Delta-5 desaturases and their use in making polyunsaturated fatty acids
37 claims: 11 independent, 26 dependent
- 1Claims Reivindicações 1. ISOLATED POLYNUCLEOTIDE, comprising:1. POLINUCLEOTÍDEO ISOLADO, que compreende: (a) a nucleotide sequence encoding a polypeptide that has delta-5 desaturase activity, where the polypeptide has at least 80% amino acid identity, based on the Clustal V method of alignment, compared to an amino acid sequence as described in SEQ ID No. 13;(a) uma sequência de nucleotídeos que codifica um polipeptídeo que possui atividade de delta-5 dessaturase, em que o polipeptídeo possui identidade de aminoácidos de pelo menos 80%, com base no método Clustal V de alinhamento, em comparação com uma sequência de aminoácidos conforme descrito em SEQ ID N° 13;(b) a nucleotide sequence that encodes a polypeptide that has delta-5 desaturase activity, where the nucleotide sequence has sequence identity of at least 80%, based on the BLASTN method of alignment, compared to a sequence of nucleotides as described in SEQ ID No. 12;(b) uma sequência de nucleotídeos que codifica um polipeptídeo que possui atividade de delta-5 dessaturase, em que a sequência de nucleotídeos possui identidade de sequências de pelo menos 80%, com base no método BLASTN de alinhamento, em comparação com uma sequência de nucleotídeos conforme descrito em SEQ ID N° 12;(c) a nucleotide sequence encoding a polypeptide that has delta-5 desaturase activity, wherein the nucleotide sequence hybridizes under stringent conditions to a nucleotide sequence as described in SEQ ID No. 12;or (d) a complement of the nucleotide sequence of (a), (b) or (c), where the complement and the nucleotide sequence consist of the same amount of nucleotides and are 100% complementary. (c) uma sequência de nucleotídeos que codifica um polipeptídeo que possui atividade de delta-5 dessaturase, em que a sequência de nucleotídeos hibridiza-se sob condições estringentes em uma sequência de nucleotídeos conforme descrito em SEQ ID N° 12;ou (d) um complemento da sequência de nucleotídeos de (a), (b) ou (c), em que o complemento e a sequência de nucleotídeos consistem da mesma quantidade de nucleotídeos e são 100% complementares.
- 8BUILDING RECOMBINANT DNA, comprising the polynucleotide according to any of claims 1, 5, 6 or 7, operably linked to at least one regulatory sequence. 8. CONSTRUÇÃO DE DNA RECOMBINANTE, que compreende o polinucleotídeo de acordo com qualquer das reivindicações 1, 5, 6 ou 7, ligado operativamente a pelo menos uma sequência reguladora.
- 11METHOD OF PRODUCTION OF A TRANSFORMED PLANT, comprising the transformation of a plant cell with the polynucleotide according to any of claims 1, 5, 6 or 7 and regeneration of a plant from the transformed plant cell. 11. MÉTODO DE PRODUÇÃO DE UMA PLANTA TRANSFORMADA, que compreende a transformação de uma célula vegetal com o polinucleotídeo de acordo com qualquer das reivindicações 1, 5, 6 ou 7 e regeneração de uma planta a partir da célula vegetal transformada.
- 16OIL OR BY-PRODUCTS obtained from seed, 16. ÓLEO OU SUBPRODUTOS obtidos a partir da semente, 10 according to claim 14. 10 de acordo com a reivindicação 14.
- 17METHOD OF PREPARING POLYINSATURATED FATTY ACIDS, long chain in a plant cell, comprising:17. MÉTODO DE ELABORAÇÃO DE ÁCIDOS GRAXOS PÓLIINSATURADOS, de cadeia longa em uma célula vegetal, que compreende: (a) transformação de uma célula vegetal com a construção recombinante de acordo com a reivindicação 8;e (a) transforming a plant cell with the recombinant construct according to claim 8;and 15 (b) selection of transformed plant cells that produce long-chain polyunsaturated fatty acids. 15 (b) seleção das células vegetais transformadas que elaboram ácidos graxos póli-insaturados de cadeia longa.
- 18METHOD OF PRODUCTION OF AT LEAST ONE POLL-INSATURATED FATTY ACID, in an oilseed cell, comprising:18. MÉTODO DE PRODUÇÃO DE PELO MENOS UM ÁCIDO GRAXO PÓLI-INSATURADO, em uma célula de planta oleaginosa, que compreende: 20 (a) transformation of an oilseed cell with a first recombinant DNA construct comprising an isolated polynucleotide encoding at least one delta-5 desaturase polypeptide, operably linked to at least one regulatory sequence and at least one additional recombinant DNA construct which comprises 20 (a) transformação de uma célula de planta oleaginosa com uma primeira construção de DNA recombinante que compreende um polinucleotídeo isolado que codifica pelo menos um polipeptídeo delta-5 dessaturase, ligado operativamente a pelo menos uma sequência reguladora e pelo menos uma construção de DNA recombinante adicional que compreende 25 an isolated polynucleotide, operably linked to at least one regulatory sequence, encoding a polypeptide selected from the group consisting of a delta-4 desaturase, delta-5 desaturase, delta-6 desaturase, delta-8 desaturase, delta-12 desaturase , delta-15 desaturase, delta-17 desaturase, delta-9 desaturase, delta-9 elongase, Ci elongase4.i6, elongase C16-18, C18-20 elongase and C20-22 elongase;25 um polinucleotídeo isolado, ligado operativamente a pelo menos uma sequência reguladora, que codifica um polipeptídeo selecionado a partir do grupo que consiste de uma delta-4 dessaturase, delta-5 dessaturase, delta-6 dessaturase, delta-8 dessaturase, delta-12 dessaturase, delta-15 dessaturase, delta-17 dessaturase, delta-9 dessaturase, delta-9 elongase, elongase Ci4.i6, elongase C16-18, elongase C18-20 e elongase C20-22;(b) regeneration of an oleaginous plant from the transformed cell of step (a);and (c) selecting the seeds obtained from the plants in step (b) that have an altered level of polyunsaturated fatty acids compared to the level in seeds obtained from an unprocessed oil plant. (b) regeneração de uma planta oleaginosa a partir da célula transformada da etapa (a);e (c) seleção das sementes obtidas a partir das plantas da etapa (b) que possuem um nível alterado de ácidos graxos póli-insaturados em comparação com o nível em sementes obtidas a partir de uma planta oleaginosa não transformada.
- 21OLEAGINOSA PLANT, comprising:21. PLANTA OLEAGINOSA, que compreende: (a) a first recombinant DNA construct comprising an isolated polynucleotide that encodes at least one delta-5 desaturase polypeptide operably linked to at least one regulatory sequence;and (b) at least one additional recombinant DNA construct comprising an isolated polynucleotide, operably linked to at least one regulatory sequence, which encodes a polypeptide selected from the group consisting of a delta-4 desaturase, delta-5 desaturase, delta-6 desaturase, delta-8 desaturase, delta-12 desaturase, delta-15 desaturase, delta-17 desaturase, delta-9 desaturase, delta-9 elongase, elongase Ci4.6, elongase C16-18. elongase Ci8.20 and elongase C2o-2222. OIL PLANT, according to either of claims 20 or 21, wherein the oilseed plant is selected from the group consisting of soybeans, Brassica species, sunflower, corn, cotton, flax and saffron. (a) uma primeira construção de DNA recombinante que compreende um polinucleotídeo isolado que codifica pelo menos um polipeptídeo delta-5 dessaturase ligado operativamente a pelo menos uma sequência reguladora;e (b) pelo menos uma construção de DNA recombinante adicional que compreende um polinucleotídeo isolado, ligado operativamente a pelo menos uma sequência reguladora, que codifica um polipeptídeo selecionado a partir do grupo que consiste de uma delta-4 dessaturase, delta-5 dessaturase, delta-6 dessaturase, delta-8 dessaturase, delta-12 dessaturase, delta-15 dessaturase, delta-17 dessaturase, delta-9 dessaturase, delta-9 elongase, elongase Ci4.i6, elongase C16-18. elongase Ci8.20 e elongase C2o-2222. PLANTA OLEAGINOSA, de acordo com qualquer das reivindicações 20 ou 21, em que a planta oleaginosa é selecionada a partir do grupo que consiste de soja, espécies de Brassica, girassol, milho, algodão, linho e açafrão.
- 3738. PROLEY PLANTS, obtained from the oilseed plant 5 according to any of claims 20 or 21. 38. PLANTAS DE PROLE, obtidas a partir da planta oleaginosa 5 de acordo com qualquer das reivindicações 20 ou 21. 1/13 1/13 Stearic acid Acid for| mythical Miristic acid [C18:0] Ciezie elongase [C16: 0] Cu ,,;elongase [C14.0] Ácido esteárico Ácido pa|mítico Ácido mirístico [C18:0] Ciezie elongase [C16:0] Cu,,;elongase [C14.0] 2/13 2/13 3/13 3/13
Independent claims11
794 paragraphs in 9 sections, as filed
(54) Title: ISOLATED POLYNUCLEOTIDE, RECOMBINANT DNA CONSTRUCTION, VEGETABLE CELL, METHODS FOR TRANSFORMING A VEGETABLE CELL, FOR PRODUCTION OF A TRANSFORMED PLANT, FOR THE PREPARATION OF POLLUCY-INSURED POLYNESYLATED FATTY ACIDS, PURPLE HAIR PRODUCTION Unsaturated, transgenic seeds, oils or
BY-PRODUCTS, PLANTAOLEAGINOSA, FOOD OR FEED AND PROLEET PLANTS.
(51) Int. Cl .: C12N 15/53; C12N 9/02; C12P 7/64 (30) Unionist Priority: 05/03/2007 US 60 / 915,733 (73) Holder (s): EIDU PONT DE NEMOURS & COMPANY (72) Inventor (s): HOWARD G. DAMUDE; QUINN QUN ZHU (74) Attorney (s): PRISCILA PENHA DE BARROS THEREZA (86) International Application: PCT US2008062173 of 01/05/2008 (87) International Publication: WO
2008/137516 of 11/13/2008 i | Γ,! Í Λ<sup>1</sup>! li \
P «ií« |? 1"
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“ISOLATED POLYNUCLEOTIDE, RECOMBINANT DNA CONSTRUCTION, PLANT CELL, TRANSFORMATION METHODS
FROM A VEGETABLE CELL, FROM THE PRODUCTION OF A TRANSFORMED PLANT, FROM THE PREPARATION OF UNSATURED POLLINE FATTY ACIDS, FROM THE PRODUCTION OF AT LEAST ONE POLY-UNSATURATED FATTY ACID, TRANSGENIC SEEDS, OILS OR
BY-PRODUCTS, OIL PLANT, FOOD OR FEED AND PROLEY PLANTS ”
This application claims the benefit of the Interim Application
North American No. 60 / 915,733, filed on May 3, 2007, the full content of which is incorporated herein as a reference.
Field of the Invention
The present invention is in the field of biotechnology. In particular, it refers to polynucleotide sequences that encode delta-5 desaturases and the use of these desaturases in the elaboration of long-chain polyunsaturated fatty acids (PUFAs).
Background of the Invention
The importance of PUFAs is unquestionable. Certain PUFAs are, for example, important biological components of healthy cells and are recognized as “essential” fatty acids that cannot be synthesized as new substances in mammals and, therefore, need to be obtained from food or derivatives through further elongation and desaturation linoleic acid (LA; 18: 2 ω-6) or α-linolenic acid (ALA; 18: 3 ω-3); components of cell plasma membranes, in which they can be found in forms such as phospholipids or triacylglycerols; necessary for proper development (particularly in the brain of developing babies) and for tissue formation and repair; and precursors of several important biologically active eicosanoids in mammals (such as prostacyclins, eicosanoids, leukotrienes and prostaglandins). In addition, high intake of long-chain ω-3 PUFAs produces cardiovascular protective effects (Dyerberg et al, Amer. J. Clin. Nutr. 28: 958-966 (1975); Dyerberg et al, Lancet 2 (8081): 117 -119 (1978); Shimokawa, H., World Rev.
Nutr. Diet 88: 100-108 (2001); Von Schacky et al, World Rev. Nutr. Diet 88: 9099 (2001)). Numerous other studies document a wide variety of health benefits conferred by the administration of omega 3 and / or omega 6 PUFAs against a range of symptoms and diseases (such as asthma, psoriasis, eczema, diabetes and cancer).
Currently, several different hosts including plants, algae, fungi and yeasts are being researched as a means of commercial production of PUFAs through various divergent efforts. Although the production capabilities of natural PUFAs from host organisms are sometimes essential to a given methodology, genetic engineering has also proven that the natural capabilities of some hosts (even those natively limited to the production of LA and ALA fatty acids) can be substantially altered to result in high level production of long chain omega 3 / omega 6 PUFAs. Whether this effect is the result of natural capabilities or recombinant technology, the production of arachidonic acid (ARA; 20: 4 ω-6), eicosapentaenoic acid (EPA; 20: 5 ω-3) and docosahexaenoic acid (DHA; 22: 6 ω3) requires the expression of the delta-9 elongase and delta-8 desaturase process (which operates in some organisms, such as euglenoid species, and which is characterized by the production of eicosadienoic acid (EDA; 20: 2 ω-6) and / or eicosatrienoic acid (ETrA; 20: 3 ω-3)) or the delta-6 desaturase / delta-6 elongase process (which is found predominantly in algae, mosses, fungi, nematodes and humans and which is characterized by the production of γ-linoleic acid (GLA ; 18: 3 ω-6) and / or stearidonic acid (STA;
18: 4 ω-3) (Fig. 1). A delta-6 elongase is also known as a C18 / 20 elongase
The delta-8 desaturase enzymes identified so far have the ability to convert EDA into dihomo-v-linolenic acid (DGLA; 20: 3) and
ETrA in eicosatetraenoic acid (ETA; 20: 4) (where ARA and EPA are subsequently synthesized from DGLA and ETA, respectively, forming a reaction with a delta-5 desaturase, while DHA synthesis requires subsequent expression of a C20 elongase / 22 additional and a delta-4 desaturase).
Based on the role played by delta-8 desaturase enzymes in the synthesis of, for example, ARA, EPA and DHA, efforts were made to identify and characterize these enzymes. Initial efforts have been reported on the isolation and characterization of Euglena gracilis' delta-8 desaturases, and several sequence variations in Euglena gracilis delta-8 desaturase (see, for example, Wallis et al, Arch. Biochem. And Biophys. 365 (2): 307-316 (1999); PCT Patent No. WO 2000/34439; United States Patent No. 6,825,017; PCT Patent No. WO 2004/057001). In addition, the depositor's copendent requests from depositors who have North American Order numbers 11 / 166,003 and 11 / 166,993, filed on June 24, 2005 (Lawyer files No. BB-1547 and CL-3150, respectively (Publications PCT No. WO 2006/012325 and WO 2006/012326; both published on February 2, 2006)) describe amino acid and nucleic acid sequences for a Euglena gracilis delta-8 desaturase.
More recently, PCT Publication No. WO 2005/103253 (published April 22, 2005) describes sequences of amino acids and nucleic acids for a delta-8 desaturase enzyme in Pavlova salina (see also North American Publication No. 2005 / 0273885). Sayanova et al (FEBS Lett. 580: 1946-1952 (2006)) describe the isolation and characterization of a cDNA from the freely living soil amoeba Acanthamoeba castellanii which, when expressed in Arabidopsis, encodes a C20 delta-8 desaturase · In addition, the copending request from assignee of depositors who have a US Patent Application number
11 / 737,772 (filed April 20, 2007; attorney's file No. BB1566) describes amino acid and nucleic acid sequences for a delta-8 desaturase enzyme from Pavlova lutheri (CCMP459). US Patent Application No. 11 / 876,115 (filed October 22, 2007; Lawyer's Folder No. BB-1574) describes sequences of amino acids and nucleic acids for a delta-8 desaturase enzyme Tetruetreptia pomquetensis CCMP1491, Eutreptiella sp. CCMP389 and Eutreptiella cf_gymnastica CCMP1594.
Based on the usefulness of the expression of delta-8 desaturases in conjunction with delta-9 elongases, efforts have been made to identify and characterize delta-9 elongases from various sources. Most of the delta-9 elongase enzymes identified so far have the ability to convert l_A into EDA and ALA into ETrA (where DGI_A and ETA are then synthesized from EDA and ETrA, respectively, after reaction with an Δ8 desaturase ; ARA and EPA are subsequently synthesized from DGI_A and ETA, respectively, after reaction with an Δ5 desaturase; and DHA synthesis requires the subsequent expression of an additional C20 / 22 elongase and an Δ4 desaturase). A delta-9 elongase from Isochrysis galbana has been made available to the public (described in GenBank Access No. AAL37626, as well as in PCT Application No. WO 02/077213). The copending request of the depositor's assignee with a North American Order number 11 / 601,563 (filed on November 16, 2006 and published on May 24, 2007; Lawyer's Folder No. BB-1562) describes a delta-9 elongase from Euglena gracilis. The copending assignment of the depositor's assignee who has North American Order number 11 / 601,564 filed on November 16, 2006 (Lawyer File No. CL3600) describes a delta-9 elongase of Eutreptiella sp CCMP389.
Most delta-5 desaturase enzymes identified up to 5 here have the primary ability to convert dihomogammalinolenic acid (20: 3, DGLA) into ARA, with secondary activity in converting eicosatetraenoic acid (20: 4, ETA) to EPA (where DHA is then synthesized from EPA after reaction with an additional C20 / 22 elongase and a delta-4 desaturase). Delta-5 desaturase has a role in the process of delta-6 desaturase / delta-6 elongase (which is found predominantly in algae, mosses, fungi, nematodes and humans and which is characterized by the production of gamma linoleic acid (“GLA”, 18: 3 ω-6) and / or stearidonic acid (“STA”; 18: 4 ω-3)) and the delta-9 elongase / delta-8 desaturase process (which is operated on some organisms, such as euglenoid species , and which is characterized by the production of eicosadienoic acid (“EDA”; 20: 2 ω-6) and / or eicosatrienoic acid (“ETrA”; 20: 3 ω-3)) (Fig. 1).
In addition, based on the role played by delta-5 desaturase enzymes in the synthesis of, for example, ARA, EPA and DHA, efforts have been made to identify and characterize these enzymes from various sources. In this way, delta-5 desaturases have been described in the open literature (such as Accesses GenBank ri AF199596, AF226273, AF320509, AB072976, AF489588, AJ510244, AF419297, AF07879, AF067654 and AB022097) and in the patent literature (such as US Patent 5,972,664 and United States Patent 6,075,183).
The depositor's assignee has a series of patent applications relating to the production of PUFAs in oilseed yeasts (ie Yarrowia lipolytica), which include: PCT publications WO 2004/101757 and WO 2004/101753 (both published on November 25, 2004); North Order6
American No. 11 / 265,761 (deposited on November 2, 2005); North American Application No. 11 / 264,784 (filed on November 1, 2005); and North American Order No. 11 / 264,737 (filed on November 1, 2005).
Relatedly, PCT Patent No. WO 2004/071467 (published on August 26, 2004; Lawyer's Folder No. BB-1538) refers to the production of PUFAs in plants, while PCT Patent No. WO 2004/071178 ( published on August 26, 2004) refers to annexin promoters and their use in the expression of transgenes in plants; both are copendent requests from the depositor's assignee.
Brief Description of the Invention
The present invention relates to an isolated polynucleotide which comprises;
(a) a nucleotide sequence encoding a polypeptide that has delta-5 desaturase activity, in which the polypeptide has at least 80% amino acid identity, based on the Clustal V method of alignment, compared to an amino acid sequence as described in SEQ ID No. 13;
(b) a nucleotide sequence encoding a polypeptide that has delta-5 desaturase activity, where the nucleotide sequence has at least 80% sequence identity, based on the BLASTN method of alignment, compared to a nucleotide sequence as described in SEQ ID No. 12;
(c) a nucleotide sequence encoding a polypeptide that has delta-5 desaturase activity, wherein the nucleotide sequence hybridizes under stringent conditions to a nucleotide sequence as described in SEQ ID No. 12; or (d) a complement of the nucleotide sequence of (a), (b) or (c), where the complement and the nucleotide sequence consist of the same number of nucleotides and are 100% complementary.
In a second embodiment, the present invention relates to a recombinant DNA construct that comprises any of the isolated polynucleotides according to the present invention operably linked to at least one regulatory sequence.
In a third embodiment, the present invention relates to a plant cell that comprises in its genome the construction of recombinant DNA according to the present invention.
In a fourth embodiment, the present invention relates to a method of transforming plant cells, which comprises transforming a plant cell with a recombinant construction according to the present invention or an isolated polynucleotide according to the present invention and selection of plant cells transformed with the recombinant construct or the isolated polynucleotide.
In a fifth embodiment, the present invention relates to transgenic seeds that comprise in their genome the recombinant construction according to the present invention or a transgenic seed obtained from a plant elaborated by means of a method according to the present invention. Also of interest are the oil or by-products obtained from these transgenic seeds.
In a sixth embodiment, the present invention relates to a method of making long-chain polyunsaturated fatty acids in plant cells that comprises:
(a) transforming a plant cell with the recombinant construct according to the present invention; and (b) selection of transformed plant cells that produce long-chain polyunsaturated fatty acids.
In a seventh embodiment, the present invention relates to a method of producing at least one polyunsaturated fatty acid in an oil plant cell, which comprises:
(a) transformation of oilseed plant cells with a first recombinant DNA construct comprising an isolated polynucleotide encoding at least one delta-5 desaturase polypeptide, operably linked to at least one regulatory sequence and at least one additional recombinant DNA construct comprises an isolated polynucleotide, operably linked to at least one regulatory sequence, encoding a polypeptide selected from the group consisting of a delta-4 desaturase, delta-5 desaturase, delta-6 desaturase, delta-8 desaturase, delta-12 desaturase, delta-15 desaturase, delta-17 desaturase, delta- 9 desaturase, delta-9 elongase, Cu / ie elongase, C16 / 18 θ elongase C20 / 22 elongase;
(b) regeneration of oilseed plants from the transformed cell of step (a); and (c) selecting the seeds obtained from the plants in step (b) that have an altered level of polyunsaturated fatty acids compared to the level in seeds obtained from an untransformed oil plant.
In an eighth embodiment, the present invention relates to an oleaginous plant that comprises in its genome the recombinant construction according to the present invention. Suitable oil plants include, but are not limited to, soy, Brassica, sunflower, corn, cotton, flax and saffron species.
In a ninth embodiment, the present invention relates to an oil plant that comprises:
(a) a first recombinant DNA construct comprising an isolated polynucleotide that encodes at least one delta-5 desaturase polypeptide, operably linked to at least one regulatory sequence; and (b) at least one additional recombinant DNA construct comprising an isolated polynucleotide, operably linked to at least one regulatory sequence, which encodes a polypeptide selected from the group consisting of delta-4 desaturase, delta-5 desaturase, delta -6 desaturase, delta-8 desaturase, delta-12 desaturase, delta-15 desaturase, delta-17 desaturase, delta-9 desaturase, delta-9 elongase, elongase C14 / 16. elongase C16 / 18. elongase C18 / 20 θ elongase C20 / 22 ·
Also of interest are transgenic seeds obtained from these oilseeds, as well as oil or by-products obtained from these transgenic seeds. A preferred by-product is lecithin.
In a tenth embodiment, the present invention relates to foods or feed that incorporate an oil or seed according to the present invention or foods or feed that comprise an ingredient derived from the processing of seeds.
In an eleventh embodiment, the present invention relates to offspring plants obtained from a plant made using the method according to the present invention or an oleaginous plant according to the present invention.
Biological Deposits
The following plasmid was deposited with the North American Collection of Type Cultures (ATCC), 10801 University Boulevard, Manassas VA 20110-2209 and contains the designation, Accession Number and deposit date below (Table 1).
Table 1
ATCC Deposit
<td>Plasmid</td><td>Access Number</td><td>Deposit Date</td>
<td>ppKR72</td><td>PTA-6019</td><td>May 28, 2004</td>
Brief Description of Figures and Sequence Listings
The present invention can be more fully understood 5 from the following detailed specification and drawings and
Attached strings, which are part of this application.
Figure 1 is a representative omega 3 and omega 6 fatty acid process that provides the conversion of myristic acid through various DHA intermediates.
Figure 2A is a schematic of EgD5.
Figure 2B is a map of plasmid pZUF17 (SEQ ID NO: 7).
Figure 2C is a map of plasmid pDMW267 (SEQ ID NO: 8).
Figure 3 is a map of plasmid pY115 (SEQ ID NO: 19).
Figure 4 is a map of plasmid pY159 (SEQ ID NO: 23).
Figure 5 is a map of plasmid pY169 (SEQ ID NO: 24).
Figure 6 are the fatty acid profiles for Yarrowia lipolytica that expresses pY169.
Figure 7 is a map of pKR1153 (SEQ ID NO: 44).
Figures 8A, 8B and 8C show a comparison of the nucleotide sequences of EaD5 (identical to EaD5Des1) (SEQ ID No. 12) and EaD5S (SEQ ID No. 45).
Figure 9 is a map of plasmid pEaD5S (SEQ ID NO: 46).
Figure 10 shows a chromatogram of the lipid profile of an extract from Euglena anabaena cells as described in the Examples.
Figure 11 shows ten events that have the highest correct mean delta-5 desaturase activities (mean of the five somatic soy embryos analyzed) of about thirty events transformed with pKR1153 (Experiment MSE2140). Fatty acids are identified as 16: 0 (palmitate), 18: 0 (stearic acid), 18: 1 (oleic acid), LA, ALA, EDA, SCI, DGLA, ARA, ERA, JUP, ETA and EPA. Fatty acid compositions for an individual embryo were expressed as a percentage by weight (weight%) of the total fatty acids and the average fatty acid composition is an average of six individual embryos for each event. The delta-5 desaturase activity is expressed as a percentage of delta-5 desaturation (“% delta-5 dessat”) calculated according to the following formula:
([product] / [substrate + product]) * 100. More specifically, the percentage of delta-5 desaturation was determined as: ([ARA + EPA] / [DGLA + ETA + ARA + EPA]) * 100.
The sequence descriptions summarize the Sequence Listing attached to this. The Sequence Listing contains one-letter codes for nucleotide sequence characters and the one- and three-letter amino acid codes as defined in the IUPAC-IUB standards described in Nucleic Acids Research 13: 3021-3030 (1985) and in the Biochemical Journal 219 (2): 345-373 (1984).
SEQ ID NO: 1 is the cDNA sequence for delta-5 desaturase 1 from
Euglena anabaena (EaD5Des1).
SEQ ID NO: 2 is the nucleotide sequence of the Euglena gracilis delta-5 desaturase 1 (EgD5) coding sequence.
SEQ ID NO: 3 is the nucleotide sequence of the Euglena gracilis YL794 delta-5 desaturase oligonucleotide.
SEQ ID NO: 4 is the nucleotide sequence of the Euglena gracilis YL797 delta-5 desaturase oligonucleotide.
SEQ ID NO: 5 is the nucleotide sequence of the Euglena gracilis YL796 delta-5 desaturase oligonucleotide.
SEQ ID NO: 6 is the nucleotide sequence of the Euglena gracilis YL795 delta-5 desaturase oligonucleotide.
SEQ ID NO: 7 is the nucleotide sequence of the plasmid pZUF17.
SEQ ID NO: 8 is the nucleotide sequence of plasmid pDMW367.
SEQ ID N ° 9 is the nucleotide sequence of the universal primer
M13F.
SEQ ID NO: 10 is the nucleotide sequence of M13-28Rev.
SEQ ID NO: 11 is the nucleotide sequence of plasmid pLF119.
SEQ ID NO: 12 is the nucleotide sequence of the Euglena anabaena delta-5 desaturase 1 coding sequence (EaD5Des1).
SEQ ID NO: 13 is the amino acid sequence of Euglena anabaena delta-5 15 desaturase 1 (EaD5Des1).
SEQ ID NO: 14 is the amino acid sequence of the Thalassiosira pseudonana delta-8 fatty acid desaturase.
SEQ ID NO: 15 is the amino acid sequence of the Phaeodactylum tricomutum delta-5 fatty acid desaturase.
SEQ ID NO: 16 is the amino acid sequence of the delta-5 desaturase from Euglena gracilis (EgD5).
SEQ ID NO: 17 is the nucleotide sequence of plasmid pDMW263.
SEQ ID NO: 18 is the nucleotide sequence of plasmid pDMW237.
SEQ ID NO: 19 is the nucleotide sequence of plasmid pY115.
SEQ ID N ° 20 is the nucleotide sequence of the oligonucleotide
0YFBA1.
SEQ ID NO: 21 is the nucleotide sequence of the oligonucleotide oYFBAI-6.
SEQ ID NO: 22 is the nucleotide sequence of plasmid pY158.
SEQ ID NO: 23 is the nucleotide sequence of plasmid pY159.
SEQ ID NO: 24 is the nucleotide sequence of plasmid pY169.
SEQ ID No. 25 is the nucleotide sequence of the delta-9 elongase from Euglena gracilis (EgD9e).
SEQ ID NO: 26 is the nucleotide sequence of the Euglena gracilis delta-8 desaturase (EgD8).
SEQ ID N ° 27 is the nucleotide sequence of oligonucleotide 15 with elongase sense from Euglena gracilis oEugEL1-1.
SEQ ID No. 28 is the nucleotide sequence of the elongase nonsense oligonucleotide of Euglena gracilis oEugEL1-2.
<td>pKR906.</td><td>SEQ</td><td>ID</td><td>No.</td><td> 29</td><td>is</td><td>The</td><td>sequence</td><td>in</td><td>nucleotides</td><td>of</td><td>plasmid</td>
<td>20 pKR72.</td><td>SEQ</td><td>ID</td><td>No.</td><td> 30</td><td>is</td><td>The</td><td>sequence</td><td>in</td><td>nucleotides</td><td>of</td><td>plasmid</td>
<td>KS102.</td><td>SEQ</td><td>ID</td><td>No.</td><td> 31</td><td>is</td><td>The</td><td>sequence</td><td>in</td><td>nucleotides</td><td>of</td><td>plasmid</td>
<td>25 pKR197.</td><td>SEQ</td><td>ID</td><td>No.</td><td> 32</td><td>is</td><td>The</td><td>sequence</td><td>in</td><td>nucleotides</td><td>of</td><td>plasmid</td>
<td>pKR911.</td><td>SEQ</td><td>ID</td><td>No.</td><td> 33</td><td>is</td><td>The</td><td>sequence</td><td>in</td><td>nucleotides</td><td>of</td><td>plasmid</td>
SEQ ID NO: 34 is the nucleotide sequence of plasmid pKR680.
SEQ ID NO: 35 is the nucleotide sequence of plasmid pKR913.
SEQ ID NO: 36 is the nucleotide sequence of the oligonucleotide oEAd5-1-1.
SEQ ID NO: 37 is the nucleotide sequence of the oligonucleotide oEAd5-1-2.
SEQ ID NO: 38 is the nucleotide sequence of plasmid pKR1136.
SEQ ID NO: 39 is the nucleotide sequence of plasmid pKR767.
SEQ ID NO: 40 is the nucleotide sequence of the Mortierella alpina delta-5 desaturase coding sequence (MaD5).
SEQ ID NO: 41 is the nucleotide sequence of plasmid pKR974.
SEQ ID NO: 42 is the nucleotide sequence of the delta-5 desaturase (SdD5) coding sequence of Saprolegnia diclina.
SEQ ID NO: 43 is the nucleotide sequence of plasmid pKR1139.
SEQ ID NO: 44 is the nucleotide sequence of plasmid pKR1153.
SEQ ID NO: 45 is the nucleotide sequence of the Euglena anabaena codon-optimized delta-5 desaturase gene (EaD5S).
SEQ ID NO: 46 is the nucleotide sequence of the plasmid pEaD5S.
Detailed Description of the Invention The descriptive report of each reference indicated herein is fully incorporated into the present as a reference.
As used herein and in the appended claims, the singular forms "one", "one", "o" and "a" include reference to the plural, unless the context clearly indicates otherwise. Thus, reference, for example, to "a plant" indicates a series of these plants, reference to "a cell includes one or more cells and their equivalents known to those skilled in the art and so on.
The present invention relates to delta-5 desaturase enzymes and nucleic acid to encode them isolated from Euglena anabaena. These are useful, among others, for the manipulation of biochemical processes for the production of PUFAs. The present invention therefore finds many applications.
PUFAs or their derivatives, elaborated using the methodology described in the present, can be used as food substitutes or supplements, particularly infant formulas, for patients undergoing intravenous feeding or to prevent or treat malnutrition. Alternatively, the purified PUFAs (or their derivatives) can be incorporated into cooking oils, fats or margarines formulated in such a way that, in normal use, the patient receives the desired amount of food supplementation. PUFAs can also be incorporated into baby formulas, nutritional supplements or other food products and can find use as anti-inflammatory or cholesterol-lowering agents. Optionally, the compositions can be used for pharmaceutical use (human or veterinary). In this case, PUFAs are generally administered orally, but they can be administered through any route by which they can be successfully absorbed, such as parenteral (for example, subcutaneous, intramuscular or intravenous), rectal, vaginal or topical (such as as in the form of ointment or skin lotion).
Supplementation of humans or animals with PUFAs produced by recombinant means may result in higher levels of
Added PUFAs, as well as their metabolic offspring. Treatment with EPA, for example, can result not only in higher levels of EPA, but also EPA products downstream, such as eicososanoids (ie, prostaglandins, leukotrienes, thromboxanes). Complex regulatory mechanisms may make it desirable to combine multiple PUFAs or add different PUFA conjugates in order to avoid, control or overcome these mechanisms to achieve the desired levels of specific PUFAs in an individual.
In this specification, a number of terms and abbreviations are used. The following definitions are provided.
“Open reading structure” is abbreviated ORF.
"Polymerase chain reaction" is abbreviated PCR.
“North American Collection of Type Cultivation” is abbreviated
ATCC.
"Polyunsaturated fatty acid (s)" is (are) abbreviated
PUFA (s).
"Triacylglycerols" are abbreviated TAGs.
The term “fatty acids” means long chain aliphatic acids (alkanoic acids) with variable chain length, from about C12 to C22 (although acids with longer and shorter chain length are known). The predominant chain lengths are C<sub>16</sub> to C22 · Additional details referring to the differentiation between "saturated fatty acids" and "unsaturated fatty acids", "monounsaturated fatty acids and" polyunsaturated fatty acids "(or" PUFAs ") and" omega 6 fatty acids "(ω- 6 or n-6) and "omega 3 fatty acids" (ω-3 or n-3) are provided in PCT Patent No. WO 2004/101757.
Fatty acids are described here by a simple “X: Y” notation system, where X is the total number of carbon atoms (C) in the specific fatty acid and Y is the number of double unions. The number after the fatty acid designation indicates the position of the double bond from the carboxyl end of the fatty acid with the affix “c” for the c / s configuration of the double bond (eg palmitic acid (16: 0), stearic acid (18: 0), oleic acid (18: 1, 9c), petroselinic acid (18: 1, 6c), LA (18: 2, 9c, 12c), GLA (18: 3, 6c, 9c, 12c) and ALA (18: 3, 9c, 12c, 15c)). Unless otherwise specified, 18: 1, 18: 2 and 18: 3 designate oleic fatty acids, LA and ALA, respectively. If not specifically stated otherwise, double joints are considered to have a c / s configuration. Double joints in 18: 2 (9,12), for example, would be considered in the cis configuration.
The nomenclature used to describe PUFAs in this specification is shown below in Table 2. In the column entitled “Abbreviated notation”, the omega reference system is used to indicate the number of carbons, the number of double joints and the position of the double joint closest to the omega carbon, from the omega carbon (which receives the number 1 for this purpose). The rest of the Table summarizes the common names of omega 3, omega 6 and their precursor fatty acids, the abbreviations that will be used throughout the specification and the chemical name of each compound.
Table 2
Nomenclature of Poli-Unsaturated Fatty Acids and Precursors
<td>Common name</td><td>Abbreviation</td><td>Chemical name</td><td>Short notation</td>
<td>Miristic</td><td> -</td><td>tetradecanoic</td><td> 14:0</td>
<td>Palmitic</td><td>PAN</td><td>hexadecanoic</td><td> 16:0</td>
<td>Palmitoleico</td><td> -</td><td>9-hexadecene</td><td> 16:1</td>
<td>Stearic</td><td> -</td><td>octadecanoic</td><td> 18:0</td>
<td>Oleic</td><td> -</td><td>w / s-9-octadecenoic</td><td> 18:</td>
<td>Common name</td><td>Abbreviation</td><td>Chemical name</td><td>Short notation</td>
<td>Linoleic</td><td>OVER THERE</td><td>w / s-9.12- octadecadienoic</td><td>18: 2 ω-6</td>
<td>gamma-Linoleic</td><td>GLA</td><td>w / s-6,9,12- octadecatrienoic</td><td>18: 3 ω-6</td>
<td>Eicosadiene</td><td>EDA</td><td>w / s-11.14- eicosadienoic</td><td>20: 2 ω-6</td>
<td>dihomogammalinoleic</td><td>DGLA</td><td>w / s-8,11,14- eicosatrienoic</td><td>20: 3 ω-6</td>
<td>Sciadonic</td><td>SCI</td><td>w / s-5,11,14- eicosatrienoic</td><td>20: 3b ω-6</td>
<td>Arachidonic</td><td>ARA</td><td>w / s-5,8,11,14- eicosatetraenoico</td><td>20: 4 ω-6</td>
<td>a-Linolenic</td><td>ALLAH</td><td>w / s-9,12,15- octadeatrienic</td><td>18: 3 ω-3</td>
<td>Stearidonic</td><td>STA</td><td>w / s-6,9,12,15- ocatadecatetraenoico</td><td>18: 4 ω-3</td>
<td>Eicosatrienoic</td><td>ETrA or ERA</td><td>w / s-11,14,17- eicosatrienoic</td><td>20: 3 ω-3</td>
<td>Eicosatetraenoic</td><td>ETA</td><td>w / s-8,11,14,17- eicosatetraenoico</td><td>20: 4 ω-3</td>
<td>Juniperonic</td><td>JUP</td><td>cis-5,11,14,17- eicosatetraenoico</td><td>20: 4b ω-3</td>
<td>Eicosapentaenoic</td><td>EPA</td><td>w / s-5,8,11,14,17- eicosapentaenoico</td><td>20: 5 ω-3</td>
<td>Docosapentaenoico</td><td>DPA</td><td>c / s-7,10,13,16,19- docosapentaenoico</td><td>22: 5 ω-3</td>
<td>Common name</td><td>Abbreviation</td><td>Chemical name</td><td>Short notation</td>
<td>Docosa-hexaenoico</td><td>DHA</td><td>c / s-4,7,10,13,16,19- docosahexaenoico</td><td>22: 6 ω-3</td>
A metabolic or biosynthetic process, in the biochemical sense, can be considered a series of chemical reactions that take place inside a cell, catalyzed by enzymes, to achieve the formation of a metabolic product to be used or stored by the cell or the beginning of another metabolic process (called a flow generation step). Many of these processes are designed and involve a step-by-step modification of the starting substance to shape it into a product that has the exact chemical structure desired.
The term “PUFA biosynthetic process” refers to a metabolic process that converts oleic acid to l_A, EDA, GLA, DGLA, ARA, ALA, STA, ETrA, ETA, EPA, DPA and DHA. This process is well described in the literature (see, for example, PCT Patent No. WO 2006/052870). Simplistically, this process involves elongating the carbon chain by adding carbon atoms and desaturating the molecule by adding double bonds, using a series of special elongation and desaturation enzymes (ie, “ enzymes from the PUFA biosynthetic process ”) present in the endoplasmic reticulum membrane. More specifically, “PUFA biosynthetic process enzyme” means any of the following enzymes (and genes encoding said enzymes) associated with the biosynthesis of a PUFA, which include: delta-4 desaturase, delta-5 desaturase, delta-6 desaturase , delta-12 desaturase, delta-15 desaturase, delta-17 desaturase, delta-9 desaturase, delta-8 desaturase, delta-9 elongase, elongase C14 / 16. elongase Cie / ie, elongase C18 / 20 θ / or elongase C20 / 22 ·
The term "biosynthetic process of omega 3 and omega 6 fatty acids" designates a set of genes that, when expressed under the appropriate conditions, encode enzymes that catalyze the production of either omega 3 and omega 6 fatty acids or both. Typically, the genes involved in the biosynthetic process of omega 3 and omega fatty acids
6 encode enzymes from the biosynthetic process of PUFAs. A representative process is illustrated in Figure 1, which provides conversion of myristic acid through various intermediates to DHA, which demonstrates how the two omega 3 and omega 6 fatty acids can be produced from a common source. The process is naturally divided into two parts, one part of which will generate omega 3 fatty acids and the other part, omega 6 fatty acids.
The term "functional", as used in the present in conjunction with the omega 3 and omega 6 fatty acid biosynthetic process, indicates that some (or all) of the genes in the process express active enzymes, which results in in vivo catalysis or conversion of substrate. It should be understood that “omega 3 and omega 6 fatty acid biosynthetic processes” or “functional omega 3 and omega 6 fatty acid processes” do not indicate that all enzyme genes in the PUFA biosynthetic process are necessary because a series of fatty acid products will only require the expression of a subset of the genes in this process.
The term “delta-9 elongase / delta-8 desaturase process” indicates a biosynthetic process for producing long-chain PUFAs. This process comprises, at least, a delta-9 elongase and a delta-8 desaturase, in order to allow the biosynthesis of DGLA and / or ETA from
LA and ALA, respectively. With expression of other desaturases and elongases, ARA, EPA, DPA and DHA can also be synthesized. This process can be advantageous in some embodiments, as the biosynthesis of GLA and / or STA is excluded.
The term "intermediate fatty acid" means any fatty acid produced in a fatty acid metabolic process that can be further converted into a desired fatty acid product in this process through the action of other metabolic process enzymes.
When EPA is produced using the delta-9 elongase / delta-8 desaturase process, EDA, ETrA, DGLA, ETA and ARA can be produced and are considered “intermediate fatty acids”, as these fatty acids can be additionally converted to EPA by through the action of other enzymes of metabolic processes.
The term “fatty acid by-product” means any fatty acid produced in a fatty acid metabolic process that is not the intended fatty acid product of the process, nor an “intermediate fatty acid” in the process. When EPA is produced using the delta-9 elongase / delta-8 desaturase process, for example, sciadonic acid (SCI) and juniperonic acid (JUP) can also be produced through the action of a delta-5 desaturase on EDA or ETrA , respectively. They are considered “fatty acid by-products”, since none of them can be further converted to EPA through the action of other enzymes of metabolic processes.
The terms "triacylglycerol", "oil" and "TAGs" refer to neutral lipids composed of three fatty acyl residues esterified in a glycerol molecule (and these terms will be used interchangeably throughout this specification). These oils may contain long-chain PUFAs, as well as shorter saturated and unsaturated fatty acids and longer-chain saturated fatty acids. In this way, “oil biosynthesis” generically designates the synthesis of TAGs in the cell.
“Percentage (%) of PUFAs in the total lipid and oil fractions designates the percentage of PUFAs in relation to the total fatty acids in those fractions. The term “total lipid fraction” or “lipid fraction” refers to the sum of all lipids (that is, neutral and polar) in an oleaginous organism, to include the lipids that are located in the phosphatidylcholine fraction ( PC), phosphatidylethanolamine (PE) fraction and triacylglycerol (TAG or oil) fraction. The terms "lipid" and "oil" will be used, however, interchangeably throughout the specification.
The terms "conversion efficiency" and "percentage of substrate conversion" refer to the efficiency with which a specific enzyme (such as a desaturase) can convert substrate into product. Conversion efficiency is measured according to the following formula: ([product] / [substrate + product]) * 100, where "product" includes the immediate product and all products in the process derived therefrom.
“Desaturase” is a polypeptide that can desaturate, that is, introduce a double bond in one or more fatty acids to produce a fatty acid or precursor of interest. Despite the use of the omega reference system throughout the specification for reference to specific fatty acids, it is more convenient to indicate the activity of a desaturase counting from the carboxyl end of the substrate, using the delta system. Of particular interest in the present delta-5 are desaturases which will desaturate a fatty acid between the fifth and sixth carbon atoms numbered from the carboxyl-terminal end of the molecule and which can, for example, catalyze the conversion of DGLA into ARA and / or ETA in EPA. Other useful fatty acid desaturases include, for example: (1) delta-8 desaturases that catalyze the conversion of EDA to DGLA and / or ERA to ETA;
(2) delta-6 desaturases that catalyze the conversion of LA to GLA and / or ALA to STA; (3) delta-4 desaturases that catalyze the conversion of DPA to DHA; (4) delta-12 desaturases that catalyze the conversion of oleic acid to LA; (5) delta-15 desaturases that catalyze the conversion of ARA to ALA and / or GLA to ETA; (6) delta-17 desaturases that catalyze the conversion of ARA to EPA and / or DGLA to ETA; and (7) delta-9 desaturases that catalyze the conversion of palmitic acid to palmitoleic acid (16: 1) and / or stearic acid to oleic acid (18: 1). In the art, delta-15 and delta-17 desaturases are also occasionally called “omega-3 desaturases”, “w-3 dessaturases” and / or “ω-3 dessaturases”, based on their ability to convert omega-6 fatty acids its omega-3 partners (conversion, for example, from LA to ALA and ARA to EPA, respectively). In some embodiments, it is more desirable to determine empirically the specificity of a fatty acid desaturase by transforming an appropriate host with the gene for that fatty acid desaturase and determining its effect on the host's fatty acid profile.
The term delta-5 desaturase refers to an enzyme that desatures a fatty acid between the fifth and sixth carbon atoms numbered from the carboxyl-terminal end of the molecule. Preferably, a delta-5 desaturase converts dihomogamalinolenic acid (20: 3, DGLA) to arachidonic acid (20: 4, ARA) or converts eicosatetraenoic acid (20: 4, ETA) to eicosapentaenoic acid (20: 5, EPA).
For the purposes of the present, the terms "EaD5Des1 or" EaD5 "refer to a delta-5 desaturase enzyme (SEQ ID N ° 13) isolated from Euglena anabaena, encoded by SEQ ID N ° 12 at present. Similarly, the term "EaD5S (SEQ ID N ° 45) designates a codon-optimized delta-5dessaturase for expression in Yarrowia lipolytica.
For the purposes of this, the term “lgD9e” designates a delta-9 elongase (SEQ ID N ° 15) (NCBI Access no. AAL37626 (Gl 17226123), site AAL37626, CDS AF390174; GenBank access no. AF390174) isolated from of Isochrysis galbana. On the other hand, the term "lgD9eS" designates a synthetic delta-9 elongase (codon-optimized) derived from the DNA sequence of the delta-9 elongase from Isochrysis galbana that can be used for expression in Yarrowia lipolytica.
Similarly for the purposes of the present, the term “EgD9e” 5 designates a delta-9 elongase isolated from Euglena gracilis. EgD9e is described in North American Order No. 11 / 601,563 (filed on November 16, 2006, published on May 24, 2007; Lawyer's Folder No. BB-1562).
Similarly, the term "EgD8" designates a delta-8 desaturase enzyme isolated from Euglena gracilis. EgD8 is 100% identical and functionally equivalent to “Eg5”, as described in PCT Patent No. WO 2006/012325 and WO 2006/012326 (SEQ ID No. 2 of Published North American Patent No. 20050287652-A1).
The term “elongase system” refers to a suite of four enzymes that are responsible for elongating a fatty acid carbon chain to produce a fatty acid that is two carbons longer than the fatty acid substrate on which the fatty acid system acts. elongase. More specifically, the stretching process occurs in association with fatty acid synthase, whereby CoA is the acyl vehicle (Lassner et al, Plant Cell 8: 281-292 (1996)). In the first stage, which was found to be substrate specific and also speed limiting, malonyl-CoA is condensed with a long-chain acyl-CoA to generate carbon dioxide (CO<sub>2</sub>) and a β-ketoacyl-CoA (in which the acyl portion was elongated by two carbon atoms). Subsequent reactions include reduction in β-hydroxyacyl-CoA, dehydration in an enoyl-CoA and second reduction to generate the elongated acyl-Coa.
Examples of reactions catalyzed by elongase systems are the conversion of GLA to DGLA, STA to ETA, LA to EDA, ALA to ETrA and EPA to DPA.
For the purposes of the present, an enzyme that catalyzes the first condensation reaction (ie conversion of malonyl-CoA and acyl25
Long-chain CoA in β-ketoacyl-CoA) will be generically called an “elongase”. In general, the elongase substrate selectivity is somewhat broad, but segregated by the chain length and the degree of unsaturation. Consequently, elongases can have different specificities. A C elongase<sub>14</sub>.16 will use a C substrate<sub>i4</sub> (such as myristic acid), a Ci elongase<sub>6</sub>-18 will use a Ci substrate<sub>6</sub> (such as palmitate), a C18-20 elongase will use a C- |<sub>8</sub> (such as GLA, STA) and a C20-22 elongase will use a C substrate<sub>2</sub>o (such as EPA). Similarly, a “delta-9 elongase” may be able to catalyze the conversion of LA to EDA and / or ALA to ETrA. It is important to note that some elongases have broad specificity and, therefore, a single enzyme may be able to catalyze various elongase reactions. In this way, for example, a delta-9 elongase can also act as a Ci6-ie elongase, Ci elongase<sub>8</sub>.<sub>2</sub>oe / or elongase C20-22 and may have alternative, but not preferred, specificities for delta-5 and delta-6 fatty acids such as EPA and / or GLA, respectively.
The term "substitution of conservative amino acids" indicates a substitution of an amino acid residue in a given protein with another amino acid, without changing the chemical or functional nature of that protein. It is well known in the art, for example, that changes in a gene that result in the production of a chemically equivalent amino acid at a given location (but that do not affect the structural and functional properties of the encoded folded protein) are common. For the purposes of the present invention, "conservative amino acid substitutions" are defined as exchanges within one of the following five groups:
1. small, non-polar or slightly polar aliphatic residues: Ala [A], Ser [S], Thr [T] (Pro [P], Gly [G]);
2. negatively charged polar wastes and their amids:
Asp [D], Asn [N], Glu [E], Gin [Q];
3. positively charged polar residues: His [H], Arg [R], Lys [K];
4. large aliphatic non-polar residues: Met [M], Leu [L], Ile [I], Val [V] (Cys [C]); and
5. large aromatic residues: Phe [F], Tyr [Y], Trp [W].
Conservative amino acid substitutions generally maintain: 1) the structure of the polypeptide backbone in the substitution area; 2) the charge or hydrophobicity of the molecule at the target site; or 3) the volume of the side chain. In addition, in many cases, changes in the N-terminal and C-terminal parts of the protein molecule would not be expected to alter the activity of the protein.
As used herein, "nucleic acid" indicates a polynucleotide and includes single or double stranded polymer with deoxyribonucleotide or ribonucleotide bases. Nucleic acids can also include fragments and modified nucleotides. In this way, the terms "polynucleotide", "nucleic acid sequence", "nucleotide sequence" or "nucleic acid fragment are used interchangeably and are a RNA or DNA polymer that has single or double strands and optionally contains bases of synthetic, unnatural or altered nucleotides. Nucleotides (normally found in their 5'-monophosphate form) are named after their letter as follows: "A" for adenylate or deoxyadenylate (for RNA or DNA, respectively), "C" for cytidylate or deosicitidylate, "G ”For guanylate or deoxyguanilate,“ U ”for uridlate,“ T ”for deositimidylate,“ R ”for purines (A or G), Ύ” for pyrimidiens (C or T), “K” for G or T, “H” for A, C or T, "I" for inosine and "N" for any nucleotide.
The terms "subfragment that is functionally equivalent" and "functionally equivalent subfragment" are used interchangeably in the present. These expressions designate a part or subsequence of an isolated nucleic acid fragment in which the ability to alter gene expression or produce a certain phenotype is retained, whether or not the fragment or subfragment encodes an active enzyme. The fragment or subfragment can be used, for example, in the design of chimeric genes to produce the desired phenotype in a transformed plant. Chimeric genes can be designed for use in suppression by ligating a fragment of nucleic acid or its subfragment, whether or not it encodes an active enzyme, in or without direction with respect to a plant promoter sequence.
The expression "conserved domain or" motif "indicates a set of amino acids conserved in specific positions along an aligned sequence of evolutionarily related proteins. Although amino acids in other positions can vary between homologous proteins, amino acids that are highly conserved in specific positions indicate amino acids that are essential in the structure, stability or activity of a protein. Because they are identified for their high degree of conservation in aligned sequences of a family of protein homologs, they can be used as identifiers or “signatures”, to determine whether a protein with a newly determined sequence belongs to a family of proteins previously identified .
The terms "homology", "homologous, substantially similar and substantially corresponding" are used interchangeably in the present. They designate nucleic acid fragments in which changes in one or more nucleotide bases do not affect the nucleic acid fragment's ability to mediate gene expression or produce a certain phenotype. These expressions also designate modifications of the nucleic acid fragments according to the present invention, such as the deletion or insertion of one or more nucleotides that do not substantially alter the functional properties of the resulting nucleic acid fragment with respect to the unmodified starting fragment. It is understood, therefore, how those skilled in the art will appreciate that the present invention encompasses more than specific sequence examples.
In addition, those skilled in the art recognize that substantially similar nucleic acid sequences encompassed by the present invention are also defined by their ability to hybridize (under moderately stringent conditions, such as 0.5X SSC, 0.1% SDS, 60 ° C) with the sequences exemplified herein or with any part of the nucleotide sequences described herein that are functionally equivalent to any of the nucleic acid sequences described herein. Stringency conditions can be adjusted to select moderately similar fragments, such as homologous sequences from distantly related organisms, to highly similar fragments, such as genes that duplicate functional enzymes from closely related organisms. Post-hybridization washes determine stringency conditions.
The term "selectively hybridizes" includes reference to hybridization, under stringent hybridization conditions, of a nucleic acid sequence in a specified nucleic acid target sequence to a detectably greater degree (such as at least twice as much as the background) that their hybridization to non-target nucleic acid sequences and substantial exclusion of non-target nucleic acids. Selective hybridization sequences typically have sequence identity of at least 80%, or sequence identity of 90%, up to and including 100% sequence identity (that is, fully complementary).
The term "stringent conditions" or "stringent hybridization conditions" includes reference to conditions under which a probe will selectively hybridize to its target sequence. Strict conditions are sequence dependent and will be different in different circumstances. By controlling the stringency of the hybridization and / or washing conditions, target sequences can be identified that are 100% complementary to the probe (homologous probe). Alternatively, stringency conditions can be adjusted to allow for some mismatch of the sequences, such that lesser degrees of similarity are detected (heterologous probing). Generally, a probe is less than about a thousand nucleotides in length, optionally less than five hundred nucleotides in length.
Typically, stringent conditions will be those in which the salt concentration is less than about 1.5 M Na ion, typically a concentration of about 0.01 to 1.0 M Na ion (or other salts) under pH 7.0 to 8.3 and the temperature is at least about 30 ° C for short probes (such as ten to fifty nucleotides) and at least about 60 ° C for long probes (such as more than fifty nucleotides) . Strict conditions can also be achieved with the addition of destabilizing agents, such as formamide. Examples of low stringency conditions include hybridization with a buffer solution of 30 to 35% formamide, 1 M NaCI, 1% SDS (sodium dodecyl sulfate) at 37 ° C and washing in 1X to 2X SSC (20X SSC = 3 , 0 M NaCI / 0.3 M trisodium citrate) at 50 to 55 ° C. Examples of moderate stringency conditions include hybridization to 40 to 45% formamide, 1 M NaCI, 1% SDS at 37 ° C and a wash in 0.5X to 1X SSC at 55 to 60 ° C. Examples of high stringency conditions include hybridization in 50% formamide, 1 M NaCI, 1% SDS at 37 ° C and a wash in 0.1 X SSC at 60 to 65 ° C.
Specificity is typically the function of post-hybridization washes, where the critical factors are the ionic resistance and the temperature of the final washing solution. For DNA-DNA hybrids, T<sub>m</sub> can be calculated approximately from the equation of Meinkoth et al, Anal.
Biochem. 138: 267-284 (1984): T<sub>m</sub> = 81.5 ° C + 16.6 (log M) + 0.41 (% GC) 0.61 (% form) - 500 / I; where M is the molarity of monovalent cations,% GC is the percentage of guanosine and cytosine nucleotides in the DNA,% shape is the percentage of formamide in the hybridization solution and L is the length of the hybrid in base pairs. AT<sub>m</sub> it is the temperature (under pH and defined ionic resistance) at which 50% of a complementary target sequence hybridizes in a perfectly matched probe. T<sub>m</sub> is reduced by about 1 ° C for each 1% mismatch; in this way, T<sub>m</sub>, hybridization and / or washing conditions can be adjusted for hybridization in the sequences with the desired identity. If streams with £ 90% identity are desired, the
T<sub>m</sub> can be reduced by 10 ° C. Generally, stringent conditions are selected about 5 ° C below the thermal melting point (T<sub>m</sub>) of the specific sequence and its complement at a defined pH and ionic resistance. Severely stringent conditions may, however, use hybridization and / or washing 1, 2, 3 or 4 ° C below the thermal melting point (T<sub>m</sub>); moderately stringent conditions may use hybridization and / or washing 6, 7, 8, 9 or 10 ° C lower than the thermal melting point (T<sub>m</sub>); low stringency conditions may use hybridization and / or washing 11, 12, 13, 14, 15 or 20 ° C lower than the thermal melting point (T<sub>m</sub>). Using the equation, wash and hybridization compositions and T<sub>m</sub> desired, those skilled in the art will understand that variations in hybridization stringency and / or washing solutions are inherently described. If the desired degree of mismatch results in a T<sub>m</sub> less than 45 ° C (aqueous solution) or 32 ° C (formamide solution), it is preferred to increase the concentration of SSC, so that a higher temperature can be used. Extensive guidance on nucleic acid hybridization is found in Tijssen, Laboratory Techniques in Biochemistry and Molecular Biology Hybridization with Nucleic Acid Probes, Part I, Chapter 2, OverView of Principies of Hybridization and the Strategy of Nucleic Acid Probe Assays, Elsevier, New York ( 1983); and Current Protocols in Molecular Biology, Chapter 2, Ausubel et al, Eds., Greene Publishing and Wiley-ltersterscience, New York (1995). Washing and / or hybridization conditions can be applied for at least ten, thirty, sixty, ninety, 120 or 240 minutes.
"Sequence identity" or "identity" in the context of nucleic acid or polypeptide sequences indicates the nucleic acid bases or amino acid residues in two sequences that are identical when aligned for maximum matching over a specified comparison window.
In this way, “percentage of sequence identity” designates the value determined by comparing two sequences ideally aligned over a comparison window, where the part of the polynucleotide or polypeptide sequence in the comparison window can comprise additions or deletions. (ie spaces) compared to the reference sequence (which does not include additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions in which identical amino acid residue or nucleic acid base occurs in the two sequences to generate the number of matching positions, dividing the number of matching positions by the total number of positions in the window. comparison and multiplying the results by one hundred to generate the sequence identity percentage. Useful examples of percentages of sequence identities include, but are not limited to, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%,
90%, 95% or any percentage of 50% to 100%. These identities can be determined using any of the programs described herein.
Sequence alignments and similarity or percent identity calculations can be determined using a series of comparison methods designed to detect homologous sequences that include, but are not limited to, the Megalign® program in the LASERGENE bioinformatics computing suite (DNASTAR Inc., Madison Wl ). Within the context of this application, it will be understood that, when using sequence analysis software for analysis, the results of the analysis will be based on the “default values” of the indicated program, unless otherwise specified. As used herein, “default values” will indicate any set of values or parameters originally loaded with the software when first started.
The “Clustal V method of alignment” corresponds to the alignment method called Clustal V (described by Higgins and Sharp, CABIOS. 5: 151-153 (1989); Higgins, DG et al (1992), Comput. Appl. Biosci. 8 : 189-191) and found in the MegAlign® program of the LASERGENE bioinformatics computing suite (DNASTAR Inc., Madison Wl). For multiple alignments, the default values correspond to INTERVAL PENALTY = 10 and INTERVAL LENGTH PENALTY = 10. The standard parameters for paired alignments and calculation of the percentage of protein sequence identity using the Clustal method are WORD LENGTH = 1, INTERVAL PENALTY = 3, VISUALIZATION OF THE
BEST RESULT = 5 and DIAGONAL SPACING = 5. For nucleic acids, these parameters are WORD LENGTH = 1, INTERVAL PENALTY = 5, BEST RESULT VIEWING = 4 and DIAGONAL SPACING = 4. After the alignment of the sequences using the program Clustal V, it is possible to obtain a “percentage of identity” by observing the table “sequence distances” in the same program.
"BLASTN method of alignment" is an algorithm provided by the National Center for Biotechnological Information (NCBI) to compare nucleotide sequences using standard parameters.
Those skilled in the art understand that many levels of sequence identity are useful in identifying polypeptides, from other species, in which these polypeptides have the same or similar function or activity. Useful examples of identity percentages include, but are not limited to, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or any entire percentage from 50% to 100 %. In fact, any entire amino acid identity from 50% to 100% can be useful in describing the present invention, such as 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59 %, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92% , 93%, 94%, 95%, 96%, 97%, 98% or 99%. In addition, any partial or full length complement of this isolated nucleotide fragment is of interest.
"Gene" means a fragment of nucleic acid that expresses a specific protein, which includes anterior regulatory sequences (non-coding sequences 5j and later (non-coding sequences 3j to the coding sequence. "Native gene" indicates a gene found in nature with its own regulatory sequences. "Chimeric gene" indicates any gene that is not a native gene, which comprises regulatory and coding sequences that are not found together in nature. Consequently, a chimeric gene can comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged differently than is normally found in nature. An “exogenous” gene indicates a gene not normally found in the host organism, but which is introduced into the host organism through gene transfer. Exogenous genes can comprise native genes inserted into a non-native organism or chimeric genes. A "transgene" is a gene that was introduced into the genome through a transformation procedure.
The term “genome”, when applied to a plant cell, encompasses not only the chromosomal DNA found inside the nucleus, but also organelle DNA found in subcellular components (such as mitochondria, plastids) of the cell.
"Codon-optimized gene" is a gene that has its codon usage frequency designed to mimic the host cell's preferred codon usage frequency.
"Allele" is one of several alternative forms of a gene that occupies a given location on a chromosome. When all the alleles present at a given location on a chromosome are identical, that plant is homozygous at that location. If the alleles present at a given location on a chromosome are different, that plant is heterozygous at that location.
"Coding sequence" indicates a DNA sequence that encodes a specific amino acid sequence. “Regulatory sequences” indicate nucleotide sequences located above (non-coding sequences 5 '), in or below (non-coding sequences 3') a coding sequence and that influence the transcription, stability or processing of RNA or translation of the sequence of associated coding. Regulatory sequences can include, but are not limited to, promoters, leading translation sequences, introns, polyadenylation recognition sequences, RNA processing sites, effector joining sites, and stem and loop structures.
"Promoter" means a DNA sequence capable of controlling the expression of a coding sequence or functional RNA. The promoter sequence consists of elements closer and more distant in the flow, with the latter often referred to as amplifiers. Consequently, an "amplifier" is a DNA sequence that can stimulate promoter activity and can be an innate element of the promoter or a heterologous element inserted to amplify the level or tissue specificity of a promoter. Promoters can be derived in their entirety from a native gene or be composed of different elements derived from different promoters found in nature, or they can even comprise synthetic DNA segments. Those skilled in the art understand that different promoters can direct the expression of a gene in different tissues or cell types, at different stages of development, or in response to different environmental conditions. It is also recognized that, as in most cases the exact boundaries of the reulatory sequences have not been completely defined, DNA fragments with some variation may have identical promoter activity. The promoters that cause a gene to be expressed in most cell types are most often referred to as "constitutive promoters". New promoters of various types useful in plant cells are constantly being discovered; numerous examples can be found in the compilation of Okamuro, JK and
Goldberg, RB, Biochemistry of Plants 15: 1-82.
"Leader translation sequence" means a polynucleotide sequence located between the promoter sequence of a gene and the coding sequence. The leading translation sequence is present in the fully processed mRNA after the translation start sequence. The leading translation sequence can affect the processing of the primary mRNA transcript, the stability of the mRNA or the efficiency of the translation. Examples of leading translation sequences have been described (Turner, R. and Foster, G.
D., Mol. Biotechnol. 3; 225-236 (1995)).
“Non-coding sequences 3” ', “transcription termination” or “termination sequences” means DNA sequences after a coding sequence and includes polyadenylation recognition sequences and other regulatory coding sequences capable of affecting the mRNA processing or gene expression. The polyadenylation signal is typically characterized by affecting the addition of traces of polyadenyl acid to the 3 'end of the mRNA precursor. The use of different 3 'non-coding sequences is exemplified by Ingelbrecht et al, Plant Cell V. 671-680 (1989).
"RNA transcript" means the product resulting from the RNA polymerase-catalyzed transcription of a DNA sequence. When the RNA transcript is a perfect complementary copy of the DNA sequence, it is called a primary transcript. An RNA transcript is called a mature RNA when it is an RNA sequence derived from the post-transcriptional processing of the primary transcript. "Messenger RNA" or "mRNA" means RNA that does not contain introns and that can be translated into protein by the cell. "CDNA" means DNA that is complementary to an mRNA model and synthesized from it using the enzyme reverse transcriptase. The cDNA can be single-stranded or converted to double-stranded form using the Klenow fragment of
DNA polymerase I. "Sense" RNA refers to an RNA transcript that includes mRNA and can be translated into protein in a cell or in vitro. “Nonsense RNA” means an RNA transcript that is complementary to a target primary mRNA or transcript, in whole or in part, and that blocks the expression of a target gene (U.S. Patent No. 5,107,065). The complementarity of a nonsense RNA can occur with any part of the specific genetic transcript, that is, in the 5 'non-coding sequence, 3' non-coding sequence, introns or in the coding sequence. “Functional RNA” means nonsense RNA, ribozyme RNA or other RNA that may not be translated, but that still has an effect on cellular processes. The terms "complement" and "reverse complement are used interchangeably in the present with respect to mRNA transcripts and are intended to define the RNA meaningless of the message.
The term "operably linked" refers to the association of nucleic acid sequences over an isolated nucleic acid fragment, such that the function of one is regulated by the other. A promoter is operably linked to a coding sequence, for example, when it is able to regulate the expression of that coding sequence (i.e., the coding sequence is under the transcriptional control of the promoter). The coding sequences can be operatively linked to regulatory sequences in meaningful or meaningless orientation. In another example, the complementary RNA regions according to the present invention can be operatively linked, either directly or indirectly, 5 'to the target mRNA, or 3' to the target mRNA, or to the target mRNA, or a first complementary region is 5 'and its complement is 3' for the target mRNA.
The standard recombinant DNA and molecular cloning techniques used in the present are well known in the art and are more fully described in Sambrook, J., Fritsch, EF and Maniatis, T., Molecular
Cloning: A Laboratory Manual; Cold Spring Harbor Laboratory Press: Cold Spring Harbor NY (1989). Transformation methods are well known to those skilled in the art and are described below.
"PCR" or "Polymerase Chain Reaction" is a technique for synthesizing large amounts of specific DNA segments and consists of a series of repetitive cycles (Perkin Elmer Cetus Instruments, Norwalk CT). Typically, double-stranded DNA is heat denatured, the two primers complementary to the 3 'boundaries of the desired segment are combined under low temperature and then extended at intermediate temperature. A set of these three consecutive steps is called a "cycle".
The term "recombinant" indicates an artificial combination of two differently separated sequence segments, for example, by means of chemical synthesis or by manipulating isolated nucleic acid segments by means of genetic engineering methods.
The terms "plasmid", "vector" and "set" designate an additional chromosomal element that often carries genes that are not part of the cell's central metabolism, usually in the form of circular double-stranded DNA fragments. These elements can be autonomous reproduction sequences, genome integration sequences, nucleotide or phage sequences, linear or circular, from a single or double stranded DNA or RNA, derived from any source, in which a series of nucleotide sequences has been joined or recombined in an exclusive construct that is capable of introducing a promoter fragment and sequence of
DNA for a selected gene product along with appropriate 3 'untranslated sequence in a cell. “Transformation set” indicates a specific vector that contains an exogenous gene and contains additional elements to the exogenous gene that facilitates the transformation of a specific host cell. “Expression set” means a specific vector that contains an exogenous gene and has elements in addition to the exogenous gene that allow enhanced expression of that gene in an exogenous host (that is, in a discrete nucleic acid fragment to which you can move a nucleic acid fragment or sequence).
The terms "recombinant construction", "expression construction", "chimeric construction", "construction" and "recombinant DNA construction are used interchangeably at present. A recombinant construct comprises an artificial combination of nucleic acid fragments, such as regulatory and coding sequences that are not found together in nature. A chimeric construct can comprise, for example, regulatory sequences and coding sequences derived from different sources or regulatory sequences and coding sequences derived from the same source, but arranged differently from that found in nature. This construction can be used on its own or can be used in conjunction with a vector. If a vector is used, the selection of the vector depends on the method to be used to transform the host cells, as is well known to those skilled in the art. For example, a plasmid vector can be used. Those skilled in the art are well aware of the genetic elements that need to be present in the vector in order to successfully transform, select and propagate host cells that comprise any of the isolated nucleic acid fragments according to the present invention. Those skilled in the art will also recognize that different and independent transformation events will result in different levels and patterns of expression (Jones et al, EMBO J. 4: 2411-2418 (1985); De Almeida et al, Mol. Geri. Genetics 218: 78-86 (1989)) and, therefore, that several events must be selected in order to obtain lineages that exhibit the desired level and pattern of expression. This selection can be achieved through Southern DNA analysis, Northern mRNA expression analysis, immunoblot analysis of protein expression or phenotypic analysis, among others.
The term "expression", as used in the present, indicates the elaboration of a functional final product (such as an mRNA or a protein (whether it is a precursor or a mature one)).
The term "introduced" indicates the delivery of a nucleic acid (such as expression construct "or protein in a cell. Introduced includes reference to the incorporation of a nucleic acid into a eukaryotic or prokaryotic cell, where the nucleic acid can be incorporated into the genome of the cell, and includes reference to the transient delivery of a nucleic acid or protein to the cell. Introduced includes reference to stable or transient transformation methods, as well as sexual crossing. Thus, “introduced” in the context of insertion of a fragment of nucleic acid (such as a recombinant DNA construct / expression construct) into a cell indicates “transfection”, transformation ”or“ transduction ”and includes reference to the incorporation of a nucleic acid fragment in a eukaryotic or prokaryotic cell, where the nucleic acid fragment can be incorporated into the cell's genome (such as chromosome, plasmid, plastid or mitochondria DNA), converted into a stand-alone replica or expressed in a transient manner (such as transfected mRNA).
"Mature" protein means a polypeptide processed after translation (that is, one from which any pre- or pro-peptides present in the original translation product have been removed). "Precursor" protein designates the original mRNA translation product (that is, with pre- and propeptides still present). Pre- and pro-peptides can be, but are not limited to, signs of intracellular localization.
“Stable transformation” means the transfer of a nucleic acid fragment to the genome of a host organism, including nuclear and organellar genomes, resulting in genetically stable inheritance. On the other hand, "transient transformation" indicates the transfer of a fragment of nucleic acid to the nucleus, or organelle that contains DNA, from a host organism, which results in genetic expression without integration or stable inheritance. The host organisms that contain the transformed nucleic acid fragments are called "transgenic" organisms.
As used at present, "transgenic" refers to a plant or cell that comprises a heterologous polynucleotide in its genome. Preferably, the heterologous polynucleotide is integrated stably within the genome, such that the polynucleotide is passed on to successive generations. The hetreologist polynucleotide can be integrated into the genome alone or as part of an expression construct. Transgenic is used at present to include any cell, cell line, callus, tissue, part of a plant or plant whose genotype has been altered by the presence of heterologous nucleic acid, including transgenics altered in this way and those created by sexual crosses or asexual spread from the initial transgenic. The term “transgenic”, as used at present, does not include altering the genome (chromosomal or extrachromosomal) by means of conventional methods of plant cultivation or naturally occurring events, such as random cross-fertilization, non-recombinant viral infections, transformation non-recombinant bacterial, non-recombinant transposition or spontaneous mutation.
"Nonsense inhibition" means the production of nonsense RNA transcripts capable of suppressing expression of the target protein. “Cossupression” means the production of sense RNA transcripts capable of suppressing the expression of identical or substantially similar endogenous or exogenous genes (US Patent No. 5,231,020). Cossupressure constructs in plants were previously designed by focusing on the overexpression of a nucleic acid sequence that has homology to an endogenous mRNA, in sense orientation, which results in the reduction of all RNA that has homology to the overexpressed sequence (see Vaucheret et al, Plant J. 16: 651-659 (1998); and Gura, Nature 404: 804-808 (2000)). The overall efficiency of this phenomenon is low and the extent of RNA reduction varies widely. More recent work has described the use of “hairpin” structures that incorporate, in whole or in part, an mRNA coding sequence in complementary orientation that results in a potential “stem circuit” structure for the expressed RNA (PCT patent WO 99/53050, published on October 21, 1999; PCT Patent WO 02/00904, published on January 3, 2002).
This increases the frequency of cosuppression in recovered transgenic plants. Another variation describes the use of viral plant sequences to direct the suppression or "silencing" of nearby mRNA coding sequences (PCT Patent No. WO 98/36083, published on August 20, 1998). Both of these phenomena of cosuppression have not been elucidated mechanically, although genetic evidence has begun to unravel this complex situation (Elmayan et al, Plant Cell 10: 1747-1757 (1998)).
The term “oilseed” means organisms that tend to store their energy source in the form of lipids (Weete, in Fungai Lipid
Biochemistry, second edition, Plenum, 1980). A class of plants identified as oilseeds is commonly referred to as "oilseed" plants. Examples of oilseed plants include, but are not limited to, soy (Glycine and Soja sp.), Flax (Linum sp), rapeseed (Brassica sp), corn, cotton, saffron (Carthamus sp) and sunflower (Helianthus sp).
In oleaginous microorganisms, the cellular oil or TAG content generally follows a sigmoid curve, in which the lipid concentration increases until it reaches its maximum in the initial stationary or later logarithmic growth phase and then is gradually reduced during the phases. stationary and dead (Yongmanitchai and Ward, Appl. Environ. Microbiol. 57: 41925 (1991)). The expression oleaginous yeast indicates microorganisms classified as yeasts that manufacture oil. It is not uncommon for oilseed microorganisms to accumulate more than about 25% of their dry cell weight in the form of oil. Examples of oleaginous yeast include, but are not limited to, the following genera: Yarrowia, Candida, Rhodotorula, Rhodosporidium, Cryptococcus, Trichosporon and Lipomyces.
The term "Euglenophyceae" indicates a group of photosynthetic or colorless unicellular flagella ("euglenoids") found alive in fresh, salt water, soil and parasitic environments. The class is characterized by solitary single cells, in which the majority swim freely and have two flagella (one of which may be non-emergent) that arise from a previous invagination known as a reservoir. Photosynthetic Euglenoids contain one to several grass-green chloroplasts, ranging from simple discs to expanded plates or strips. Colorless Euglenoids depend on osmotrophy or phagotrophy for assimilation of nutrients. About a thousand species have been described and classified into forty genera and six orders. Examples of Euglenophyceae include, but are not limited to, the following genera: Euglena, Eutreptiella and Tetruetreptia.
The term "plant" indicates whole plants, plant organs, plant tissues, seeds, plant cells, seeds and their offspring. Plant cells include, without limitation, seed cells, suspension cultures, embryos, meristematic regions, callus tissue, leaves, roots, shoots, gametophytes, sporophytes, pollen and microspores.
“Offspring comprise any subsequent generation of a plant.
General analysis: microbial biosynthesis of fatty acids and triacylglycerols
In general, the accumulation of lipids in oleaginous microorganisms is triggered in response to the general ratio between carbon and nitrogen present in the growth medium. This process, which generates the synthesis of free palmitate (16: 0) in the form of a new substance in oleaginous microorganisms, is described in detail in PCT Publication No. WO 2004/101757. Palmitate is the precursor to derivatives of longer chain saturated and unsaturated fatty acids, which are formed through the action of elongases and desaturases (Fig. 1).
TAGs (the primary storage unit for fatty acids) are formed by a series of reactions involving: (1) the esterification of an acyl-CoA molecule into glycerol 3-phosphate by means of an acyltransferase to produce lysophosphatidic acid; (2) esterification of a second acyl-CoA molecule by means of an acyltransferase to generate 1,2-diacylglycerol phosphate (commonly identified as phosphatidic acid); (3) removal of a phosphate by phosphatidic acid phosphatase to generate 1,2 diacylglycerol (DAG); and (4) adding a third fatty acid through the action of an acyltransferase to form TAG. A wide spectrum of fatty acids can be incorporated into TAGs, including saturated and unsaturated fatty acids and short- and long-chain fatty acids.
Biosynthesis of omega fatty acids
The metabolic process in which oleic acid is converted to long-chain omega 3 / omega 6 fatty acids involves elongating the carbon chain by adding carbon atoms and desaturating the molecule by adding double bonds. This requires a series of special stretching and desaturation enzymes present in the endoplasmic reticulum membrane. As seen in Fig. 1 and described below, however, there are often several alternative processes for producing a specific long-chain omega 3 / omega 6 fatty acid.
Specifically, all processes require the initial conversion of oleic acid to LA, the first of the omega 6 fatty acids, by a delta-12 desaturase. Using the “delta-9 elongase / delta-8 desaturase process”, then long-chain omega 6 fatty acids are formed as follows: (1) LA is converted to EDA by a delta-9 elongase; (2) EDA is converted to DGLA by a delta-8 desaturase; and (3) DGLA is converted to ARA by a delta-5 desaturase. Alternatively, the “delta-9 elongase / delta-8 desaturase process” can be used for the formation of long-chain omega 3 fatty acids as follows: (1) LA is converted to ALA, the first of the omega 3 fatty acids, by a delta-15 desaturase; (2) ALA is converted to ETrA by a delta-9 elongase; (3) ETrA is converted to ETA by a delta-8 desaturase; (4) ETA is converted to EPA by a delta-5 desaturase; (5) EPA is converted to DPA by elongase
C20-22; θ (6) DPA is converted to DHA by a delta-4 desaturase.
Optionally, omega 6 fatty acids can be converted to omega 3 fatty acids; ETA and EPA, for example, are produced from DGLA and ARA, respectively, by delta-17 desaturase activity.
Alternative biosynthesis processes of omega fatty acids
3 / omega 6 use a delta-6 desaturase and elongase C18-20 (also known as delta-6 elongase, the terms can be used interchangeably) (ie, the “delta-6 desaturase / delta-6 elongase process ”). More specifically, LA and ALA can be converted to GLA and STA, respectively, by a delta-6 desaturase; then, a C18-20 elongase converts GLA to DGLA and / or STA to ETA.
It is contemplated that the specific functionalities that need to be introduced in a specific host organism for the production of omega 3 / omega 6 fatty acids will depend on the host cell (and its native PUFA profile and / or desaturase / elongase profile), availability of the substrate and the desired final product (s). The expression of the delta-9 elongase / delta-8 desaturase process may be preferred, for example, in some embodiments, unlike the expression of the delta-6 desaturase / delta-6 elongase process, since PUFAs produced through the process above are exempt from GI_A.
Those skilled in the art will be able to identify several possible genes that encode each of the desired enzymes for the biosynthesis of omega 3 / omega 6 fatty acids. Useful desaturase and elongase sequences can be derived from any source, such as isolated from a natural source. (from bacteria, algae, fungi, plants, animals, etc.), produced using a semi-synthetic process or synthesized as new substances. Although the specific source of the desaturase and elongase genes introduced into the host is not critical, considerations for the selection of a specific polypeptide that has desaturase or elongase activity include: (1) the substrate specificity of the polypeptide; (2) whether the polypeptide or one of its components is a rate-limiting enzyme; (3) whether desaturase or elongase is essential for the synthesis of a desired PUFA; and / or (4) cofactors required by the polypeptide. The expressed polypeptide preferably has parameters compatible with the biochemical environment of its location in the host cell (see PCT Patent No. WO 2004/101757 for further details).
In additional embodiments, it will also be useful to consider the conversion efficiency of each specific desaturasse and / or elongase. More specifically, as each enzyme rarely works with 100% efficiency of converting substrate to product, the final lipid profile of unpurified oils produced in a host cell will typically be a mixture of several PUFAs consisting of omega 3 / omega fatty acid desired, as well as several intermediate PUFAs above in the flow. Thus, the consideration of the conversion efficiency of each enzyme is also a variable when optimizing the biosynthesis of a desired fatty acid that must be considered in the light of the desired final lipid profile of the product.
With each of the above considerations in mind, possible genes that have the appropriate desaturase and elongase activities (such as delta-6 desaturases, elongases C18-20, delta-5 desaturases, delta-17 desaturases, delta-15 desaturases, delta- 9 desaturases, delta-12 desaturases, elongases C14-16, elongases Cie-ie. delta-9 elongases, delta-8 desaturases, delta-4 desaturases and elongases C20-22) can be identified according to publicly available literature (such as GenBank), patent literature and experimental analysis of organisms that have the production capacity of PUFAs. These genes will be suitable for introduction into a specific host organism, to allow or enhance the synthesis of PUFAs by the organism.
Identification of innovative delta-5 desaturases sequences
In the present invention, nucleotide sequences encoding delta-5 desaturases were isolated from Euglena anabaena (referred to herein as "EaD5Des1").
Thus, the present invention relates to an isolated polynucleotide that comprises:
(a) a nucleotide sequence encoding a polypeptide that has delta-5 desaturase activity, where the polypeptide has at least 80% amino acid identity, based on the method
Clustal V alignment, compared to an amino acid sequence as described in SEQ ID No. 13 (EaD5Des1);
(b) a nucleotide sequence encoding a polypeptide that has delta-5 desaturase activity, where the nucleotide sequence has at least 80% sequence identity, based on the BLASTN method of alignment, compared to a nucleotide sequence as described in SEQ ID No. 12 (EaD5Des1); or (c) a complement of the nucleotide sequence of (a) or (b), wherein the complement and the nucleotide sequence consist of the same number of nucleotides and are 100% complementary.
In yet another aspect, the present invention relates to an isolated polynucleotide comprising a nucleotide sequence that encodes a polypeptide that has delta-5 desaturase activity, wherein the nucleotide sequence has sequence identity of at least 90%, with based on the BLASTN method of alignment, compared to a nucleotide sequence as described in SEQ ID No. 12.
The EaD5Des1 sequences of the present can be codon-optimized for expression in a specific host organism (see SEQ ID No. 45). As is well known in the art, this can be a useful means to further optimize the expression of the enzyme in the alternative host, as the use of preferred codons by the host can substantially increase the expression of the exogenous gene encoding the polypeptide. In general, codons preferred by the host can be determined in a specific host species of interest by examining the use of codons in proteins (preferably those expressed in greater quantities) and determining which codons are used with the highest frequency. Then, the coding sequence for a polypeptide of interest that has, for example, desaturase activity can be synthesized, in whole or in part, using the preferred codons in the host species.
EaD5Des1 can be optimized by codons for expression in Yarrowia lipolytica, as taught in PCT Patent No. WO 04/101757 and in US Patent No. 7,125,672. In one embodiment, it may be desirable to modify a part of the codons encoding EaD5Des1 (as described in SEQ ID NO: 12) to increase gene expression in a host organism that includes, but is not limited to, a plant or plant part.
Those skilled in the art would be able to use the 5 teachings of the present to create several other codon-optimized delta-5 desaturase proteins for optimal expression in alternative hosts, based on the wild type EaD5Des1 sequence. Accordingly, the present invention relates to any codon-optimized delta-5 desaturase protein that is derived from wild type EaD5Des1 (i.e., encoded by SEQ ID NO: 12).
Identification and isolation of counterparts
Any of the present desaturase sequences (ie, EaD5Des1) or parts thereof can be used to search for delta-5 desaturase homologs in the same or other species of bacteria, algae, fungus, euglenoid or plant using sequence analysis software. In general, this computer software matches similar strings by assigning degrees of homology to various substitutions, exclusions and other modifications.
Alternatively, any of the present desaturase sequences or parts thereof can also be employed as hybridization reagents for identifying delta-5 desaturase homologs. The basic components of a nucleic acid hybridization test include a probe, a sample suspected of containing the gene or genetic fragment of interest, and a specific hybridization method. The probes according to the present invention are typically single stranded nucleic acid sequences that are complementary to the nucleic acid sequences to be detected. The probes are "hybridizable" in the sequence of nucleic acids to be detected. Although the probe length can vary from five bases to tens of thousands of bases, a probe length of about fifteen bases to about thirty bases is typically appropriate. Only part of the probe molecule needs to be complementary to the nucleic acid sequence to be detected. In addition, the complementarity between the probe and the target sequence need not be perfect. Hybridization occurs between imperfectly complementary molecules with the result that a certain fraction of the bases in the hybridized region is not paired with the appropriate complementary base.
Hybridization methods are well defined. Typically, the probe and the sample should be mixed under conditions that allow hybridization of nucleic acids. This involves contacting the probe and sample in the presence of an organic or inorganic salt under the appropriate temperature and concentration conditions. The sample and probe nucleic acids must be in contact for a sufficiently long time so that any possible hybridization between the probe and the nucleic acid sample can occur. The concentration of probe or target in the mixture will determine the time required for hybridization to occur. The higher the target or probe concentration, the shorter the required hybridization incubation time. Optionally, a chaotropic agent (such as guanidinium chloride, guanidinium thiocyanate, sodium thiocyanate, lithium tetrachloroacetate, sodium perchlorate, rubidium tetrachloroacetate, potassium iodide, cesium trifluoroacetate) can be added. If desired, formamide can be added to the hybridization mixture, typically 30 to 50% (v / v).
Various hybridization solutions can be employed. Typically, these comprise about 20 to 60% by volume, preferably 30%, of a polar organic solvent. A common hybridization solution employs about 30 to 50% v / v formamide, about 0.15 to 1 M sodium chloride, about 0.05 to 0.1 M buffers (such as sodium citrate, Tris -HCI, PIPES or HEPES (pH in the range of about 6 to 9), about 0.05 to 0.2% detergent (such as sodium dodecyl sulfate) or 0.5 to 20 mM EDTA, FICOLL (Pharmacia Inc.) (about 300 to 500 kdal), polyvinylpyrrolidone (about 250 to 500 kdal) and serum albumin. Also included in the typical hybridization solution are unlabeled carrier nucleic acids to about 0.1 to 5 mg / ml, fragmented nucleic DNA (such as calf's thymus, salmon sperm DNA or yeast RNA) and, optionally, about from 0.5 to 2% weight / volume of glycine. Other additives can also be included, such as volume exclusion agents that include a series of swellable or water-soluble polar agents (such as polyethylene glycol), anionic polymers (such as polyacrylate or polymethylacrylate) and anionic saccharide polymers (such as dextran sulfate ).
Hybridization of nucleic acids is adaptable to a number of test formats. One of the most appropriate is the sandwich test format.
The sandwich test is particularly adaptable to hybridization under non-denaturation conditions. A major component of a sandwich type test is a solid support. The solid support absorbed or covalently attached an immobilized nucleic acid probe to it that is not labeled and is complementary to a part of the sequence.
In additional embodiments, any of the delta-5 desaturase nucleic acid fragments described herein (or any of their identified counterparts) can be used to isolate genes encoding homologous proteins from the same or another species of bacteria, algae, fungus, euglenoid or plant. The isolation of homologous genes using sequence-dependent protocols is well known in the art. Examples of sequence-dependent protocols include, but are not limited to: (1) nucleic acid hybridization methods; (2) DNA and RNA amplification methods, as exemplified by various uses of nucleic acid amplification technologies (such as polymerase chain reaction (PCR), Mullis et al, U.S. Patent No. 4,683,202; ligase chain (LCR), Tabor et al, Proc. Acad. Sci. USA 82: 1074 (1985); or tape displacement amplification (SDA), Walker et al, Proc. Natl. Acad.
Know. USA, 89: 392 (1992)); and (3) methods of building libraries and selection through complementation.
Genes that encode proteins or polypeptides similar to those of delta-5 desaturases described herein may, for example, be isolated directly using the nucleic acid fragments of the present or a part of them as DNA hybridization probes to select libraries from, for example, any yeast or fungus desired using methodology well known to those skilled in the art (where organisms that produce ARA and / or EPA would be preferred). Specific oligonucleotide probes based on the present nucleic acid sequences can be designed and synthesized by methods known in the art (Maniatis, above). In addition, the complete sequences can be used directly to synthesize DNA probes by methods known to those skilled in the art (such as DNA staining of random primers, Nick translation or later staining methods) or RNA probes using transcription systems in vitro available. In addition, specific primers can be designed and used to amplify the sequences of the present, in whole or in part. The resulting amplification products can be labeled directly during amplification reactions or marked after amplification reactions and used as probes to isolate fragments of
Full-length DNA under conditions of appropriate stringency.
Typically, in PCR-type amplification methods, primers have different sequences and are not complementary to each other. Depending on the desired test conditions, primer sequences should be designed to provide efficient and reliable reproduction of the target nucleic acid. PCR primer design methods are common and well known in the art (Thein and Wallace, The Use of Oligonucleotide as Specific Hybrídization Probes in the Diagnosis of Genetic Disorders, in Human Genetic
Diseases: A Practical Approach, KE Davis Ed. (1986), p. 33-50, IRL: Herndon VA; and Rychlik, W. in Methods in Molecular Biology, White, BA, Ed. (1993), Vol. 15, p. 31-39, PCR Protocols: Current Methods and Applications, Humania: Totowa NJ).
Generally, two short segments of the 10 sequences of the present can be used in PCR protocols to amplify fragments of longer nucleic acids that encode homologous genes from DNA or RNA. PCR can also be performed on a library of cloned nucleic acid fragments in which the sequence of one primer is derived from the nucleic acid fragments of the present and the sequence of the other primer uses the presence of traces of polyadenic acid towards the end 3 'of the mRNA precursor encoding eukaryotic genes.
Alternatively, the second primer sequence can be based on sequences derived from the cloning vector. Technicians in the subject can follow, for example, the RACE protocol (Frohman et al, PNAS
USA 85: 8998 (1988)) to generate cDNAs using PCR to amplify copies of the region between a single point in the transcript and the 3 'or 5' end. Primers oriented in 3 'and 5' directions can be designed from the sequences of the present. Using commercially available 3 'RACE or 5' RACE systems (Gibco / BRL, Gaithersburg MD), specific 3 'or 5' cDNA fragments can be isolated (Ohara et al, PNAS USA 86: 5673 (1989); Loh et al , Science 243: 217 (1989)).
In other embodiments, any of the delta-5 desaturase nucleic acid fragments described herein (or any of their identified counterparts) can be used to create new and improved fatty acid desaturases. As is well known in the art, mutagenesis and in vitro selection, chemical mutagenesis, genetic switching methods or other means can be employed to obtain naturally occurring desaturase gene mutations. Alternatively, enhanced fatty acids can be synthesized by domain switching, in which a functional domain of any of the delta-5 desaturase nucleic acid fragments described herein is exchanged with a functional domain in an alternative desaturase gene, in order to result in an innovative protein. As used herein, "domain" or "functional domain" designates the sequence (s) of nucleic acids that is (are) capable of allowing a biological reaction in plants.
Methods of producing various omega 3 and / or omega 6 fatty acids
The introduction of chimeric genes encoding the delta-5 desaturase described herein (ie, EaD5Des1 or other mutant enzymes, codon-optimized enzymes or their counterparts) is expected, under the control of the appropriate promoters, to result in an increase in production of ARA and / or EPA in the transformed host organism, respectively. Thus, the present invention encompasses a method of direct production of PUFAs which comprises the exposure of a fatty acid substrate (ie, DGI_A and / or ETA) to the desaturase enzymes described in the present (such as EaD5Des1), in such a way that the substrate is converted into the desired fatty acid product (ie ARA and / or EPA).
More specifically, it is an object of the present invention to provide a method of producing ARA in a plant host cell (such as soybeans), wherein the plant host cell comprises:
(a) a recombinant construct encoding a delta-5 desaturase polypeptide selected from the group consisting of SEQ ID NO:
13; and (b) a source of DGLA;
wherein the host plant cell is grown under conditions such that delta-5 desaturase is expressed and DGLA is converted to ARA, where ARA is optionally recovered.
In alternative embodiments of the present invention, delta-5 desaturase can be employed for the use of the enzyme for converting ETA to EPA. Consequently, the present invention provides a method of producing EPA, wherein the host cell comprises:
(a) a recombinant construct encoding a delta-5 desaturase polypeptide selected from the group consisting of SEQ ID NO: 13; and (b) a source of ETA;
wherein the host plant cell is grown under conditions such that delta-5 desaturase is expressed and ETA is converted to EPA, where EPA is optionally recovered.
Alternatively, each delta-5 desaturase gene and its corresponding enzyme product described herein can be used indirectly to produce various omega 6 and omega 3 PUFAs, which include, for example, DGLA, ETA, ARA, EPA, DPA and / or DHA (see Fig. 1; see also PCT Patent No. WO 2004/101757). The indirect production of omega 3 / omega 6 PUFAs occurs when the fatty acid substrate is converted indirectly into the desired fatty acid product, through one or more intermediate or intermediate process steps. Thus, it is contemplated25 that the delta-5 desaturases described in the present (that is, EaD5Des1 or other mutant enzymes, codon-optimized enzymes or their counterparts) can be expressed together with additional genes that encode enzymes in the PUFA biosynthetic process (such as such as delta-6 desaturases, elongases C18-20, delta-17 dessaturases, delta-8 dessaturas, delta-15 dessaturases, delta-9 dessaturasses, delta-12 dessaturases, elongases C<sub>14</sub>.<sub>16</sub>, elongases C<sub>16</sub>-18. delta-9 elongases, delta-5 desaturases, delta-4 desaturases, elongases C20-22) to result in higher levels of longer chain omega 3 / omega 6 fatty acid production (such as ARA, EPA, DPA and DHA ).
In preferred embodiments, the delta-5 desaturases according to the present invention will be minimally expressed together with a delta-9 elongase and delta-8 desaturases (such as a delta-8 desaturase or a codon-optimized delta-8 desaturase). The delta-5 desaturase may also be expressed minimally together with a delta-6 desaturase and elongases C<sub>18</sub>-2o- The specific genes included in a specific expression set will, however, depend on the host cell (and its PUFA profile and / or desaturase / elongase profile), the availability of the substrate and the product (s) desired end (s).
When the desired end product is SCI and / or JUP, the delta-5 desaturase will be minimally expressed together with a delta-9 elongase in an organism that manufactures EDA and / or ERA, respectively.
The term “delta-6 desaturase / delta-6 elongase process” also refers to a biosynthetic process for producing long-chain PUFAs. This process comprises at least one delta-6 desaturase and one delta-6 elongase, in order to allow the biosynthesis of DGLA and / or ETA from LA and ALA, respectively. With the expression of other desaturases and elongases, ARA, EPA, DPA and DHA can also be synthesized.
Occasionally, a delta-6 elongase can elongate fatty acids in addition to the intended fatty acid. Delta-6 elongases generally convert, for example, GLA to DGLA, but some delta-6 elongases can also convert unwanted substrates, such as LA or ALA to EDA or ETrA, respectively. In a delta-6 desaturase / delta-6 elongase process, EDA and ETrA would be considered “fatty acid by-products” as defined herein. The addition of a delta-8 desaturase to a delta-6 desaturase / delta-6 elongase process would provide a means of converting the “fatty acid by-products” EDA and ETrA back to intermediate fatty acids ”(as defined above) DGLA and ETA, respectively.
Plant expression systems, sets, vectors and transformation
In one embodiment, the present invention relates to a recombinant construct comprising any of the delta-5 desaturase polynucleotides according to the present invention operably linked to at least one regulatory sequence appropriate for expression in a plant. A promoter is a DNA sequence that directs a plant's cellular machinery to produce RNA from the contiguous coding sequence below in the promoter (3 ') stream. The promoter region influences the speed, stage of development and cell type in which the gene's RNA transcript is performed. The RNA transcript is processed to produce mRNA that serves as a model for translating the RNA sequence into the amino acid sequence of the encoded polypeptide. The 5 'untranslated leader sequence is a region of the above mRNA in the flow of the protein coding region that can play a role in the mRNA initiation and translation. The 3 'polyadenylation and transcription termination signal is an untranslated region below in the flow of the protein coding region that functions in the plant cell to cause the termination of the RNA transcript and the addition of polyadeniate nucleotides to the 3' end of the RNA .
The origin of the promoter selected to direct the expression of the delta-5 desaturase coding sequence is not important, as long as there is sufficient transcriptional activity to carry out the present invention expressing translatable mRNA for the desired nucleic acid fragments in the desired host tissue at the right time . Heterologous or non-heterologous (i.e., endogenous) promoters can be used to practice the present invention. Suitable promoters include, but are not limited to, the prime alpha subunit of the beta conglycinin promoter, the Kunitz trypsin inhibitor 3 promoter, the annexin promoter, the glycine promoter Gy1, the beta subunit of the beta promoter conglycinin, the promoter of 30 K P34 / Gly Bd m, the albumin promoter, the Leg A1 promoter and the Leg A2 promoter.
The annexin promoter, or P34, is described in PCT Patent No. WO
2004/071178 (published on August 26, 2004). The level of activity of the annexin promoter is comparable to that of many known strong promoters, such as: (1) the CaMV 35S promoter (Atanassova et al, Plant Mol. Biol. 37: 275-285 (1998); Battraw and Hall , Plant Mol. Biol. 15: 527-538 (1990);
Holtorf et al, Plant Mol. Biol. 29: 637-646 (1995); Jefferson et al, EMBO J. 6: 3901-3907 (1987); Wilmink et al, Plant Mol. Biol. 28: 949-955 (1995)); (2) Arabidopsis oleosin promoters (Plant et al, Plant Mol. Biol. 25: 193-205 (1994); Li, Pd.D dissertation at Texas A&M University, pp. 107-128 (1997)) ; (3) ubiquitin extension protein promoters from
Arabidopsis (Callis et al, J. Biol. Chem. 265 (21): 12486-93 (1990)); (4) a tomato ubiquitin gene promoter (Rollfinke et al, Gene 211 (2): 267-76 (1998)); (5) a soy hot shock protein promoter (Schoffl et al, Mol. Gen. Genet. 217 (2-3): 246-53 (1989)); and (6) a corn histone H3 gene promoter (Atanassova et al, Plant Mol. Biol. 37 (2): 275-85 (1989)).
Another useful feature of the annexin promoter is its expression profile in developing seeds. The annexin promoter is most active in developing seeds in the early stages (ten days before pollination) and is largely dormant in later stages.
The expression profile of the annexin promoter is different from many specific seed promoters, such as seed storage protein promoters, which often provide higher activity in later stages of development (Chen et al, Dev. Genet. 10: 112 -122 (1989);
Ellerstrom et al, Plant Mol. Biol. 32: 1019-1027 (1996); Keddie et al, Plant Mol. Bioi. 24: 327-340 (1994); Plant et al (above); Li (above)). The annexin promoter has a more conventional expression profile, but remains distinct from other known seed-specific promoters. In this way, the annexin promoter will be a very attractive candidate when it is desired to overexpress, or suppress, a gene in embryos at an early stage of development. It may be desirable, for example, to overexpress a gene that regulates early embryo development or a gene involved in metabolism before seed maturation.
After identifying a suitable promoter for the expression of a specific delta-5 desaturase coding sequence, the promoter is then operably linked in sense orientation using conventional means well known to those skilled in the art.
The methods of molecular cloning and standard recombinant DNA used herein are well known in the art and described more fully in Sambrook, J. et al, Molecular Cloning: A Laboratory Manual, second edition; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, New York, 1989 (hereinafter “Sambrook et al, 1989”) or Ausubel, FM, Brent, R., Kingston, RE, Moore, DD, Seidman, JG, Smith, ALREADY and Struhl, K., Eds., Current Protocols in Molecular Biology, John Wiley and Sons,
New York, 1990 ("Ausubel et al, 1990").
After making the recombinant construct, it can then be introduced into a selected plant cell using methods well known to those of ordinary skill in the art (such as transfection, transformation and electroporation). Oilseed plant cells are the preferred plant cells. The transformed plant cell is then cultured and regenerated under appropriate conditions, which allows expression of the long chain PUFA which is optionally recovered afterwards and purified.
The recombinant constructs according to the present invention can be introduced into a plant cell; or, alternatively, each construct can be introduced into separate plant cells.
Expression in a plant cell can be carried out in a transient or stable manner, as described above.
The desired long-chain PUFAs can be expressed in seeds. Also within the scope of the present invention are seeds or plant parts obtained from such transformed plants.
Plant parts include differentiated and non-differentiated tissues, which include, but are not limited to, the following: roots, stems, buds, leaves, pollen, seeds, tumor tissues and various forms of cells and cultivation (such as isolated cells , protoplasts, embryos and callus tissue). The plant tissue can be in a plant or in an organ, tissue or plant cell culture.
The term "plant organ" means a plant tissue or group of tissues that constitute a morphologically and functionally distinct part of a plant. The term “genome” means the following: (1) the complete complement of genetic material (genes and non-coding sequences) is present in each cell of an organism, virus or organelle; (2) a complete set of chromosomes inherited as a parent (haploid) unit.
Thus, the present invention also relates to a method of transforming cells, which comprises transforming a cell with the recombinant construct according to the present invention and selecting the cells transformed with the recombinant construct according to the present invention.
Also of interest is a method of producing a transformed plant 5 which comprises transforming a plant cell with the delta-5 desaturase polynucleotides according to the present invention and regenerating plants from the transformed plant cell.
Methods for transforming dicots (using mainly Agrobacterium tumefaciens) and obtaining transgenic plants have been published, among others, for: cotton (US Patent No. 5,004,863); United States Patent No. 5,159,135); soy (North American Patent No. 5,569,834; North American Patent No. 5,416,011); Brassica (United States Patent No. 5,463,174); peanuts (Cheng et al, Plant Cell Rep. 15: 653-657 (1996); McKently et al, Plant Cell Rep. 14: 699-703 (1995));
papaya (Ling, K. et al, Bio / Technology 9: 752-758 (1991)); and pea (Grant et al, Plant Cell Rep. 15: 254-258 (1995)). For analysis of other commonly used methods of plant transformation, see Newell, CA (Mol. Biotechnol. 16: 53-65 (2000)). One of these transformation methods uses Agrobacterium rhizogenes (Tepfler, M. and Casse-Delbart, F., Microbioi. Sci. 4:
24-28 (1987)). Transformation of soybeans using direct DNA supply was published using PEG fusion (PCT Patent No. WO 92/17598), electroporation (Chowrira, GM et al, Mol. Biotechnol. 3: 17-23 (1995); Christou, P. et al, Proc. Natl. Acad. Sci. USA 84: 3962-3966 (1987)), microinjection and particle bombardment (McCabe, DE et al, Bio / Technology 6: 923 (1988); Christou et al, Piant Physioi. 87: 671-674 (1988)).
There are a number of methods of plant regeneration from plant tissue. The specific regeneration method will depend on the initial plant tissue and the specific plant species to be regenerated. The regeneration, development and cultivation of plants from isolated plant protoplasty transformers or from several transformed explants is well known in the art (Weissbach and Weissbach, Methods for Plant Molecular Biology (Eds.), Academic: San Diego CA (1988)) . This process of regeneration and growth typically includes the stages of selecting transformed cells and cultivating individualized cells along the usual stages of embryonic development throughout the rooted planticle stage. Embryos and transgenic seeds are regenerated in a similar way. The resulting transgenic rooted shoots are then planted in an appropriate plant growth medium, such as soil. Preferably, the regenerated plants are self-pollinated to provide homozygous transgenic plants. Otherwise, pollen obtained from regenerated plants is crossed with plants grown with seeds of agronomically important strains. On the other hand, pollen from plants of these important strains is used to pollinate regenerated plants. A transgenic plant according to the present invention that contains a desired polypeptide is grown using methods well known to those skilled in the art.
In addition to the procedures discussed above, those skilled in the art are familiar with standard resource materials that describe specific conditions and procedures for the construction, manipulation and isolation of macromolecules (such as DNA molecules, plasmids, etc.), generation of recombinant DNA fragments , recombinant expression constructs and selection and isolation of clones. See, for example, Sambrook et al,
Molecular Cloning: A Laboratory Manual, Cold Spring Harbor: New York (1989); Maliga et al, Methods in Plant Molecular Biology, Cold Spring Harbor: New York (1995); Birren et al, Genome Analysis: Detecting Genes, Vol. 1, Cold Spring Harbor: New York (1998); Birren et al, Genome Analysis:
Analyzing DNA, vol. 2, Cold Spring Harbor: New York (1988); Plant Molecular Biology: A Laboratory Manual, eds. Clark, Springer: New York (1997).
Examples of oilseed plants include, but are not limited to soy, species of Brassica, sunflower, corn, cotton, flax and saffron.
Examples of PUFAs that contain at least twenty carbon atoms and four or more carbon-carbon double bonds include, but are not limited to, omega 3 fatty acids such as EPA, DPA and DHA and ARA omega 6 fatty acid. Seeds obtained from these plants are also within the scope of the present invention, as well as the oil obtained from these seeds.
In one embodiment, therefore, the present invention relates to an oil plant comprising:
(a) a first recombinant DNA construct comprising an isolated polynucleotide that encodes a delta-5 desaturase polypeptide, operably linked to at least one regulatory sequence; and (b) at least one additional recombinant DNA construct comprising an isolated polynucleotide, operably linked to at least one regulatory sequence, which encodes a polypeptide selected from the group consisting of delta-4 desaturase, delta-5 desaturase, delta -6 desaturase, delta-8 desaturase, delta-9 desaturase, delta-9 congratase, delta-12 desaturase, delta-15 desaturase, delta-17 desaturase, elongase Ci<sub>4</sub>.<sub>16</sub>, elongase Ci<sub>6</sub>-i8, elongase C18-20 and elongase C2022 ·
Additional desaturases are discussed, for example, in
US Patents No. 6,075,183, 5,968,809, 6,136,574, 5,972,664, 6,051,754, 6,410,288 and PCT Patent No. WO 98/46763, WO 98/46764, WO 00/12720 and WO 00/40705.
The selection of combination sets used depends, in part, on the PUFA profile and / or desaturase / elongase profile of the oil plant cells to be transformed and the long chain PUFA that must be expressed.
In another aspect, the present invention relates to a method of making long-chain PUFAs in a plant cell comprising:
(a) transforming a cell with the recombinant construct according to the present invention; and (b) selection of the transformed cells that manufacture long-chain PUFAs.
In yet another aspect, the present invention relates to a method of producing at least one PUFA in a soybean cell comprising:
(a) transforming a soybean cell with a first recombinant DNA construct comprising:
(i) an isolated polynucleotide encoding a delta-5 desaturase polypeptide, operably linked to at least one regulatory sequence; and (ii) at least one additional recombinant DNA construct 20 comprising an isolated polynucleotide, operably linked to at least one regulatory sequence, which encodes a polypeptide selected from the group consisting of a delta-4 desaturase, delta-5 desaturase , delta-6 desaturase, delta-8 desaturase, delta-9 desaturase, delta-9 elongase, delta-12 desaturase, delta-15 desaturase, delta-17 desaturase, elongase C<sub>14</sub>.16, elongase C-ie-ie, elongase C18-20 and elongase C<sub>20</sub>.
22, (b) regeneration of a soybean plant from the transformed cell of step (a); and (c) selecting the seeds obtained from the plants in step (b) that have an altered level of PUFAs compared to the level in seeds obtained from an unprocessed soy plant.
In other preferred embodiments, the at least one additional recombinant DNA construct 5 encodes a polypeptide that has delta-9 elongase activity, such as delta-9 elongase isolated or derived from Isochrysis galbana (GenBank Accession No. AF390174; lgD9e) or delta-9 elongase isolated or derived from Euglena gracilis.
In other preferred embodiments, the at least one additional recombinant DNA construct encodes a polypeptide that has delta-8 desaturase activity. PCT Patent No. WO 2005/103253 (published April 22, 2005), for example, describes amino acid and nucleic acid sequences for a Pavlova saline delta-8 desaturase enzyme (see also North American Publication no.
2005/0273885). Sayanova et al (FEBS Lett. 580: 1946-1952 (2006)) describe the isolation and characterization of an amoeba cDNA that lives freely in the soil Acanthamoeba castellanii which, when expressed in Arabidopsis, encodes a delta-8 desaturase C<sub>2</sub>o- In addition, the applicant's copending assignment with a US patent application number 11/737772 (filed April 20, 2007; attorney's portfolio No. BB-1566) describes amino acid and acid sequences nucleic acids for a Pavlova lutheri delta-8 desaturase enzyme (CCMP459). US Patent Application No. 11/876115 (filed on October 22, 2007; attorney's brief No.
BB-1574) describes nucleic acid and amino acid sequences for a Tetruetreptia pomquetensis delta-8 desaturase enzyme CCMP1491, Eutreptiella sp CCMP389 and Eutreptiella cf_gymnastica CCMP1594.
Microbial expression systems, sets, vectors and transformation
The delta-5 desaturase genes and genetic products described herein (ie, EaD5Des1 or other mutant enzymes, codon-optimized enzymes or their counterparts) can also be produced in heterologous microbial host cells, particularly in oil yeast cells (such as Yarrowia lipolytica).
Microbial expression systems and expression vectors that contain regulatory sequences that drive high-level expression of exogenous proteins are well known to those skilled in the art. Any of these can be used to build chimeric genes for the production of any of the genetic products in the sequences of the present. These chimeric genes can then be introduced into appropriate microorganisms by means of transformation to provide high-level expression of the encoded enzymes.
Vectors or sets of DNA useful for the transformation of appropriate microbial host cells are well known in the art. The specific selection of sequences present in the construct depends on the desired expression products (above), the nature of the host cell and the proposed means of separating transformed cells against untransformed cells. Typically, however, the vector or set contains sequences that direct the transcription and translation of the relevant gene (s), a selectable marker, and sequences that allow for autonomous reproduction or chromosomal integration. Suitable vectors comprise a 5 'region of the gene that controls transcription initiation (such as a promoter) and a 3' region of the DNA fragment that controls transcription termination (i.e., a terminal). It is preferably superior when the two control regions are derived from genes of the transformed host cell, although it should be understood that these control regions do not need to be derived from the native genes for the specific species selected as the production host.
Promoters or early control regions that are useful for directing the expression of delta-t desaturase ORFs present in the desired microbial host cell are numerous and familiar to those skilled in the art. Virtually any promoter capable of directing the expression of these genes in the selected host cell is suitable for the present invention. Expression in a microbial host cell can be carried out in a transient or stable manner. Transient expression can be accomplished by inducing the activity of a regulating promoter operatively linked to the gene of interest. Stable expression can be achieved using a constitutive promoter operably linked to the gene of interest. When the host cell is a yeast, for example, functional transcription and translation regions are provided in yeast cells, particularly the host species (see, for example, PCT Patents No. WO 2004/101757 and WO 2006/052870 for regions preferred transcriptional regulatory agents for use in Yarrowia lipolytica). Any one of a series of regulatory sequences can be used, depending on whether constitutive or induced transcription is desired, the promoter's efficiency in expressing the ORF of interest, ease of construction and the like.
It was concluded that nucleotide sequences around the translation start codon “ATG” affect expression in yeast cells. If the desired polypeptide is poorly expressed in yeast, the nucleotide sequences of exogenous genes can be modified to include an efficient yeast translation start sequence for optimal gene expression. For yeast expression, this can be done through site-directed mutagenesis of an inefficiently expressed gene by fusing it in frame with an endogenous yeast gene, preferably a highly expressed gene. Alternatively, one can determine the sequence of initiation of consensus translation in the host and elaborate this sequence in heterologous genes for its ideal expression in the host of interest.
The termination region can be derived from the 3 'region of the gene from which the start region was obtained or from a different gene. A large number of termination regions are known and work satisfactorily in a number of hosts (when used in identical and different genera and species from which they were derived). The termination region is usually selected more for convenience than because of a specific property. Preferably, when the microbial host is a yeast cell, the termination region is derived from a yeast gene (particularly Saccharomyces, Schizosaccharomyces, Candida, Yarrowia or Kluyveromyces). The 3 'regions of mammalian genes encoding γ-interferone and a-2 interferone are also known to function in yeast. Termination control regions can also be derived from various genes native to preferred hosts. Optionally, a termination location may be unnecessary; it is most preferred, however, if included. Although not intended to be limited, the termination regions useful in this specification include: about 100 bp of the 3 'region of the Yarrowia lipolytica extracellular protease (XPR; GenBank Accession No. M17741); acyl-coA oxidase (Aco3: GenBank Access No. AJ001301 and CAA04661; Pox3 terminals: GenBank Access No. XP_503244); the Pex20 terminal (GenBank Access No. AF054613); the Pex16 terminal (GenBank Access No. U75433); the Lip1 terminal (GenBank Access No. Z50020); the Lip2 terminal (GenBank Access No. AJ012632); and the 3-oxoacyl-CoA thiolase terminal (OCT; GenBank Accession No. X69988).
As ordinary technicians in the subject know, the mere insertion of a gene into a cloning vector does not guarantee that it will be successfully expressed at the necessary level. In response to the need for a high speed of expression, many specialized expression vectors have been created by manipulating a number of different genetic elements that control aspects of transcription, translation, protein stability, oxygen limitation and microbial host cell secretion. . More specifically, some of the molecular characteristics that have been manipulated to control gene expression include: (1) the nature of the relevant transcription promoter and terminator sequences; (2) the number of copies of the gene being spun and whether the gene is contained in a plasmid or integrated into the host cell genome; (3) the final cell location of the synthesized exogenous protein; (4) the efficiency of translation and the correct folding of the protein in the host organism; (5) the intrinsic stability of the mRNA and protein of the gene cited within the host cell; and (6) the use of codons in the cited gene, so that their frequency is close to the preferred codon use frequency of the host cell. Each of these types of modifications is encompassed in the present invention as a means of further optimization of the delta-5 desaturase expression described herein.
After obtaining the DNA encoding an appropriate polypeptide for expression in an appropriate microbial host cell (such as oleaginous yeast) (for example, a chimeric gene comprising a promoter, ORF and terminal), it is placed in a plasmid vector capable of autonomous reproduction in a host cell; or it is integrated directly into the host cell's genome. The integration of expression sets can occur randomly within the host genome or can be directed using constructs that contain regions of homology with the host genome sufficient to direct recombination within the host site. When constructions are directed to an endogenous site, all or part of the translation and transcription regulatory regions can be provided by the endogenous site.
The preferred method of gene expression in Yarrowia lipolytica is through integration of linear DNA into the host genome and integration at various locations within the genome can be particularly useful when high-level gene expression is desired (for example, at the site Ura3 (GenBank Access n ° AJ306421), the Leu2 gene site (GenBank Access n ° AF260230), the Lys5 gene (GenBank Access η<sup>θ</sup> M34929), the Aco2 gene site (GenBank Access No. AJ001300), the Pox3 gene site (Pox3: GenBank Access No. XP_503244); or Aco3: GenBank Access No. AJ001301), the delta-12 desaturase gene site (PCT Patent No. WO 2004/104167), the Lip1 gene site (GenBank Access No. Z50020) and / or the Lip2 gene site ( GenBank Accession No. AJ012632)).
Conveniently, the Ura3 gene can be used repeatedly in combination with selection of 5-fluoro-orotic acid (acid monohydrate
5-fluorouracil-6-carboxylic; “5-FOA”) (below), to allow easy integration of genetic modifications into the Yarrowia genome in an easy way.
When two or more genes are expressed from separate reproduction vectors, it is desirable that each vector has a different means of selection and should not have homology to the other construct (s), to maintain stable expression and to avoid the new disposition of elements between the constructions. Careful selection of regulatory regions, means of selection and method of propagation of the construction (s) introduced can be determined experimentally, so that all the introduced genes are expressed at the levels necessary to provide the synthesis of the desired products.
The constructs that comprise the gene of interest can be introduced into a microbial host cell using any standard method. These methods include transformation (such as lithium acetate transformation (Methods in Enzymology, 194: 186-187 (1991)), protoplast fusion, bolistic impact, electroporation, microinjection or any other method that introduces the gene of interest into the host cell. More specific teachings applicable to oleaginous yeasts (ie Yarrowia lipolytica) include U.S. Patent No. 4,880,741, U.S. Patent No. 5,071,764 and Chen, DC et al (Appl. Microbiol. Biotechnol. 48 ( 2): 232-235 (1997)).
For convenience, a host cell that has been manipulated by any method to absorb a sequence of
DNA (such as an expression set) will be called "transformed" or "recombinant" in the present. The expressions “transformed” and “recombinant” are, therefore, used interchangeably in the present. The transformed host will contain at least one copy of the expression construct and may contain two or more, depending on whether the gene is integrated into the genome, amplified or is present on an extrachromosomal element that contains several copy numbers.
The transformed host cell can be identified using various selection methods, as described in PCT Patent Nos. WO 2004/101757 and WO 2006/052870. The preferred selection methods for use in the present are resistance to kanamycin, hygromycin and the amino glycoside G418, as well as the ability to grow on media that do not contain uracil, leucine, lysine, tryptophan or histidine. In alternative embodiments, 5-FOA is used for the selection of yeast Ura mutants. The compound is toxic to yeast cells that have a functioning URA3 gene that encodes orotidine 5'-monophosphate decarboxylase (OMP decarboxylase); therefore, based on its toxicity, 5-FOA is especially useful for the selection and identification of mutant yeast strains Ura '(Bartel, PL and Fields, S., Yeast 2-Hybrid System, University of Oxford: New York, vol. 7, pages
109-147, 1997). More specifically, one can first kill the native Ura3 gene to produce a strain that contains a Ura phenotype, in which the selection occurs based on 5-FOA resistance. Then, a set of several chimeric genes and a new Ura3 gene could be integrated into a different location in the Yarrowia genome, in order to produce a new strain that contains a Ura + phenotype. Subsequent integration produces a new strain of Ura3 (again identified using 5-FOA selection), when the introduced Ura3 gene is killed. In this way, the Ura3 gene (in combination with 5-FOA selection) can be used as a selection marker in several rounds of transformation.
After transformation, suitable substrates for delta-5 desaturase (and, optionally, other PUFA enzymes that are coexpressed in the host cell) can be produced by the host naturally or transgenically, or can be supplied exogenously.
The microbial host cells for expression of the genes and fragments of the present nucleic acid may include hosts that grow on a series of food stocks, which include simple or complex carbohydrates, fatty acids, organic acids, oils and alcohols and / or hydrocarbons throughout wide range of temperature and pH values. Based on the needs of the Depositor Assignee, the genes described in the present invention will be expressed in an oleaginous yeast (particularly in Yarrowia lipolytica) ', however, it is contemplated that, due to the transcription, translation and high conservation of the protein biosynthetic apparatus , any bacteria, yeast, algae and / or fungus will be an appropriate microbial host for expression of the nucleic acid fragments of the present.
The preferred microbial hosts are, however, oilseeds. These organisms are naturally capable of oil synthesis and accumulation, in which the oil may comprise more than about 25% of the dry cell weight, more preferably more than about 30% of the dry cell weight, and preferably more than about 40% of the dry cell weight. Genera typically identified as oilseeds include, but are not limited to: Yarrowia, Candida, Rhodotorula, Rhodosporidium, Cryptococcus, Trichosporon and Lipomyces. More specifically, illustrative oil-synthesizing yeasts include: Rhodosporidium toruloides, Lipomyces starkeyii, L. lipoferus, Candida revkaufí, C. pulcherrima, C. tropicalis, C. utilis, Trichosporon pullans, T. cutaneum, Rhodotorula glutinus, R. graminis and Yarrowia lipolytica (previously classified as Candida lipolytica).
It is preferably superior to the oleaginous yeast Yarrowia lipolytica-, and, in an additional embodiment, Y. lipolytica strains called ATCC No. 20362, ATCC No. 8862, ATCC No. 18944, ATCC No. 76982 and / or LGÃM S (7) 1 (Papanikoiaou, S. and Aggelis, G., Bioresour. Technol. 82 (1): 43-9 (2002)).
Historically, several strains of Y. lipolytica have been used for the manufacture and production of: isocitrate lyase; lipases; polyhydroxyalkanoates; Citric acid; erythritol; 2-oxoglutaric acid; γ-decalactone; γdodecalactone; and pyruvic acid. Specific teachings applicable to the elaboration of the production of ARA, EPA and DHA in Y. lipolytica are provided in North American Patent Application No. 11/264784 (WO 2006/055322), North American Patent Application No. 11/265761 (WO 2006/052870) and North American Patent Application No. 11 / 264737 (WO 2006/052871), respectively.
Other preferred microbial hosts include oilseed bacteria, algae and other fungi; and, within this broad group of microbial hosts, microorganisms that synthesize omega 3 / omega 6 fatty acids (or those that can be genetically engineered for this purpose (such as other yeasts like Saccharomyces cerevisiae)) are of particular interest. Thus, for example, the transformation of Mortierella alpina (which is used commercially for the production of ARA) with any of the delta-5 desaturase genes present under the control of inducible or regulated promoters may generate a transformer organism capable of synthesizing larger quantities of DGLA. The transformation method of M. alpina is described by Mackenzie et al (Appl. Environ. Microbiol. 66: 4655 (2000)). Similarly, methods for transforming Thraustochytriales microorganisms are described in US 7,001,772.
Metabolic elaboration of omega 3 and / or omega 6 fatty acid biosynthesis in microbe
Methods of manipulating biochemical processes are well known to those skilled in the art; and it is expected that several manipulations are possible to maximize the biosynthesis of omega 3 and / or omega 6 fatty acids in oleaginous yeasts and, particularly, in Yarrowia lipolytica. This manipulation may require metabolic elaboration directly in the PUFA biosynthetic process or additional coordinated manipulation of several other metabolic processes.
In the case of manipulations in the PUFA biosynthetic process, it may be desirable to increase the production of LA to allow greater production of omega 3 and / or omega 6 fatty acids. The introduction and / or amplification of genes encoding delta-9 and / or delta-12 desaturases can accomplish this. To maximize the production of unsaturated omega 6 fatty acids, those skilled in the art are well aware that production is favored in a host micro25 organism that is substantially free of ALA; this way, preferably, the host is selected or obtained by removing or inhibiting desaturase activity type delta 15 or omega 3 that allows the conversion of LA into ALA. Alternatively, it may be desirable to maximize the production of omega 3 fatty acids (and minimize the synthesis of omega 6 fatty acids). In this example, a host microorganism could be used in which the delta-12 desaturase activity that allows the conversion of oleic acid into LA is removed or inhibited; then, appropriate expression sets would be introduced into the host, along with appropriate substrates (such as ALA) for conversion to derivatives of ALA omega 3 fatty acids (such as STA, ETrA, ETA, EPA, DPA, DHA).
In alternative embodiments, biochemical processes that compete with the biosynthetic processes of omega 3 and / or omega 6 fatty acids for energy or carbon, or enzymes from the native PUFA biosynthetic process that interfere with the elaboration of a specific PUFA end product eliminated by genetic disruption or down-regulated by other means (such as nonsense mRNA).
Detailed discussion of manipulations within the PUFA biosynthetic process as a means of increasing ARA, EPA or DHA (and their associated methods) is presented in PCT Patent No. WO 2006/055322, WO 2006/052870 and WO 2006/052871, respectively, as they are desired manipulations in the TAG biosynthetic process and in the TAG degradation process (and its associated methods).
Within the context of the present invention, it may be useful to modulate the expression of the biosynthetic fatty acid process using any of the strategies described above. The present invention provides, for example, methods by which genes encoding key enzymes in the delta-9 elongase / delta-8 desaturase biosynthetic processes are introduced into plants for the production of omega 3 and / or omega 6 fatty acids. It will be particularly useful to express the delta-5 desaturase genes present in plants that do not naturally have omega 3 and / or omega 6 fatty acid biosynthetic processes and coordinate the expression of these genes, to maximize the generation of processed PUFA products using various means of metabolic elaboration of the host organism.
Microbial fermentation processes for RUFA production
The transformed host cell is grown under conditions that optimize the expression of chimeric desaturase genes and produce the highest and most economical yield of the preferred PUFAs. In general, the conditions of media that can be optimized include the type and amount of carbon source, the type and amount of nitrogen source, the ratio of carbon to nitrogen, the amount of different mineral ions, the level of oxygen, growth temperature, pH, duration of the biomass production phase, duration of the oil accumulation phase and the time and method of cell harvesting. Yarrowia lipolytica is generally grown in complex media (such as dextrose-peptone-yeast extract broth (YPD)) or a minimally defined medium that does not contain a component necessary for growth and thus forces selection of expression sets (such as yeast nitrogen base (DIFCO Laboratories, Detroit Ml)).
The fermentation media can contain an appropriate carbon source. Appropriate carbon sources are taught in PCT Patent No.
WO 2004/101757. Although it is contemplated that the carbon source used may encompass a wide variety of carbon containing sources, preferred carbon sources are sugars, glycerol and / or fatty acids. It is preferably higher than glucose and / or fatty acids containing 10 to 22 carbons.
Nitrogen can be supplied from an inorganic source (such as (NH<sub>4</sub>)<sub>2</sub>ONLY<sub>4</sub>) or organic source (such as urea or glutamate). In addition to appropriate sources of carbon and nitrogen, the fermentation medium must also contain appropriate minerals, salts, cofactors, buffers, vitamins and other components known to those skilled in the art appropriate for the growth of the oil host and the promotion of enzymatic processes necessary for production of PUFA. Specific attention is paid to various metal ions (such as Mn<sup>+2</sup>, Co<sup>+2</sup>, Zn<sup>+2</sup>, Mg<sup>+2</sup>) that promote the synthesis of lipids and PUFAs (Nakahara, T. et al, Ind. Appl. Single Cell Oils, DJ Kyle and R. Colin, eds., pp. 61-97 (1992)).
Preferred growth media in the present invention are common commercially prepared media, such as yeast nitrogen base (DIFCO Laboratories, Detroit Ml). Other synthetic or defined growth media can also be used and the appropriate growth medium for the transforming host cells will be known to those skilled in the art of microbiology or fermentation science. A suitable pH range for fermentation is typically about pH 4.0 to pH 8.0, where pH 5.5 to pH 7.5 is preferred as the range for initial growth conditions. Fermentation can be conducted under aerobic or anaerobic conditions and microaerobic conditions are preferred.
Typically, the accumulation of high levels of PUFAs in oleaginous yeast cells requires a two-step process, as the metabolic state must be “balanced” between growth and fat synthesis / storage. Thus, more preferably, a two-stage fermentation process is required for the production of PUFAs in oleaginous yeast (such as Yarrowia lipolytica). This approach is described in PCT Patent No. WO 2004/101757, as well as several appropriate fermentation process designs (i.e., batch, fed and continuous batches) and considerations during growth.
Purification and processing of PUFA oils
PUFAs can be found in host microorganisms and plants in the form of free fatty acids or in esterified forms, such as acylglycerols, phospholipids, sulpholipids or glycolipids, and can be extracted from host cells by a number of means well known in the art. An analysis of extraction methods, quality analysis and acceptability standards for yeast lipids is that of Z. Jacobs (Critical Reviews in Biotechnology 12 (5/6): 463-491 (1992)). A quick analysis of processing downstream is also available through A. Singh and O. Ward (Adv. Appl. Microbiol. 45: 271-312 (1997)).
Generally, means of purifying PUFAs may include extraction with organic solvents, sonication, extraction of supercritical fluids (using, for example, carbon dioxide), saponification and physical media such as presses or combinations thereof. One refers to the teachings of PCT Patent No. WO 2004/101757 for further details. Methods for isolating seed oils are well known in the art (Young et al, Processing of Fats and Oils, in The Lipid Handbook, Gunstone et al, eds., Chapter 5, pp. 253-257; Chapman & Hall: London ( 1994)). Soya oil is produced, for example, using a series of steps that involve the extraction and purification of an edible oil product from the seed that contains oil. Soy oils and soy by-products are produced using the generalized steps shown in Table 3.
Table 3
Generalized Stages of Production of Oil and Soy By-Products
<td>Step of process</td><td>Process</td><td>Impurities removed and / or obtained by-products</td>
<td>n ° 1</td><td>soybean seed</td><td></td>
<td>n ° 2</td><td>oil extraction</td><td>pasta</td>
<td>n ° 3</td><td>fat removal</td><td>lecithin</td>
<td>n ° 4</td><td>physical refinement or alkali</td><td>gums, free fatty acids, pigments</td>
<td>Step of process</td><td>Process</td><td>Impurities removed and / or obtained by-products</td>
<td>n ° 5</td><td>water wash</td><td>soap</td>
<td>n ° 6</td><td>bleaching</td><td>color, soap, metal</td>
<td>n ° 7</td><td>(hydrogenation)</td><td></td>
<td>n ° 8</td><td>(winterization)</td><td>stearin</td>
<td>n ° 9</td><td>deodorization</td><td>free fatty acids, tocopherols, sterols, volatiles</td>
<td>n ° 10</td><td>oil products</td><td></td>
More specifically, soybean seeds are cleaned, seasoned, peeled and made into flakes, in order to increase the efficiency of oil extraction. Oil extraction is normally carried out by means of solvent extraction (such as hexane), but it can also be achieved through a combination of physical pressure and / or solvent extraction. The resulting oil is called crude oil. The crude oil can have its gum removed by hydrating phospholipids and other neutral and polar lipid complexes that facilitate its separation from the triglyceride fraction without hydration (soybean oil). The resulting lecithin gums can be further processed to make commercially important lecithin products used in a number of food and industrial products as emulsifying and releasing agents (ie, anti-caking agents). Oil with removed gum can be further refined to remove impurities (mainly free fatty acids, pigments and residual gums). Refining is carried out by adding a caustic agent that reacts with the free fatty acid to form soap and phosphate hydrates and proteins in the crude oil. Water is used to wash traces of soap formed during refining. The soap by-product can be used directly in animal feed or acidulated to recover free fatty acids. The coloring is removed by adsorption with a bleaching soil that removes most of the chlorophyll and carotenoid compounds. The refined oil can be hydrogenated, in order to result in fats with different melting properties and textures. Winterization (fractionation) can be used to remove stearin from the hydrogenated oil by crystallization under carefully controlled cooling conditions. Deodorization (mainly through vacuum steam distillation) is the last step and is designed to remove compounds that provide odor or aroma to the oil. Other valuable by-products, such as tocopherols and sterols, can be removed during the deodorization process. Deodorized distillate containing these by-products can be sold for the production of natural vitamin E and other pharmaceutical products with high value. Refined, bleached (hydrogenated, fractionated) and deodorized fats and oils can be packaged and sold directly or further processed into more specialized products. A more detailed reference to soybean seed processing, soybean oil production and use of by-products can be found in Erickson, Practical Handbook of Soybean Processing and Utilization, The
American Oil Chemists' Society and United Soybean Board (1995). Soy oil is liquid at room temperature because it has a relatively low content of saturated fatty acids compared to oils such as coconut, palm, palm seed and cocoa butter.
Vegetable and microbial oils that contain PUFAs that have been refined and / or purified can be hydrogenated, in order to result in fats with different textures and melting properties. Many processed fats (including spreaders, confectionery fats, hard butters, margarines, cooking toppings, etc.) require varying degrees of strength at room temperature and can only be produced by changing the physical properties of the source oil. This is most commonly achieved through catalytic hydrogenation.
Hydrogenation is a chemical reaction in which hydrogen is added to the double joints of unsaturated fatty acid with the aid of a catalyst such as nickel. High oleic soybean oil, for example, contains linolenic, LA and unsaturated oleic fatty acids and each of these can be hydrogenated. Hydrogenation has two primary effects. First, the oxidative stability of the oil increases as a result of the reduction in the unsaturated fatty acid content. Second, the physical properties of the oil are altered because the changes in fatty acids increase the melting point, which results in a solid or semi-liquid fat at room temperature.
There are many variables that affect the hydrogenation reaction, which, in turn, alters the composition of the final product. Operating conditions, which include pressure, temperature, type and concentration of catalyst, agitation and reactor design, are among the most important parameters that can be controlled. Selective hydrogenation conditions can be used to hydrogenate the most unsaturated fatty acids in preference to the less unsaturated ones. Very light hydrogenation or brushing is often used to increase the stability of liquid oils. Additional hydrogenation converts a liquid oil into a physically solid fat. The degree of hydrogenation depends on the desired performance and fusion characteristics designed for the specific final product. Liquid toppings (used in the manufacture of baking products, solid fats and toppings used for commercial frying and roasting operations) and base stocks for the manufacture of margarine are among the series of possible oil and fat products achieved through hydrogenation . A more detailed description of hydrogenation and hydrogenated products can be found in Patterson, Η. B. W., Hydrogenation of Fats and Oils: Theory and Practice, The American Oil Chemists' Society (1994).
Hydrogenated oils have also become somewhat controversial due to the presence of isomers of trans fatty acids that result from the hydrogenation process. Ingestion of large amounts of trans isomers has been linked to harmful health effects that include higher ratios between low density and high density lipoproteins in the blood plasma and increased risk of coronary heart disease.
OILS CONTAINING PUFA FOR FOOD USE
The market currently supports a wide variety of foods and food products, which incorporate omega 3 and / or omega 6 fatty acids (particularly ARA, EPA and DHA). It is believed that plant / seed oils, altered seeds and microbial oils that comprise PUFAs will work in foods and food products to provide the health benefits of current formulations. In comparison with other vegetable oils, oils according to the present invention are believed to work similarly to other oils in food applications from the physical point of view (partially hydrogenated oils, such as soybean oil, are widely used, for example , such as spreading ingredients, margarine and toppings for cooking and frying).
Plant / seed oils, altered seeds and microbial oils containing omega 3 and / or omega 6 fatty acids as described herein will be suitable for use in a variety of foods and food products that include, but are not limited to: analogs of food, meat products, cereal products, cooked foods, snacks and food products. In addition, the plant / seed oils, altered seeds and microbial oils of the present can be used in formulations to provide health benefits in medical foods that include medical nutritional products, food supplements, infant formulas as well as pharmaceuticals. Those skilled in the subject of food processing and food formulation will understand how the amount and composition of plant and microbial oils in the present can be added to foods or food products. This quantity will be indicated in the present as "effective" quantity and will depend on the food or food product, the diet that the product intends to supplement or the average condition that the medical food or medical nutritional product is intended to correct or treat.
Food analogs can be made using processes well known to those skilled in the art. Meat analogs, cheese analogs, milk analogs and the like can be mentioned. Meat analogues made from soy beans contain soy protein or tofu and other ingredients mixed together to simulate different types of meat. These meat alternatives are sold in the form of frozen, canned or dried foods. Typically, they can be used in the same way as the foods they replace. Meat alternatives made from soybeans are excellent sources of protein, iron and B vitamins. Examples of meat analogues include, but are not limited to ham analogues, sausage analogues, bacon analogues and the like.
Food analogues can be classified as imitations or substitutes, depending on their functional and composition characteristics. A cheese imitation, for example, needs only to recall the cheese that it is designed to replace. A product can generally be called a cheese substitute, for example, only if it is nutritionally equivalent to the cheese it is replacing and meets the minimum composition needs of that cheese. In this way, substitute cheese will often contain higher levels of protein than imitations of cheese and will be fortified with vitamins and minerals.
Analogs of milk or non-dairy food products include, but are not limited to, imitations of milk and frozen non-dairy desserts (such as those made with soy beans and / or soy protein products).
Meat products encompass a wide variety of products.
In the United States, "meat" includes "red meat" produced with oxen, pigs and sheep. In addition to red meats, there are poultry products that include chickens, turkeys, geese, guinea hens, ducks, fish and seafood. There is a wide variety of processed and seasoned meat products: fresh, cured and fried, cured and cooked. Sausages and sausages are examples of processed meat products. Thus, the expression “meat products”, as used in the present, includes, but is not limited to, processed meat products.
A cereal food product is a food product derived from the processing of cereal grains. A grain of cereal includes any plant in the grass family that generates edible grains (seeds). The most popular grains are barley, corn, white corn, oats, quinoa, rice, rye, sorghum, triticale, wheat and wild rice. Examples of cereal food products include, but are not limited to, whole grains, chopped grains, debris, flour, bran, germ, breakfast cereals, extruded foods, pasta and the like.
A cooked food product comprises any of the aforementioned cereal food products that have been cooked or processed in a manner comparable to cooking (i.e., drying or hardening by submitting to heat). Examples of baked food products include, but are not limited to, breads, cakes, donuts, bars, pastas, bread crumbs, baked snacks, mini-cookies, mini-cookies, minicookies and minipretzels. As mentioned earlier, the oils according to the present invention can be used as ingredients.
A food snack product comprises any of the food products described above or below.
A fried food product comprises any of the food products described above or below that has been fried.
A healthy food product is any food product that provides a health benefit. Many food products derived from oilseeds can be considered healthy foods.
The drink can be presented in liquid or dry powder form.
One can mention, for example, non-carbonated drinks such as fruit juices, fresh, frozen, canned or concentrated; whole milk or flavored drinks etc. Nutritional formulas for adults and babies are well known in the art and commercially available (such as Similac®, Ensure®, Jevity® and Alimentum® from Ross Products Division, Abbott Laboratories).
Baby formulas are liquid or reconstituted powders administered to babies and young children. “Baby formula” is defined as an enteral nutritional product that can be substituted for human breast milk in infant feeding and is typically composed of a desired percentage of fat mixed with desired percentages of carbohydrates and proteins in an aqueous solution (see, for example, U.S. Patent No. 4,670,285). Based on worldwide composition studies, as well as at levels specified by expert groups, average human breast milk typically contains about 0.20% to 0.40% of total fatty acids (considering about 50% of calories from fat) ; and generally the ratio between DHA and ARA would range from about 1: 1 to 1: 2 (see, for example, formulations of Enfamil LIPIL® (Mead Johnson & Company) and Similac Advance® (Ross Products Division, Abbott Laboratories )). Baby formulas have a special role to play in feeding babies because they are often the only source of nutrients for babies; and while breastfeeding is still the best nutrition for babies, baby formulas are a close enough alternative for babies to not only survive, but are also well nourished.
Dairy product is a product derived from milk. An analogous milk or non-dairy product is derived from a different source of milk, such as soy milk, as discussed above. These products include, but are not limited to, whole milk, skim milk, fermented milk products such as yogurt or sour milk, sour cream, butter, condensed milk, powdered milk, coffee whitener, coffee cream, ice cream, cheese etc.
Additional food products in which PUFA-containing oils according to the present invention may be included are, for example, chicles, confectionery and frozen foods, gelatins and puddings, hard and soft candies, jellies and gelatins, white granulated sugar, sugar substitutes , sweet sauces, toppings, syrups and powder mixes mixed dry.
OILS CONTAINING PUFA RARE FOR USE IN HEALTHY FOOD PRODUCTS AND
PHARMACEUTICALS
A healthy food product is any food product that provides a health benefit and includes functional foods, medical foods, medical nutritional products and food supplements. In addition, plant oils and seeds, altered seeds and microbial oils according to the present invention can be used in standard pharmaceutical compositions (oils containing long-chain PUFA can be easily incorporated, for example, in any of the products mentioned above, in order to produce a medical or functional food). More concentrated formulations comprising PUFAs include, for example, capsules, powders, lozenges, soft gels, gelatin capsules, liquid concentrates and emulsions that can be used as a food supplement in humans or animals other than humans.
Oils containing PUFA for use in animal feed:
Animal feeds are generally defined herein as products intended for use as food or for mixing in animal feed other than human beings. Plant or seed oils, altered seeds and microbial oils according to the present invention can be used as ingredients in various animal foods.
More specifically, although without limitations in the present, it is expected that the oils according to the present invention can be used in pet food products, poultry and ruminant feed products and aquaculture feed products. Pet food products are products intended to be administered to domestic animals (such as dogs, cats, birds, reptiles and rodents). These products may include the above cereal products and healthy foods, as well as meat and meat by-products, soy protein products, grass and hay products (such as alfalfa, herd grass, oats or barley grass, vegetables). Food products for birds and ruminants are those in which the product is intended to be supplied to animals (such as turkeys, chickens, oxen and pigs). As with the pet food above, these products may include cereal products and healthy foods, soy protein products, meat and meat by-products, grass and hay products as listed above. Aquaculture feed products (or “aquatic foods”) are products intended for use in aquaculture, that is, that take care of the propagation, cultivation or creation of aquatic organisms and / or animals in fresh or salt water.
Examples
The present invention is further defined in the Examples below, in which parts and percentages are by weight and degrees are Celsius, unless otherwise indicated. It should be understood that these Examples, while indicating preferred embodiments of the present invention, are provided by way of illustration only. From the above discussion and these Examples, those skilled in the art can determine the essential features of the present invention and, without abandoning its spirit and scope, can devise various changes and modifications of the present invention to adapt it to various uses and conditions. In this way, several modifications of the present invention in addition to those shown and described herein will be evident to those skilled in the art from the above specification. These modifications are also intended to fall within the scope of the appended claims.
The abbreviations mean the following: “sec” indicates second (s), “min” indicates minute (s), “h” indicates hour (s), “d” indicates day (s), “μΙ” indicates microliter ( s), “ml” indicates milliliter (s), “I” indicates liter (s), “μΜ” indicates micromolar, “mM” indicates millimolar, “M” indicates molar, “mmol” indicates millimol (es), “μηιοΓ indicates micromol (s), “g” indicates gram (s), Vg ”indicates microgram (s),“ ng ”indicates nanogram (s),“ U ”indicates unit (s),“ bp ”indicates pair (s) of bases and “kB” indicates kilobase (s).
General methods
Transformation and cultivation of Yarrowia lipolytica
Yarrowia lipolytica strains with accession numbers ATCC 20362, 76982 and 90812 were purchased from the North American Collection of Type Crops (Rockville MD). Yarrowia lipolytica strains were typically grown at 28 ° C on YPD agar (1% yeast extract, 2% bactopeptone, 2% glucose, 2% agar).
Transformation of Yarrowia lipolytica was performed according to the method of Chen, DC et al (Appl. Microbiol. Biotechnol. 48 (2): 232-235 (1997)), unless otherwise indicated. Briefly, Yarrowia was streaked on a YPD plate and grown at 30 ° C for about eighteen hours. Several large cell circuits were scraped from the plate and resuspended in 1 ml of transformation buffer containing: 2.25 ml of 50% PEG, average MW 3350; 0.125 ml of 2 M lithium acetate, pH 6.0; 0.125 ml of 2 M DTT; and 50 pg of cut salmon sperm DNA. Then about
500 ng of linearized plasmid DNA were incubated in 100 μΙ of cells resuspended and maintained at 39 ° C for one hour with swirl mixing at fifteen minute intervals. The cells were plated on plates of selection media and kept at 30 ° C for two to three days.
For the selection of transformers, a minimum medium (“MM”) was generally used; the composition of MM is as follows: 0.17% yeast nitrogen base (Difco Laboratories, Detroit Ml) without ammonium sulfate or amino acids, 2% glucose, 0.1% proline, pH 6.1). Uracil supplements were added as appropriate to a final concentration of
0.01% (in order to produce “MMU” selection media, prepared with 20 g / l of agar).
Alternatively, transformers were selected using means of selection of 5-fluoro-orotic acid (“FOA”, also 5-fluorouracil-6-carboxylic acid monohydrate), comprising: 0.17% yeast nitrogen base ( Difco Laboratories, Detroit Ml) without ammonium sulfate or amino acids, 2% glucose, 0.1% proline, 75 mg / l uracil, 75 mg / l uridine, 900 mg / l FOA (Zymo Research Corp., Orange AC) and 20 g / l of agar.
Fatty acid analysis of Yarrowia lipolytica For fatty acid analysis, cells were harvested by centrifugation and lipids were extracted as described in Bligh, EG and Dyer, WJ (Can. J. Biochem. Physiol. 37: 911-917 (1959 )). Methyl fatty acid esters were prepared by transesterification of the lipidioc extract with sodium methoxide (Roughan, G. and Nishida, I., Arch. Biochem. Biophys. 276 (1): 38-46 (1990)) and then analyzed with a HewlettPackard 6890 GC equipped with a 30 mx 0.25 mm (internal diameter) column of HP-INNOWAX (Hewlett-Packard). The oven temperature was 170 ° C (maintenance for 25 minutes) at 185 ° C to 3.5 ° C / min.
For direct base transesterification, Yarrowia cultivation (3 ml) was harvested, washed once in distilled water and vacuum dried in SpeedVac for five to ten minutes. Sodium methoxide (100 μΙ of 1%) was added to the sample and then the sample was swirled and rocked for twenty minutes. After adding three drops of 1 M NaCI and 400 μΙ of hexane, the sample was swirled and centrifuged. The top layer was removed and analyzed by GC as described above.
Example 1
Synthesis of a Euglena anabaena UTEX 373 cDNA library
The Example of the present describes the synthesis of a Euglena anabaena UTEX 373 cDNA library. This work included the generation of RNA, synthesis of cDNA and generation of a cDNA library.
Growth of Euglena anabaena UTEX 373 and preparation of RNA
Euglena anabaena UTEX 373 was obtained through Dr. Richard Triemer's laboratory at Michigan State University (East Lansing Ml). About 2 ml of culture were removed for lipid analysis and centrifuged at 1800 xg for five minutes. The pellet was washed once with water and again centrifuged. The resulting pellet was dried for five minutes under vacuum, again suspended in 100 pl of trimethylsulfonium hydroxide (TMSH) and incubated at room temperature for fifteen minutes with shaking. After this step, 0.5 ml of hexane was added and the ampoules were incubated for fifteen minutes at room temperature with shaking. Methyl fatty acid esters (5 μΙ injected from the hexane layer) were separated and quantified using a Hewlett Packard 6890 Gas Chromatograph equipped with an Omegawax 320 fused silica capillary column (Supelco Inc., Cat. No. 24152). The oven temperature has been programmed to remain at 170 ° C for one minute, increase to 240 ° C to 5 ° C per minute and maintain for an additional minute. Vehicle gas was supplied by a Whatman hydrogen generator. The retention times were compared with those of commercially available standard methyl esters (Nu-Chek Prep, Inc., category No. U-99-A) and the resulting chromatogram is shown in Fig. 10. The presence of EDA, ERA, EPA and DHA in the fatty acid profile, with the absence of GLA and STA, suggested that Euglena anabaena uses the delta-9 elongase / delta-8 desaturase process for LC-PUFA biosynthesis and would be a good source of biosynthetic LC-PUFA genes, such as, but not limited to, delta-5 desaturases.
The remaining 5 ml of an actively growing culture were transferred to 25 ml of AF-6 Medium (Watanabe & Hiroki, NIES-Collection List of Strains, fifth edition, National Institute for Environmental Studies, Tsukuba, 127 pages. (2004)) in a 125 ml glass bottle. Cultures of Euglena anabaena grew at 22 ° C with a cycle of sixteen hours of light and eight hours of darkness for two weeks with gentle agitation.
After two weeks, the culture (25 ml) was transferred to 100 ml of AF-6 medium in a 500 ml glass bottle and the culture was grown for one month as described above. After that period, two 50 ml portions were transferred to two separate 500 ml glass bottles containing 250 ml AF-6 medium and the cultures were grown for two months as described above (generating a total of about 600 ml of culture) . Then, the cultures were pelleted by means of centrifugation at 1800 xg for ten minutes, washed once with water and again centrifuged. Total RNA was extracted from one of the resulting pellets using the STAT-60® RNA reagent (TEL-TEST, Inc., Friendswood TX) and following the manufacturer's protocol provided (use 5 ml reagent, RNA dissolved in 0.5 ml of Water). In this way, 340 pg of total RNA (680 pg / ml) were obtained from the pellet. The remaining pellet was frozen in liquid nitrogen and stored at -80 ° C. The mRNA was isolated from all 340 pg of total RNA using the mRNA Purification Kit (Amersham Biosciences, Piscataway NJ) following the protocol provided by the manufacturer. In this way, 9.0 pg of mRNA were obtained.
Preparation of Euglena Anabaena cDNA and generation of eDNAN eugIc library
A cDNA library was generated using the Cloneminer® cDNA Library Construction Kit (Cat. No. 18249-029, Invitrogen Corporation, Carlsbad CA), following the protocol provided by the manufacturer (Version B, 25-0608). Using the radiolabel method, cDNA was synthesized from 5.12 pg of mRNA (described above) using the primer
Biotin-atfB2-Oligo (dT). After synthesis of the first and second strands, the affB1 adapter was added, attached and the cDNA was fractionated in size using column chromatography. Fraction DNA was concentrated, recombined in pDONR® 222 and transformed into E. coli phage-resistant cells ElectroMAX® DH10B® T1 (Invitrogen Corporation). The library of
Euglena anabaena was called euglc.
The euglc cDNA library was placed on LBKan plates (about one hundred thousand colonies), the colonies were scraped and DNA was isolated using the QIAprep® Spin Mini Preparation Kit (Qiagen Inc., Valencia, CA) following the manufacturer's protocol. In this way, a sub-library of euglc plasmids DNA was obtained.
Example 2
Isolation of Euglena delta-5 full-length desaturases
ANABAENA UTEX 373
The present Example describes the identification of a cDNA (SEQ
ID N ° 1) encoding Euglena anabaena UTEX 373 delta-5 desaturase. This work included the generation of a probe derived from Euglena gracilis delta-5 desaturase (EgD5; SEQ ID N ° 2; which is described in the Provisional Application
North American No. 60 / 801,172 (deposited on May 17, 2006; Attorney's Folder No. CL-3486)) and probe hybridization in the euglc cDNA library in order to identify Euglena delta-5 desaturase counterparts anabaena UTEX 373.
Construction generation PDMW367, comprising EgD5
Based on the Euglena gracilis delta-5 desaturase sequence (EgD5; SEQ ID No. 2), oligonucleotides YL794 and YL797 (SEQ ID No. 3 and 4, respectively) were used as primers to amplify the first part of EgD5 ( Fig. 2A). Primer YL794 contained an Nco \ site and Primer YL797 contained a Hind III site. Then the primers YL796 and
YL795 (SEQ ID NO: 5 and 6, respectively) were used as primers to amplify the second part of EgD5. Primer YL796 contained a Hind \\\ location, while primer YL797 contained a Nott location. PCR reactions, using primer pairs YL794 / YL797 or YL796 / YL795, with Euglena gracilis cDNA (whose generation is described in North American Provisional Application No. 60 / 801,172 (deposited on May 17th, 2006; attorney No. CL-3486)) as a model were conducted individually in a total volume of 50 pl comprising: PCR buffer (containing 10 mM KCI, 10 mM (NH ^ SO ^ 20 mM Tris-HCI (pH 8 .75), 2 mM MgSO4, 0.1% Triton
Χ-100), 100 pg / ml BSA (final concentration), 200 μΜ of each deoxyribonucleotide triphosphate, 10 pmol of each primer and 1 μΙ of Pfu DNA polymerase (Stratagene, San Diego CA). The conditions of the thermal cycler were defined for 35 cycles at 95 ° C for one minute, 56 ° C for thirty seconds and 72 ° C for one minute, followed by a final extension at 7 ° C for ten minutes. The individual PCR products were purified using a Qiagen PCR purification kit. The PCR product from the amplified reaction with YL794 / 797 primers was digested with Λ / col and HincftU, while the PCR product from the amplified reaction with YL796 / YL795 primers was digested with Hind \\\ and Λ / ofl. THE
NcoVHindHl and the DNA fragments digested by HindUVNofi were purified after gel electrophoresis in 1% (w / v) agarose and then ligated directionally with Ncol / Notl digested pZUF17 (Fig. 2B; SEQ ID NO: 7; comprises a synthetic delta-17 desaturase gene (“D17st”) derived from S. diclina (North American Publication ri 2003/0196217 A1), codon-optimized for Yarrowia lipolytica (Publication PCT ri WO 2004/101757)). The product of this connection was pDMW367 (Fig. 2C; SEQ ID N ° 8), which thus contained the following components:
Table 4
Components of Plasmid PDMW367 (SEQ ID N ° 8)
<td>RE locations and nucleotides in SEQ ID N ° 8</td><td>Description of fragment and components of chimeric genes</td>
<td>EcoR 1 / BsiWI (7416-</td><td>FBAIN :: EgD5 :: Pex20, which comprises:</td>
<td> 1617)</td><td>- FBAIN: Farrow promoter of Yarrowia lipolytica (WO 2005/049805) - EgD5: Euglena gracilis delta-5 desaturase (SEQ ID N ° 2 described in the present) - Pex20: Pex20 termination sequence from Yarrowia's Pex20 gene (GenBank access n ° AF054613)</td>
<td>RE locations and nucleotides in SEQ ID N ° 8</td><td>Description of fragment and components of chimeric genes</td>
<td> 2707-1827</td><td>Reproduction origin of plasmid ColE1</td>
<td> 3637-2777</td><td>Ampicillin resistance gene (Amp®) for selection in E. coli</td>
<td> 4536-5840</td><td>Yarrowia autonomous breeding sequence (ARS18; Access GenBank No. A17608)</td>
<td> 7373-5886</td><td>Gene Ura 3 from Yarrowia (GenBank access n ° AJ306421)</td>
The expression “FBAIN promoter” or “promoter region for
FBAIN ”designates the region not translated above in flow 5 'in front of the start codon for translation“ ATG ”of the enzyme fructose-bisphospholate aldolase from Yarrowia lipolytica (EC 4.1.2.13) encoded by the fba1 gene and which is necessary for expression, more a part of the 5 'coding region that contains an intron of the fba1 gene.
Colony surveys
About 17,000 euglc cDNA library clones were plated on three large square petri dishes (24 cm x 24 cm) (Corning, Corning NY), each containing LB + 50 pg / ml kanamycin Agar media. The cells were cultured overnight at 37 ° C and the plates were then cooled to room temperature.
0.45 pm Biodyne B membrane (Cat. No. 60207, Pall Corporation, Pensacola FL) was cut to approximately 22 cm x 22 cm and the membrane was carefully deposited in layers on the agar to avoid air bubbles. After incubation for two minutes at room temperature, the membrane was marked for orientation, lifted with tweezers and placed with the colony side up on filter paper soaked with 0.5 M sodium hydroxide and 1.5 M sodium chloride. After denaturing for four minutes, the sodium hydroxide was neutralized by placing the membrane on filter paper soaked with 0.5 M Tris-HCI (pH 7.5) and 1.5 M sodium chloride for four minutes. This step was repeated and the membrane was quickly rinsed in 2X SSC buffer (20X SSC is 3M sodium chloride, 0.3M sodium citrate; pH 7.0) and air dried on filter paper.
Hybridization
The membranes were previously hybridized at 65 ° C in 200 ml of hybridization solution for two hours. The hybridization solution contained 6X SSPE (20X SSPE is 3M sodium chloride, 0.2M sodium phosphate, 20mM
EDTA; pH 7.4), 5X Denhardt's solution (100X Denhardt's reagent is 2% (w / v) Ficoll, 2% (w / v) polyvinylpyrrolidone, 2% (w / v) acetylated bovine serum albumin), 0, 5% sodium dodecyl sulfate (SDS), 100 pg / ml of cut salmon sperm DNA and 5% dextran sulfate.
A DNA probe was used using a fragment of
Ncol / Notl DNA purified with agarose gel, containing the P-labeled Euglena gracilis delta-5 desaturase gene, of pDMW367 (SEQ ID NO: 8)<sup>32 </sup>dCTP using the RadPrime DNA Marking System (Cat. No. 18428011, Invitrogen, Carlsbad CA) following the manufacturer's instructions. P<sup>32</sup> Unincorporated dCTP was separated using a NICK column (Cat. No. 17-085520 02, Amersham Biosciences, Piscataway NJ) following the manufacturer's instructions. The probe was denatured for five minutes at 100 ° C, placed on ice for three minutes and half was added to the hybridization solution.
The membrane was hybridized with the probe for one night at 65 ° C with gentle agitation and then washed the next day twice with
2X SSC containing 0.5% SDS (five minutes each) and twice with 0.2X SSC containing 0.1% SDS (fifteen minutes each). After washing, hyperfilm (Cat. No. RPN30K, Amersham Biosciences, Piscataway NJ) was exposed to the membrane for one night at -80 ° C.
Based on the alignment of plates with the exposed hyperfilm, positive colonies were taken using the obtuse end of a Pasteur pipette in 1 ml of water and swirled. Several dilutions were made and placed on small round petri dishes (82 mm) containing LB media plus 50 pg / ml kanamycin to obtain about one hundred colonies isolated in wells on a single plate. Surveys were carried out as described above except for the use of NytranN membrane circles (Cat. No. 10416116, Schleicher & Schuell, Keene NH) and hybridization was conducted in 100 ml using the remaining radiolabeled probe.
In this way, positive clones were confirmed.
Individual positive clones were cultured at 37 ° C in LB + 50 pg / ml of liquid kanamycin media and the plasmid was purified using the QIAprep® Centrifugation Mini Preparation Kit (Qiagen Inc.) following the manufacturer's requirement.
DNA inserts had ends sequenced in 384-well plates, using universal primer M13F with vector primer (SEQ ID N ° 9), primer M13rev-28 (SEQ ID N ° 10) and WobbleT oligonucleotides with poly tail primers (A ), with the Prism ABI BigDye version 3 sequencing kit. For the sequencing reaction, 100 to
200 ng of model and 6.4 pmol of primer and the following reaction conditions were repeated 25 times: 96 ° C for ten seconds, 50 ° C for five seconds and 60 ° C for four minutes. After ethanol-based cleaning, cycle sequencing reaction products were resolved and detected on Perkin-Elmer ABI 3700 automated sequencers. The WobbleT primer is an equimolar mixture of 21mer poli (T) A, poli (T) C and poli (T) G, used to sequence the 3 'end of cDNA clones.
The sequences were aligned and compared using Sequencher® (Version 4.2, Gene Codes Corporation, Ann Arbor Ml) and, thus, it was determined that all CDS in each cDNA were identical. A representative clone containing a cDNA (pLF119) is displayed in SEQ ID No. 11 and the gene contained in the cDNA was called EaD5Des1. The coding sequence for EaD5Des1 is displayed in SEQ ID No. 12. The corresponding amino acid sequence for EaD5Des1 is displayed in SEQ ID No. 13. Example 3
Analysis of primary sequences of the delta-5 desaturase sequence of
Euglena anabaena UTEX 373 (EaD5Des1) and comparison with the Euglena gracilis delta-5 desaturase sequence (EgD5)
The amino acid sequence for EaD5Des1 (SEQ ID N ° 13) was evaluated using BLASTP (Basic Local Alignment Research Tool; Altschul et al, J. Mol. Biol. 215: 403-410 (1993)) looking for similarity to sequences contained in the BLAST database “nr” (which comprises all non-redundant translations of GenBank CDS, sequences derived from the three-dimensional structure Brookhaven Protein Database, the last major publication of the SWISS-PROT protein sequence database, EMBL and DDBJ databases) using standard parameters with the filter off. For convenience, the P value (probability) of observing a coincidence of a cDNA sequence with a sequence contained in the databases researched at random as calculated by means of BLAST are reported in the present as “pLog” values, which represent the negative of the reported P-value logarithm. Consequently, the higher the pLog value, the greater the probability that the cDNA sequence and the “found” by BLAST represent homologous proteins.
BLASTP analysis with EaD5Des1 generated a pLog value of
76.52 (P value of 3e-77) against Thalassiosira pseudonana delta-8 fatty acid desaturase (TpsD8; SEQ ID N ° 14) (NCBI access n ° AAX14502 (Gl 60172920), site AAX14502, CDS AY817152; Tonon et al, FEBS J. 272: 3401-3412 (2005)) compared to the “nr” database. Although identified as a delta-8 fatty acid desaturase in the NCBI database, AY817152 was identified as a delta-5 desaturase in
Tonon et al and the designation of NCBI as a delta-8 fatty acid desaturase is probably an error. BLASTP analysis with EaD5Des1 also generated a pLog value of 75.70 (P value of 2e-76) against the Phaeodactylum tricornutum delta-5 fatty acid desaturase (SEQ ID N ° 15) (NCBI access n ° AAL92562 (Gl 19879687 ), location AAL92562, CDS AY082392; Domergue et al,
Eur. J. Biochem. 269: 4105-4113 (2002)) compared to the “nr” database.
The amino acid sequence of EaD5Des1 (SEQ ID NO: 13) was compared with the Thalassiosira pseudonana delta-8 fatty acid desaturase (SEQ ID NO: 14) and the amino acid sequence of Euglena gracilis delta-5 desaturase (EgD5; SEQ ID N ° 16; which is described in North American Provisional Application n ° 60 / 801,172 (filed May 17, 2006; Lawyer Attorney N ° CL-3486) using BlastP, Clustal V and Jotun Hein methods of comparison of strings. The percentage of identity against TpsD8 and EgD5 using each method is shown in the Table
5 and Table 6, respectively.
The calculations of percent identity of strings performed by the BlastP method are as described above. The calculations of percentages of sequence identity were performed using the Clustal V method (Higgins, DG and Sharp, PM, Comput. Appl. Biosci. 5: 151-153 (1989);
Higgins et al, Comput. Appl. Biosci. 8: 189-191 (1992)) using the MegAlign® v6.1 program from the LASERGENE bioinformatics computing suite (DNASTAR Inc., Madison Wl) with the standard parameters for pair alignments (WORD LENGTH = 1, INTERVAL PENALTY
100 = 3, VISUALIZATION OF THE BEST RESULT = 5, SPACING IN DIAGONALS = 5 and PENALTY OF THE INTERVAL = 10).
The calculations of sequence identity percentages performed using the method of Jotun Hein (Hein, JJ, Meth. Enz. 183: 6265 645 (1990)) were performed using the MegAlign® v6.1 program from the LASERGENE bioinformatics computing suite ( DNASTAR Inc., Madison Wl) with standard parameters for alignment in pairs (WORD LENGTH = 2).
Tables
Sequence Comparison Between EaD5Des1 (SEQ ID N ° 13) and TpsD8 (SEQ
IDN ° 14)
<td>Desaturase</td><td>Percent of identity for TpsD8 by BLASTP</td><td>Percent of identity for TpsD8 by Method from Jotun Hein</td><td>Percent of Identity for TpsD8 by Method Clustal V</td>
<td>EaD5Des1 (SEQ ID</td><td> 37%</td><td> 40,8%</td><td> 30,8%</td>
<td>No. 13)</td><td></td><td></td><td></td>
Table 6
Sequence Comparison Between EaD5Des1 (SEQ ID N ° 13) and EgD5 (SEQ ID
No. 16)
<td>Desaturase</td><td>Percent of identity for EgD5 by BLASTP</td><td>Percent of identity for EgD5 by Method from Jotun Hein</td><td>Percent of Identity for EgD5 by Method Clustal V</td>
<td>EaD5Des1 (SEQ ID</td><td> 73%</td><td> 72,4%</td><td> 77,1%</td>
<td>No. 13)</td><td></td><td></td><td></td>
101
Example 4
Functional analysis of the delta-5 desaturase from Euglena gracius UTEX 373 (EaD5Des1) in Yarrowia lipolytica The present Example describes the functional analysis of EaD5Des1 (SEQ ID NO: 13) in Yarrowia lipolytica. This work included the following steps: (1) construction of Yarrowia expression vector compatible with Gateway® pY159; (2) transfer of EaD5Des1 (SEQ ID NO: 12) in pY159 to produce pY169; and (3) comparison of lipid profiles in transforming organisms that comprise pY169.
Gateway-compatible Yarrowia expression vector construction
PY159
Plasmid pY5-30 (which was previously described in PCT Patent No. WO 2005/003310 (whose content is hereby incorporated by reference)) is a booster plasmid that can reproduce in E. coli and
Yarrowia lipolytica. Plasmid pY5-30 contains the following: an autonomous reproduction sequence from Yarrowia (ARS18); a ColE1 plasmid breeding source; an ampicillin resistance gene (Amp<sup>R</sup>) for selection in E. coli ', a LEU2 gene from Yarrowia for selection in Yarrowia', and a chimeric TEF :: GUS :: XPR gene. Plasmid pDMW263 (SEQ ID NO: 17) was created from pY5-30 by replacing the TEF promoter with the Yarrowia lipolytica FBAINm promoter (PCT Patent No. WO 2005/049805) using methods well known to those skilled in the art. subject matter. Briefly, this promoter refers to a modified promoter that is located in the untranslated region above in flow 5 'in front of the' ATG 'translation start codon of the fructose-bisphosphate aldolase enzyme (EC 4.1.2.13) encoded by the fba1 gene and that is required for expression, plus a part of the 5 'coding region that contains an intron, where FBAINm has a 52 bp exclusion between the ATG translation start codon and the FBAIN promoter intron (so
102 to include only 22 N-terminal amino acids) and a new translation consensus motif after the intron. Table 7 summarizes the components of pDMW263 (SEQ ID NO: 17).
Table 7
Components of Plasmid pDMW263 (SEQ ID N ° 17)
<td>RE locations and nucleotides in SEQ IDN ° 17</td><td>Description of chimeric gene fragment and components</td>
<td> 4992-4296</td><td>ARS18 sequence (GenBank access no. A17608)</td>
<td>Sall / Sacll (8505-</td><td>FBAINm :: GUS :: XPR, which comprises:</td>
<td> 2014)</td><td>- FBAINm: promoter of FBAINm (WO 2005/049805) - GUS: E. coli gene encoding β-glucuronidase (Jefferson, RA, Nature, 14: 342: 837-838 (1989) - XPR: about 100 bp of the 3 'region of the Yarrowia Xpr gene (Access GenBank No. M17741)</td>
<td> 6303-8505</td><td>Yarrowia Leu2 gene (GenBank access n ° AF260230)</td>
The pDMW263 Nco \ / Sal \ DNA fragment (SEQ ID NO: 17), which contains the Yarrowia lipolytica FBAINm promoter, was cloned into the pDMW237 Nco \ / Sal \ DNA fragment (SEQ ID NO: 18), described previously in PCT Patent No. WO 2006/012325 (whose content is hereby incorporated by reference), which contains a synthetic delta-9 elongase gene derived from Isochrysis galbana and codon-optimized for expression in Yarrowia lipolytica (lgD9eS) to produce pY115 ( SEQ ID No. 19; Fig. 3). In Fig. 3, the modified FBAINm promoter is called FBA1 + Intron. It is also FBA1 + Intron in the other figures, as well as YAR FBA1 PRO + Intron, and these terms are used interchangeably with FBAINm.
The FBAINm promoter was amplified from the plasmid
103 pY115 (SEQ ID No. 19), using PCR with oligonucleotide primers oYFBAI (SEQ ID No. 20) and 0YFBAI-6 (SEQ ID No. 21). The oYFBAI primer (SEQ ID No. 20) was designed to introduce a BglW location at the 5 'end of the promoter and the 0YFBAI-6 primer (SEQ ID No. 21) was designed to introduce a Not \ location at the 3' end of the promoter. , while removing the Nco \ location and, therefore, the ATG start codon. The resulting PCR fragment was digested with BglW and Not \ and cloned into the BglW / Nofi fragment of pY115, which contains the vector backbone, to form pY158 (SEQ ID NO: 22).
Plasmid pY158 (SEQ ID No. 22) was digested with Notl and the resulting 10 DNA ends were filled. After filling to form obtuse ends, the DNA fragments were treated with calf intestinal alkaline phosphatase and separated using agarose gel electrophoresis. The 6992 bp fragment containing the FBAINm promoter from Yarrowia lipolytica was excised from the agarose gel and purified using the QIAquick® Gel Extraction Kit (Qiagen Inc., Valencia CA) following the manufacturer's protocol. The purified 6992 bp fragment was ligated to the rfA pool using the Gateway Vector Conversion System (Cat. No. 11823-029, Invitrogen Corporation) following the manufacturer's protocol to form the Gateway® target vector of Yarrowia lipolytica pY159 (SEQ ID No. 23; Fig. 4).
Construction of Yarrowia pY169 expression vectors
Using the Clonase® II Gateway® LR enzyme mix (Cat.
No. 11791-020, Invitrogen Corporation) and following the manufacturer's protocol, the pLF119 cDNA insert (SEQ ID No. 11) was transferred to pY159 (SEQ ID No. 23) to form pY169 (SEQ ID No. 24, Fig. 5). In Fig. 5, EaD5Des1 is identified as EaD5-1, but they are identical.
Functional analysis of EaD5Des1 in Yarrowia lipolytica
The Y2224 strain was isolated as follows: Yarrowia lipolytica cells ATCC No. 20362 from a YPD Agar plate (1% extract of
104 yeast, 2% bactopeptone, 2% glucose, 2% Agar) were stained on an MM plate (75 mg / l of uracil and uridine each, 6.7 g / l of YNB with ammonium sulfate, without amino acid, and 20 g / l of glucose) containing 250 mg / l of 5-FOA (Zymo Research). The plates were incubated at 28 ° C and four of the resulting colonies were plastered separately on MM plates containing 200 mg / ml of 5-FOA and MM plates that do not contain uracil and uridine to confirm the auxotrophy of uracil Ura3.
The Y2224 strain was transformed with pY169 (SEQ ID No. 24, Fig. 5), as described in the General Methods.
Isolated colonies of the transformer Yarrowia lipolytica containing pY169 were cultured in 3 ml of minimal media containing no uracil supplemented with 0.2% tergitol at 30 ° C for one day. Then, 0.1 ml was transferred to 3 ml of the same medium supplemented with ALA, EDA, ERA, DGLA, ETA, EPA, DPA or no fatty acid. These were incubated for sixteen hours at 30 ° C, 250 rpm and then pellets were obtained by means of centrifugation. The cells were washed once with water, pelleted by means of centrifugation and dried in air. The pellets were transesterified (Roughan, G. and Nishida, I., Arch. Biochem. Biophys. 276 (1): 38-46 (1990)) with 500 pl of 1% sodium methoxide for thirty minutes at 50 ° C, after which 500 μΙ of 1 M sodium chloride and 100 μΙ of heptane were added. After complete mixing and centrifugation, fatty acid methyl esters (FAMEs) were analyzed by GC. FAMEs (5 μΙ injected from the hexane layer) were separated and quantified using a Hewlett-Packard 6890 Gas Chromatograph equipped with an Omegawax 320 fused silica capillary column (Cat. No. 24152, Supelco Inc.). The oven temperature was programmed to stay at 220 ° C for 2.6 minutes, increase to 240 ° C at 20 ° C / min and then continue for an additional 2.4 minutes. The vehicle gas was supplied by a hydrogen generator
105
Whatman. In the case of DPA feeding, GC analysis was conducted in a similar manner, except that the oven temperature was programmed to remain at 170 ° C for 1.0 min, increase to 240 ° C at 5 ° C / min and then hold for an additional 1.0 min. Retention times were compared with those of commercially available standard methyl esters (Nu-Chek Prep, Inc.).
The fatty acid profiles for Yarrowia lipolytica that expresses pY169 and various substrates fed are shown in Fig. 6. The substrates (LA (when no fatty acid is fed), ALA, EDA, ERA, DGLA, ETA or DPA) were fed to determine the activities of delta-4 (DPA for DHA), delta-5 (DGLA for ARA, DTA for EPA, EDA for SCI, ERA for JUP), delta-6 (LA for GLA, ALA for STA), delta-8 (EDA for DGLA, ERA for ETA) or omega-3 (LA for ALA, EDA for ERA, DGLA to ETA) desaturates. The percentage of desaturation (% desat) was calculated by dividing15 the percentage by weight of substrate (LA (when no fatty acid is fed), ALA, EDA, ERA, DGLA, ETA or DPA) by the sum of the weight percentage of the substrate ( LA (when no fatty acid is fed), ALA, EDA, ERA, DGLA, ETA or DPA) and product (GLA, STA, DGLA, ETA, ARA, EPA or DHA, respectively), multiplying by one hundred to express in the form of percentage, depending on which substrate was fed. In Fig. 6, the shading indicates the substrates fed and the products generated. The averages are indicated by Ave. followed by an appropriate header. From the results of Fig. 6, it is clear that EaD5Des1 functions as a delta-5 desaturase with preference for DGLA and ETA over EDA and ERA. The desaturation ratio of omega-6 substrate to omega-3 substrate (n-6 / n-3 ratio) is calculated by dividing the average percentage of desaturation for DGLA by ETA or EDA by ERA. In both cases, EaD5Des1 prefers n-6 substrates and not n-3 substrates. The desaturation ratio between the preferred substrate and the
106 non-preferred substrate (product / by-product ratio) is calculated by dividing the average percentage of desaturation for DGLA by EDA or ETA by ERA. In both cases, EaD5Des1 has a preference of about 3.5 times for DGLA or ETA over EDA or ERA, respectively.
Example 5
Construction of soybean expression vector pKR1 153 for coexpression of the delta-5 desaturase from Euglena anabaena UTEX 373 (EaD5Des1) with a delta-9 elongase derived from Euglena gracius (EgD9e) and a delta-8 desaturase derived from Euglena gracilis (EgD8)
The present example describes the construction of a soybean vector for the coexpression of EaD5Des1 with EgD9e (SEQ ID No. 25; which is described in North American Order No. 11 / 601,563 (filed on November 16, 2006 and published on 24 May 2007; Lawyer Attorney No. BB-1562) and EgD8 (SEQ ID No. 26; described as Eg5 in PCT Application No. WO
2006/012325).
Delta-9 elongase from Euglena gracius (EgD9e)
A clone of the Euglena cDNA library (eeglc), named eeg1c.pk001.n5f, which contains the Euglena gracilis delta-9 elongase (EgD9e; SEQ ID No. 25, which is described in North American Order No. 11 / 601,563 (deposited on November 16, 2006 and published on May 24, 2007; Attorney's Folder No. BB-1562), the content of which is incorporated into the present as a reference), was used as a model to amplify EgD9e with oligonucleotide primers oEugEL1-1 (SEQ ID N ° 27) and oEugEL1-2 (SEQ ID N ° 28) using VentR® DNA Polymerase (Cat. No. M0254S, New England Biolabs
Inc., Beverly MA) following the manufacturer's protocol. The resulting DNA fragment was cloned into the pCR-Blunt® cloning vector using the Zero Blunt® PCR Cloning Kit (Invitrogen Corporation), following the manufacturer's protocol, to produce pKR906 (SEQ ID NO: 29).
107
An initial plasmid pKR72 (ATCC Accession No. PTA-6019; SEQ ID No. 30, 7085 bp sequence), a derivative of pKS123 that was previously described in PCT Patent No. WO 02/008269 (the content of which is incorporated herein as reference), contains the hygromycin B phosphotransferase (HPT) gene (Gritz, L. and Davies, J., Gene 25: 179-188 (1983)), flanked by the T7 promoter and transcription termination (T7prom / HPT / T7term set) and a breeding bacterial origin (ori) for selection and breeding in bacteria (for E. coli). In addition, pKR72 also contains HPT, flanked by the 35S promoter (Odell et al, Nature 313: 810-812 (1985)) and the NOS 3 'transcription termination (Depicker et al, J. Mol. Appl. Genet. 1: 561-570 (1982)) (set 35S / HPT / NOS3 ') for selection in plants such as soybeans. pKR72 also contains a Nott restriction site, flanked by the promoter for the β-conglycinin subunit (Beachy et al, EMBO J. 4: 3047-3053 (1985)) and the 3 'transcription termination region of the gene Phaseolin (Doyle et al, J.
Biol. Chem. 261: 9228-9238 (1986)), in order to allow strong tissue-specific expression in soybean seeds of genes cloned at the Nott site.
The Ascl fragment of plasmid pKS102 (SEQ ID NO: 31), previously described in PCT Patent No. WO 02/00905 (whose content is hereby incorporated by reference), which contains the set
T7prom / hpt / T7term and bacterial ori, was combined with the Ascl fragment from plasmid pKR72 (SEQ ID No. 30), which contains the pcon / A / hi // Phas set to produce pKR197 (SEQ ID No. 32), described previously in PCT Patent No. WO 04/071467 (the content of which is hereby incorporated by reference).
The Euglena gracilis delta-9 elongase gene was released by pKR906 (SEQ ID NO: 29) via Nott digest and cloned into the Nott site of pKR197 to produce the intermediate cloning vector pKR911 (SEQ ID NO: 33).
108
Delta-8 desaturase from Euglena gracilis (EgD8)
Plasmid pKR680 (SEQ ID NO: 34), which was previously described in PCT Patent No. WO 2006/012325 (the content of which is hereby incorporated by reference), contains Euglena gracilis delta-8 desaturase (EgD8; SEQ ID N ° 26; described as Eg5 in WO 2006/012325) flanked by the soybean trypsin inhibitor promoter Kunitz (KTi) (Jofuku et al, Plant Cell 1: 1079-1093 (1989)) and by the 3 'termination region of KTi, whose isolation is described in U.S. Patent No. 6,372,965, followed by the termination of transcription of soybean albumin, which was previously described in PCT Patent No. WO 2004/071467 (set Kti // Vofl / Kti3'Salb3 ').
Plasmid pKR680 (SEQ ID NO: 34) was digested with Bsi \ N \ and the fragment containing EgD8 was cloned into the physical / WI site of pKR911 (SEQ ID NO: 33) to produce pKR913 (SEQ ID NO: 35).
Delta-5 desaturase from Euglena anabaena UTEX 373 (EaD5Des1)
In order to introduce Noti sites at the 5 'and 3' ends of the coding sequence, EaD5Des1 was amplified by PCR from pLF119 (SEQ ID No. 11) with oligonucleotide primers oEAd5-1-1 (SEQ ID No. 36 ) and oEAd5-1-2 (SEQ ID N ° 37) using Phusion® High Fidelity DNA Polymerase (Cat. N ° F553S, Finnzymes Oy, Finland), following the manufacturer's protocol. The resulting DNA fragment was cloned into the pCR-Blunt® cloning vector using the Zero Blunt® PCR Cloning Kit (Invitrogen Corporation), following the manufacturer's protocol, to produce PKR1136 (SEQ IDN ° 38).
Plasmid pKR767 (SEQ ID No. 39), which was previously described in PCT Patent No. WO 2006/012325 (the content of which is hereby incorporated by reference), contains the delta-5 desaturase from Mortierella alpina (MaD5; SEQ ID N 40), which is described in U.S. Patent No. 6,075,183 and PCT Patent No. WO 2004/071467 and WO 2005/047479)
109 flanked by the promoter for the soy glycine gene Gy1 and the pea A2 3 'leguminous transcription termination region (Gy1 / MaD5 / legA2 set; the construction of which is described in WO 2006/012325). Plasmid pKR974 (SEQ ID NO: 41) is identical to pKR767 (SEQ ID NO: 40) except for the Nofi fragment that contains MaD5, which was replaced by a Nofi fragment that contains the delta-5 desaturase from Saprolegnia diclina (SaD5 SEQ ID No. 42, which is described in PCT Patent No. WO 2004/071467). In addition, an Mfe \ site at the legA2 terminal of pKR974 (SEQ ID N ° 41) was removed by digesting with Mfe \, filling in the Mfe \ site and reconnecting (ie CAATTG converted to CAATTAATTG) and therefore the legA2 terminal of pKR974 (SEQ ID No. 41) is 770 bp against 766 bp for pKR767 (SEQ ID No. 40).
The gene for Euglena anabaena's delta-5 desaturase was released from pKR1136 (SEQ ID No. 38) by digesting with Nofí and cloned into the Nofí site of pKR974 (SEQ ID No. 41) to produce pKR1139 (SEQ ID N °
43).
Plasmid pKR1139 (SEQ ID N ° 43) was digested with Sbfí and the fragment containing Euglena anabaena delta-5 desaturase was cloned at the Sbfí site of pKR913 (SEQ ID N ° 35) to produce pKR1153 (SEQ ID N ° 44) , Fig. 7). Thus, Euglena anabaena delta-5 desaturase (EaD5Des1) can be coexpressed with Euglena gracilis delta-8 desaturase (EgD8) and Euglena gracilis delta-9 elongase (EgD9e) behind specific strong seed promoters. In Fig. 7, EaD5Des1, EgD8 and EgD9e are called EA d5 DS, eug d8-sq5 and eug el1, respectively.
Example 6
Production and transformation of a somatic soybean culture model system with soybean expression vectors and conditions
PLANT REGENERATION CULTIVATION
Cultivations of soy embryogenic suspension (cv. Jack) are
110 kept in 35 ml of SB196 liquid medium (above) on a rotating shaker, 150 rpm, 26 ° C with cold white fluorescent lights over a 16: 8 hour day / light photoperiod under 60 to 85 pE / m light intensity<sup>2</sup>/s. Cultures are subcultured every seven days to two weeks by inoculating about 35 mg of tissue in 35 ml of fresh SB196 liquid (the preferred subculture interval is every seven days).
Cultures of embryogenic soy suspension are transformed with the soybean expression plasmids using the particle trigger bombardment method (Klein et al, Nature 327 '. 70 (1987)) using a DuPont Biolistic PDS1000 / He instrument (retrofit of helium) for all transformations.
Beginning of cultivation of embryogenic soy suspension
Soy crops are started twice a month with five to seven days between each start. Pods with immature seeds of available soybean plants are taken 45 to 55 days after planting. The seeds are removed from the pods and placed in a sterile magenta box. Soya beans are sterilized by shaking them for 15 minutes in a 5% Clorox solution with a drop of ivory soap (ie 95 ml of autoclave distilled water plus 5 ml of Clorox and a drop of soap, well mixed). The seeds are rinsed using two one-liter bottles of sterile distilled water and those smaller than 4 mm are placed on individual microscope slides. The small end of the seed is cut and the cotyledons are pressed out of the seed coating. When crops are being prepared for production transformation, cotyledons are transferred to plates containing SB1 medium (25 to 30 cotyledons per plate). The plates are packed with fiber tape and are kept at 26 ° C with cold white fluorescent lights over a 16: 8 hour day / night photoperiod under 60 to 60 light intensity.
111 pE / m<sup>2</sup>/ s for eight weeks, with a change of means after four weeks. When cultures are being prepared for model system experiments, cotyledons are transferred to plates containing SB199 medium (25 to 30 cotyledons per plate) for two weeks and then transferred to SB1 for two to four weeks. The light and temperature conditions are the same as described above. After incubation on SB1 medium, secondary embryos are cut and placed in SB196 liquid medium for seven days.
Preparation of DNA for bombardment An intact plasmid or a plasmid fragment of DNA containing the genes of interest and the selectable marker gene are used for bombardment. Fragments of soybean expression plasmids are obtained by gel isolation from digested plasmids. In each case, 100 pg of plasmid DNA is used in 0.5 ml of the specific enzyme mixture described below. Plasmids are digested with Ascl (100 units) in NE 4 buffer (20 mM Tris-acetate, 10 mM magnesium acetate, 50 mM potassium acetate, 1 mM dithiothreitol, pH 7.9), 100 pg / ml of BSA and 5 mM betamercaptoethanol at 37 ° C for one and a half hours. The resulting DNA fragments are separated by means of gel electrophoresis on 1% SeaPlaque GTG agarose (BioWhitaker Molecular Applications) and the DNA fragments containing genetic sets are cut from the agarose gel. DNA is purified from agarose using the GELase digesting enzyme following the manufacturer's protocol.
A 50 pl portion of sterile distilled water containing 3 mg of gold particles (3 mg of gold) is added to 30 pl of a 10 ng / pl solution of DNA (intact plasmid or DNA fragment prepared as described herein) , 25 pl of 5 M CaCI<sub>2</sub> and 20 µl of 0.1 M spermidine. The mixture is stirred for three minutes on level 3 of a vortex shaker and centrifuged for ten seconds in a microcentrifuge.
112 stand. The supernatant is removed, followed by washing with 400 pl of 100% ethanol and another rapid centrifugation. The 400 pl of ethanol is removed and the pellet is resuspended in 40 μΙ of 100% ethanol. Five microliters of DNA suspension are released for each disc suspended from the Biolistic PDS1000 / He instrument disc. Each 5 μΙ plot contains about 0.375 mg of gold per bombardment (such as per disk).
For model system transformations, the protocol is identical, except for a few minor changes (ie, 1 mg of gold particles is added to 5 μΙ of a 1 pg / μΙ solution of DNA, 50 μΙ of 2.5 M of CaCb are used and the pellet is finally resuspended in 85 μΙ of 100% ethanol, in order to provide 0.058 mg of gold particles by bombardment).
Preparation of tissues and bombardment with DNA:
About 150 to 200 mg of seven-day-old embryogenic suspension cultures are placed in an empty sterile 60 x 15 mm petri dish and the plate is covered with a plastic net. The chamber is evacuated to a vacuum of 68 to 71 cm of mercury and the tissue is bombarded once or twice per plate with a membrane burst pressure set at 1100 psi. The fabric is placed about 9 cm from the retention / stop screen. The transformation conditions of the model system are identical, except for the use of 100 to 150 mg of embryogenic tissue, the burst pressure is set at 650 psi and the tissue is placed approximately 6.3 cm from the retention screen.
Selection of transformed embryos
The transformed embryos are selected using hygromycin (when the hygromycin B phosphotransferase (HPT) gene is used as the selectable marker) or chlorosulfurone (when the acetolactate synthase (ALS) gene is used as the selectable marker).
113
After bombardment, the tissue is placed in new SB196 media and cultured as described above. Six to eight days after the bombing, the SB196 is replaced by a new SB196 containing 30 mg / l of hygromycin or 100 ng / ml of chlorosulfone, depending on the selectable marker used. The selection means are renewed weekly. Four to six weeks after selection, transformed green tissue is seen growing from untransformed necrotic embryogenic clusters.
Ripening of embryos:
For production transformations, isolated green tissue is removed and inoculated into plates with multiple cavities to generate new embryogenic suspension cultures transformed and propagated in a clonal way. The transformed embryogenic clusters are cultured for four to six weeks in multi-well plates at 26 ° C in SB196 under cold white fluorescent lamps (Phillips Econowatt F40 / CW / RS / EW cold white) and Agro (Phillips F40 Agro) (40 watts ) over a 16: 8 hour photoperiod with a light intensity of 90 to 120 pE / m<sup>2</sup>s. After this period, the embryo sets are removed to a solid Agar medium, SB166, for one to two weeks and then subcultured in SB103 medium for three to four weeks to mature the embryos. After maturing on plates in SB103, individual embryos are removed from the pools, dried and selected to determine changes in their fatty acid compositions as described in Example 7.
For model system transformations, embryos are matured in liquid soybean maturation and histodifferentiation medium (SHaM liquid media; Schmidt et al, Cell Biology and Morphogenesis 24: 393 (2005)) using a modified procedure. Briefly, after four weeks of selection on SB196 as described above, embryo sets are removed to 35 ml of SB228 (SHaM liquid medium) in a
114 250 ml Erlenmeyer flask. The tissue is maintained in SHaM liquid medium on a rotary shaker at 130 rpm and 26 ° C with cold white fluorescent lights over a 16: 8 hour day / night photoperiod at a light intensity of 60 to 85 pE / m<sup>2</sup>/ s for two weeks as the embryos mature.
Embryos grown for two weeks in liquid SHaM media have a size and fatty acid content equivalent to embryos grown on SB166 / SB103 for five to eight weeks.
After maturing in SHaM liquid media, individual embryos are removed from the pools, dried and selected to determine changes in their fatty acid compositions as described in Example 7. Media recipes
SB 196 - FN LITE NET PROLIFERATION MEDIA (PER LITER)
<td>MS FeEDTA- 100x standard 1</td><td>10 ml</td>
<td>MS Sulfate - 100x standard 2</td><td>10 ml</td>
<td>Halides FN Lite - 100x standard 3</td><td>10 ml</td>
<td>FN Lite P, B, Mo - standard 100x 4</td><td>10 ml</td>
<td>Vitamins B5 (1 ml / l)</td><td>1.0 ml</td>
<td>2,4-D (10 mg / l final concentration)</td><td>1.0 ml</td>
<td>KNO<sub>3</sub></td><td>2.83 g</td>
<td>(NH<sub>4</sub>)<sub>2</sub>ONLY<sub>4</sub></td><td>0.463 g</td>
<td>Asparagine</td><td>1.0 g</td>
<td>Sucrose (1%)</td><td>10g</td>
<td>pH 5.8</td><td></td>
FN Lite standard solutions
<td>Pattern n °</td><td></td><td>1000 ml</td><td>500 ml</td>
<td> 1</td><td>MS Fe EDTA 100x Standard At<sub>2</sub> EDTA * FeSO<sub>4</sub> - 7H<sub>2</sub>THE</td><td>3.724 g 2.784 g</td><td>1.862 g 1.392 g</td>
115
<img file="BRPI0809877A2_D0001.tif" />
<td>Pattern n °</td><td></td><td>1000 ml</td><td>500 ml</td>
<td colspan="3">* Add first, dissolve in a dark bottle by shaking</td><td></td>
<td> 2</td><td>Standard 100x MS sulfate MgSO<sub>4</sub> - 7H<sub>2</sub>THE</td><td>37.0 g</td><td>18.5 g</td>
<td></td><td>MnSO<sub>4</sub> - H<sub>2</sub>THE</td><td>1.69 g</td><td>0.845 g</td>
<td></td><td>ZnSO<sub>4</sub> - 7H<sub>2</sub>THE</td><td>0.86 g</td><td>0.43 g</td>
<td></td><td>CuSO<sub>4</sub> - 5H<sub>2</sub>THE</td><td>0.0025 g</td><td>0.00125 g</td>
<td> 3</td><td>Halides FN Lite 100x standard CaCI<sub>2</sub> - 2H<sub>2</sub>THE</td><td>30.0 g</td><td>15.0 g</td>
<td></td><td>Kl</td><td>0.083 g</td><td>0.0715 g</td>
<td></td><td>CoCI<sub>2</sub>-6H<sub>2</sub>THE</td><td>0.0025 g</td><td>0.00125 g</td>
<td> 4</td><td>Standard FN Lite P, B, Mo 100x KH<sub>2</sub>POWDER<sub>4</sub></td><td>18.5 g</td><td>9.25 g</td>
<td></td><td>u.pn.</td><td rowspan="2">0.62 g</td><td rowspan="2">n 31 π</td>
<td></td><td></td>
<td></td><td>At<sub>2</sub>Mo0<sub>4</sub> - 2H<sub>2</sub>THE</td><td>0.025 g</td><td>0.0125 g</td>
SB1 solid medium (per liter) package of MS salts (Gibco / BRL - Cat. No. 11117-066) ml of B5 vitamins 1000x standard 31.5 g of glucose
2 ml of 2,4-D (final concentration of 20 mg / l) pH 5.7 g of TC Agar
SB199 solid medium (per liter) MS salt package (Gibco / BRL - cat. N ° 11117-066)
1 ml of B5 vitamins 1000x standard g of sucrose ml of 2,4-D (final concentration of 40 mg / l) pH 7.0 »116 g of Gelrite
SB166 solid medium (per liter) MS salts package (Gibco / BRL - cat. N ° 11117-066) ml of B5 vitamins 1000x standard
60 g of maltose
750 mg of MgCb hexahydrate 5 g of activated carbon pH 5.7 g of gelrite
SB 103 solid medium (per liter) MS salts package (Gibco / BRL - cat. No. 11117-066) ml of B5 vitamins 1000x standard 60 g maltose
750 mg of MgCb hexahydrate pH 5.7 g of gelrite
SB 71-4 solid medium (per liter) bottle of Gamborg B5 salts with sucrose (Gibco / BRL - cat. No. 21153-036) pH 5.7 g of AgarTC
2,4-D stock
Get pre-made from Phytotech cat. n ° D 295 - mg / ml concentration
Stock of B5 vitamins (per 100 ml):
Store plots at -20 ° C.
g of myoinositol 100 mg nicotinic acid
117
100 pyridoxine HCI mg 1 g thiamine
If the solution does not dissolve quickly enough, apply a low level of heat using the hot stir plate.
SB 228 - SOY HISTODIFERENTIATION AND MATURATION (SHaM) (BY LITER)
H<sub>2</sub>DDI 600 ml
Macro Salts FN-Lite for SHaM 10X 100 ml
Micro Salts MS 1000x 1 ml
MSFeEDTA100x 10 ml
CaCHOOx 6.82 ml
Vitamins B5 1000x 1 ml
L-methionine 0.149 g
Sucrose 30 g
Sorbitol 30 g
Adjust volume to 900 ml pH 5.8
Autoclave
Add cooled media (at 30 ° C):
* Glutamine (final concentration of 30 mM) 4% 110 ml * Note: the final volume will be 1010 ml after the addition of glutamine.
As glutamine degrades relatively quickly, it may be preferable to add it immediately before using the media. Validity up to two weeks after the addition of glutamine; the base media can be maintained longer without glutamine.
FN-lite Macro for SHAM 10x - Stock No. 1 (per liter) (NH<sub>4</sub>)<sub>2</sub>ONLY<sub>4</sub> (ammonium sulfate) 4.63 g
KNO<sub>3</sub> (potassium nitrate) 28.3 g
MgSO<sub>4</sub>* 7H<sub>2</sub>O (magnesium sulfate heptahydrate) 3.7 g
118
KH<sub>2</sub>POWDER<sub>4</sub> (potassium phosphate, monobasic) 1.85 g
Bring up to volume
Autoclave
MS Micro 1000X- Stock No. 2 (per liter)
H3BO3 (boric acid) 6.2 g
MnSO<sub>4</sub>* H2O (manganese sulfate monohydrate) 16.9 g ZnSO<sub>4</sub>* 7H<sub>2</sub>O (zinc heptahydrate sulfate) 8.6 g
At<sub>2</sub>MoO<sub>4</sub>* 2H<sub>2</sub>O (sodium molybdate dihydrate) 0.25 g CuSO<sub>4</sub>* 5H2O (copper sulfate pentahydrate) 0.025 g
CoCÍ2 * 6H<sub>2</sub>O (cobalt chloride hexahydrate) 0.025 g
Kl (potassium iodide) 0.8300 g
Bring up to volume
Autoclave
FeEDTA 100X - Stock No. 3 (per liter)
At<sub>2</sub>EDTA * (sodium EDTA) 3.73 g
FeSO<sub>4</sub>* 7H2O (iron heptahydrate sulfate) 2.78 g * EDTA must be completely dissolved before adding iron.
Bring up to volume
The solution is photosensitive. The bottle (s) must be packed in foil to omit the light.
Autoclave
Ca 100X - Stock No. 4 (per liter)
CaCÍ2 * 2H<sub>2</sub>O (calcium chloride dihydrate) 44 g
Bring up to volume
Autoclave
Vitamin B51000X- Stock No. 5 (per liter)
Thiamine * HCI
10g
119
Nicotinic acid
Pyridoxine * HCI
Myoinositol
9 ig 100 g
Bring up the heat volume
Store frozen
4% GLUTAMINE - STANDARD N ° 6 (PER LITER)
DDI water heated to 30 ° C L-glutamine
900 ml g
Gradually add by shaking and applying low
Do not exceed 35 ° C
Bring up to volume
Filter and sterilize
Store frozen * * Note: heat the defrosted stock in a bath to 31 ° C to completely dissolve the crystals.
Regeneration of somatic soy embryos in plants
In order to obtain whole plants from embryogenic suspension cultures, the tissue must be regenerated. Embryos are matured as described above. After subculturing on the SB103 medium for three weeks, individual embryos can be removed from the pools and selected by changes in their fatty acid compositions as described in Example 7. It should be noted that any detectable phenotype, resulting from the expression of the genes of interest, can be selected at this stage. This would include, but is not limited to, changes in the fatty acid profile, protein profile and content, carbohydrate content, growth rate, viability or normal development capacity in a soybean plant.
Ripened individual embryos are dissected through the
120 placing it in a small empty petri dish (35 x 10 mm) for about four to seven days. The plates are sealed with fiber tape (which creates a small humidity chamber). Dissected embryos are planted in SB71-4 medium, where they are kept in germination under the same cultivation conditions described above. Germinated seedlings are removed from the germination medium, rinsed thoroughly with water and then planted in Redi-Earth in a 24-cell pack tray, covered with a clear plastic dome. After two weeks, the dome is removed and the plants are hardened for another week. If the seedlings appeared to be hardened, they were transplanted into a 25.4 cm pot of Redi-Earth with up to three seedlings per pot. After ten to sixteen weeks, the mature seeds are harvested, chopped and analyzed to determine their fatty acid content.
Example 7
Fatty acid analysis of somatic transgenic soy embryos
Mature somatic soy embryos are a good model for zygotic embryos. Although in the state of a globular embryo in a liquid state, somatic soy embryos contain very low amounts of triacylglycerol or storage proteins typical of ripening zygotic soy embryos. At this stage of development, the ratio between total triacylglyceride and total polar lipid (phospholipids and glycolipid) is about 1: 4, as is typical of zygotic soy embryos in the developmental stage from which somatic embryo cultivation was started . Also in the globular stage, mRNAs for prominent seed proteins, β-conglycinin Î ± subunit, Kunitz 3 trypsin inhibitor and seed lectin are essentially absent. By transferring to hormone-free media to allow differentiation into the state of maturing somatic embryos, triacylglycerol becomes the most <
121 abundant. Likewise, mRNAs for β-conglycinin subunit, trypsin inhibitor Kunitz 3 and seed lectin become very abundant messages in the total mRNA population. Based on this, the somatic soy embryo system behaves very similarly to in vivo ripening zygotic soy embryos and is therefore a good and fast model system for analyzing the phenotypic effects of modifying gene expression in the fatty acid biosynthesis process (see PCT Patent No. WO 2002/00904, Example 3). Most importantly, the model system also provides for the fatty acid composition of plant seeds derived from transgenic embryos.
A subset of somatic embryos for each event generated from production transformation or model system transformation (as described in Example 6) is harvested as follows. Embryos (five to ten embryos) from each event are placed in GC glass ampoules and fatty acid methyl esters are prepared by transesterification. For transesterification, 50 μΙ of trimethylsulfonium hydroxide (TMSH) and 0.5 ml of hexane are added to the embryos in glass ampoules and incubated for 30 minutes at room temperature by shaking. Methyl fatty acid esters (5 μΙ injected from the hexane layer) are separated and quantified using a Hewlett-Packard 6890 Gas Chromatograph equipped with an Omegawax 320 fused silica capillary column (Catalog No. 24152, Supelco Inc.). The oven temperature is programmed to remain at 220 ° C for 2.6 minutes, increase to 240 ° C at 20 ° C / min and then maintain for an additional 2.4 min. Vehicle gas is supplied by a Whatman hydrogen generator. Retention times were compared with those of commercially available standard methyl esters (Nu-Check Prep., Inc.). Events that have a good phenotype can be analyzed again by GC using identical conditions, except for the oven temperature, which is
122 maintained at 150 ° C for one minute and then increased to 240 ° C at 5 ° C / minute.
Example 8
Construction of Alternative Soy Expression Vectors for Expression
DELTA-5 DESATURASE OF EUGLENA ANABAENA UTEX 373 (EaD5DES1)
In addition to the genes, promoters, terminals and genetic sets described herein, those skilled in the art may appreciate that other combinations of promoter, gene and terminal sets can be synthesized in a similar, but not limited, manner to that described herein for expression of EaD5Des1. Similarly, it may be desirable to express other PUFA genes (such as those described below in Table 10) for coexpression with the delta-5 desaturase according to the present invention.
PCT Patents No. WO 2004/071467 and WO 2004/071178 describe, for example, the isolation of a series of transcription termination and promoter sequences for use in specific expression of soy embryos. In addition, PCT Patent Nos. WO 2004/071467, WO 2005/047479 and WO 2006/012325 describe the synthesis of various combinations of promoter, gene and terminal sets by linking individual promoters, genes and transcription terminations between in unique combinations. Generally, a Noti site flanked by the appropriate promoter (such as those listed in Table 8, but without limitations) and a transcription terminal (such as those listed in Table 9, but without limitations) is used to clone the desired gene. Noti sites can be added to a gene of interest as listed in Table 7, but without limitation, using PCR amplification with oligonucleotides designed to introduce Noti sites at the 5 'and 3' ends of the gene. The resulting PCR product is then digested with Noti and cloned into a set of promoter, Noti and appropriate terminal.
123
In addition, PCT Patent Nos. WO 2004/071467, WO 2005/047479 and WO 2006/012325 describe the additional ligation of individual genetic sets in unique combinations, together with appropriate selectable marker sets, in order to obtain the desired phenotypic expression. Although this is done using mainly different restriction enzyme sites, those skilled in the art can appreciate that a number of methods can be used to achieve the desired combination of promoter, gene and termination of transcription. In doing so, any combination of embryo-specific promoter, gene and termination sets can be achieved. Those skilled in the art may also appreciate that these clusters may be located on individual DNA fragments or on several fragments, where gene coexpression is the result of the co-transformation of different DNA fragments.
Table 8
Seed Specific Promoters
<td>District Attorney</td><td>Body</td><td>Promoter reference</td>
<td>Β-conglycinin subunit</td><td>Soy</td><td>Beachy et al, EMBO J. 4: 3047-3053 (1985)</td>
<td>Soy trypsin inhibitor</td><td>Soy</td><td>Jofuku et al, Plant Cell 1: 1079-1093 (1989)</td>
<td>Appendine</td><td>Soy</td><td>WO 2004/071467</td>
<td>Glycine Gy1</td><td>Soy</td><td>WO 2004/071467</td>
<td>Albumin 2S</td><td>Soy</td><td>US Patent No. 6,177,613</td>
<td>Legumina A1</td><td>pea</td><td>Rerie et al, Mol. Gen. Genet. 225: 148-157 (1991)</td>
<td>Β subunit of β-conglycinin</td><td>Soy</td><td>WO 2004/071467</td>
124
<td>District Attorney</td><td>Body</td><td>Promoter reference</td>
<td>BD30 (also called P34)</td><td>Soy</td><td>WO 2004/071467</td>
<td>Leguminous Α2</td><td>pea</td><td>Rerie et al, Mol. Gen. Genet. 225: 148-157 (1991)</td>
Table 9
TRANSCRIPTION TERMINATIONS
<td>Termination of transcription</td><td>Body</td><td>Reference</td>
<td>Faseolina 3 '</td><td>bean</td><td>WO 2004/071467</td>
<td>Kunitz 3 'trypsin inhibitor</td><td>Soy</td><td>WO 2004/071467</td>
<td>BD30 (also called P34) 3 '</td><td>pea</td><td>WO 2004/071467</td>
<td>Leguminous A2 3 '</td><td>pea</td><td>WO 2004/071467</td>
<td>Albumin 2S 3 '</td><td>Soy</td><td>WO 2004/071467</td>
Table 10
Genes of the PUFA Biosynthetic Process
<td>Gene</td><td>Body</td><td>Reference</td>
<td>Delta-6 desaturase</td><td>Saprolegnia diclina</td><td>WO 2002/081668</td>
<td>Delta-6 desaturase</td><td>Mortierella alpina</td><td>US Patent No. 5,968,809</td>
<td>Elongase</td><td>Mortierella alpina</td><td>WO 2000/12720 US Patent No. 6,403,349</td>
<td>Delta-5 desaturase</td><td>Mortierella alpina</td><td>US Patent No. 6,075,183</td>
<td>Delta-5 desaturase</td><td>Saprolegnia diclina</td><td>WO 2002/081668</td>
<td>Delta-5 desaturase</td><td>Peridinium sp</td><td>North Provisional Order American n ° 60 / 801.119</td>
<td>Delta-5 desaturase</td><td>Euglena gracilis</td><td>North Provisional Order American No. 60 / 801,172</td>
125
<td>Gene</td><td>Body</td><td>Reference</td>
<td>Delta-15 desaturase</td><td>Fusarium moniliform</td><td>WO 2005 / 801.172</td>
<td>Delta-17 desaturase</td><td>Saprolegnia diclina</td><td>WO 2002/081668</td>
<td>Elongase</td><td>Thraustochytrium</td><td>WO 2002/08401</td>
<td></td><td>aureum</td><td>US Patent No. 6,677,145</td>
<td>Elongase</td><td>Pavlova sp</td><td>Pereira et al, Biochem. J. 384: 357-366 (2004)</td>
<td>Delta-4 desaturase</td><td>Schizochytrium</td><td>WO 2002/090493</td>
<td></td><td>aggregatum</td><td>US Patent No. 7,045,683</td>
<td>Delta-4 desaturase</td><td>Í3GChynSiS Çj & íbQnci</td><td>WO 2002 / Ό90493 US Patent No. 7,045,683</td>
<td>Delta-4 desaturase</td><td>Thraustochytrium</td><td>WO 2002/090493</td>
<td></td><td>aureum</td><td>US Patent No. 7,045,683</td>
<td>Delta-4 desaturase</td><td>Euglena gracilis</td><td>US Patent No. 10 / 552,127</td>
<td>Delta-9 elongase</td><td>Isochrysis galbana</td><td>WO 2002/077213</td>
<td>Delta-9 elongase</td><td>Euglena gracilis</td><td>North-American Patent Application American laughs 11 / 601,563</td>
<td>Delta-9 elongase</td><td>Eutreptiella sp</td><td>North-American Patent Application</td>
<td></td><td>CCMP389</td><td>American laughs 11 / 601,564</td>
126
<td>Gene</td><td>Body</td><td>Reference</td>
<td>Delta-8 desaturase</td><td>Euglena gracilis</td><td>WO 2000/34439 US Patent No. 6,825,017 WO 2004/057001 WO 2006/012325</td>
<td>Delta-8 desaturase</td><td>Acanthamoeba</td><td>Sayanova et al, FEBS Lett. 580:</td>
<td></td><td>castellanii</td><td> 1946-1952 (2006)</td>
<td>Delta-8 desaturase</td><td>Pavlova saline</td><td>WO 2005/103253</td>
<td>Delta-8 desaturase</td><td>Pavlova lutheri</td><td>North Provisional Order American n ° 60 / 795,810</td>
<td>Delta-8 desaturase</td><td>Tetruetreptia</td><td>North Provisional Order</td>
<td></td><td>pomquetensis CCMP1491</td><td>American n ° 60 / 853,563</td>
<td>delta-8 desaturase</td><td>Eutreptiella sp</td><td>North Provisional Order</td>
<td></td><td>CCMP389</td><td>American n ° 60 / 853,563</td>
Example 9
Synthesis of a delta-5 desaturase gene optimized by Yarrowia lipolytica (EaDS5) codons
The use of Euglena 5 anabaena delta-5 desaturase (EaD5) codons has been optimized for expression in Yarrowia lipolytica, in a manner similar to that described in PCT Patent No. WO 2004/101753. Specifically, a codon-optimized delta-5 desaturase gene (called “EaD5S”, SEQ ID No. 45) was designed based on the EaD5Des1 coding sequence (SEQ ID No. 12 and 13), according to the usage pattern codon of Yarrowia (Patent
PCT No. WO 2004/101753), the consensus sequence around the translation start codon 'ATG' and the general RNA stability rules <) ·
127 (Guhaniyogi, G. and J. Brewer, Gene 265 (1-2): 11-23 (2001)). In addition to modifying the translation start location, 183 bp of the 1362 bp coding region were modified (13.4%) and 174 codons were optimized (38.3%). The GC content was reduced by 57.6% within the wild type gene (ie,
EaD5Des1) to 54.6% within the synthetic gene (ie EaD5S). An Ncol site and Notl sites were incorporated around the translation start codon and after the EaD5S stop codon (SEQ ID No. 45), respectively. Figs. 8A, 8B and 8C show a comparison of the nucleotide sequences of EaD5Des1 (SEQ ID No. 12) and EaD5S (SEQ ID No. 45). The codon-optimized EaD5S gene did not alter any amino acid sequence of EaD5Des1 (SEQ ID NO: 13). The projected EaD5S gene was synthesized by GenScript Corporation (Piscataway NJ) and spun in pUC57 (GenBank Access No. Y14837) to generate pEaD5S (SEQ ID No. 46; Fig. 9).
Based on the teachings of the present with reference to the formation of vectors and promoters and terminals suitable for use in Yarrowia lipolytica, those skilled in the art will be able to construct additional plasmids appropriate for the expression of EaD5S (SEQ ID N ° 45).
Example 10
Functional analysis of the Euglena anabaena UTEX 373 delta-5 desaturase (EaD5Des1) coexpressed with a Euglena-derived delta-9 elongase
GRACILIS (EgD9e) A DELTA-8 DESATURASE DERIVED FROM EUGLENA GRACILIS (EgD8) and a DELTA-17 DESATURASE from Saprolegnia diclina in embryos
SOYBEAN SOYBEANS:
The present example describes the transformation and expression in somatic embryos of soybean of pKR1153 (SEQ ID NO: 44; Example 5) comprising EaD5Des1, EgD9e and EgD8 together with pKR328 (described in PCT Patent No. WO 04/071467) which comprises delta-17 desaturase from
i) <·
128
Saprolegnia diclina SdD17 under control of the annexin promoter that contains a hygromycin resistance gene for selection in plants.
Cultivation of embryogenic soy suspension (cv. Jack) was transformed with pKR1153 (SEQ ID N ° 44) and pKR328 and the embryos underwent maturation in soybean histodifferentiation and liquid maturation medium (SHaM liquid medium; Schmidt et al, Cell Biology and Morphogenesis, 24: 393 (2005)) as described in Example 6 and described previously in PCT Patent No. WO 2007/136877 (the content of which is hereby incorporated by reference).
After maturation in SHaM liquid media, a subset of 10 transformed soy embryos (i.e., five embryos per event) were harvested and analyzed to determine fatty acid profiles by GC as described in Example 7 and the present.
In this way, about thirty events transformed with pKR1153 and pKR328 (Experiment MSE2140) were analyzed and the ten events that have the highest average correct delta-5 desaturase activities (average of the five analyzed embryos) are shown in Fig. 11 .
In Fig. 11, fatty acids are identified as 16: 0 (palmitate), 18: 0 (stearic acid), 18: 1 (oleic acid), LA, ALA, EDA, SCI, DGLA, ARA, ERA, JUP, ETA and EPA. The fatty acid compositions for an individual embryo were expressed as a percentage by weight (weight%) of the total fatty acids and the average fatty acid composition is an average of six individual embryos for each event.
The delta-5 desaturase activity is expressed as a percentage of delta-5 desaturation (“% delta-5 desat.”), Calculated according to the following formula: ([product] / [substrate + product]) * 100. More specifically, the percentage of delta-5 desaturation was determined as: ([ARA + EPA] / [DGLA + ETA + ARA + EPA]) * 100.
Contents9
14 sheets
Sheet 1 Sheet 2 Sheet 3 Sheet 4 Sheet 5 Sheet 6 Sheet 7 Sheet 8 Sheet 9 Sheet 10 Sheet 11 Sheet 12 Sheet 13 Sheet 14
19 members in 7 offices
Priority claims7
| Document | Office | Kind | Date |
|---|---|---|---|
| 60915733 | United States of America | – | |
| 91573307 | United States of America | P | |
| 2008062173 | United States of America | W | |
| 2008062173 | – | – | – |
| 60915733 | – | – | – |
| US20070915733P | – | – | – |
| WO2008US62173 | – | – | – |
Members19
| Document | Office | Kind | |
|---|---|---|---|
| US2008274259A1 | United States of America | A1 | |
| US2008274521A1 | United States of America | A1 | |
| AU2008247766A1 | Australia | A1 | |
| CA2684719A1 | Canada | A1 | |
| WO2008137516A1 | World Intellectual Property Organization (WIPO) | A1 | |
| WO2008137532A1 | World Intellectual Property Organization (WIPO) | A1 | |
| EP2140006A1 | European Patent Office (EPO) | A1 | |
| EP2140007A1 | European Patent Office (EPO) | A1 | |
| US2010189868A1 | United States of America | A1 | |
| US7943365B2 | United States of America | B2 | |
| EP2471928A1 | European Patent Office (EPO) | A1 | |
| AU2008247766B2 | Australia | B2 | |
| BRPI0809877A2This record | Brazil | A2 | |
| US8957280B2 | United States of America | B2 | |
| US2015175977A1 | United States of America | A1 | |
| EP2140007B1 | European Patent Office (EPO) | B1 | |
| EP2140006B1 | European Patent Office (EPO) | B1 | |
| CA2684719C | Canada | C | |
| DK2140006T3 | Denmark | T3 |
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| Update of information on the portal [chapter 15.35 patent gazette]B350 | B350 | |
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Numbers
- Publication
- PI0809877
- Publication, DOCDB
- PI0809877
- Publication, EPODOC
- BRPI0809877
- Application
- 9877
- Application, DOCDB
- PI0809877
- Application, EPODOC
- BR2008PI09877
Titles2
- Portuguese
- POLINUCLEOTÍDEO ISOLADO, CONSTRUÇÃO DE DNA RECOMBINANTE, CÉLULA VEGETAL, MÉTODOS DE TRANSFORMAÇÃO DE UMA CÉLULA VEGETAL, DE PRODUÇÃO DE UMA PLANTA TRANSFORMADA, DE ELABORAÇÃO DE ÁCIDOS GRAXOS PÓLI-INSATURADOS, DE PRODUÇÃO DE PELO MENOS UM ÁCIDO GRAXO PÓLI-INSATURADO, SEMENTES TRANSGÊNICAS, ÓLEOS OU SUBPRODUTOS, PLANTAOLEAGINOSA, ALIMENTOS OU RAÇÃO E PLANTAS DE PROLE.
- English
- POLYNUCLEOTIDE ISOLATED, RECOMBINANT DNA CONSTRUCTION, VEGETABLE CELL, METHODS OF TRANSFORMING A VEGETABLE CELL, TRANSFORMING A CUTTING CELL, POLY-UNSATURATED FATS, PRODUCTION OF AT LEAST ONE POLY-UNSATURATED FATTY ACID, TRANSGENIC SEEDS, OILS OR BY-PRODUCTS, PLANTAOLEAGINOSA, FOOD OR FEED AND PROLEET PLANTS.
Classification
- CPC, 8
- C12N9/0071
- A23D9/00
- A23D9/02
- A23K20/158
- A23L33/115
- C12N9/0083
- C12N15/8247
- C12Y114/19
- IPC, 3
- C12N15 53
- C12N9 02
- C12P7 64
