US20070118929A1 - Delta-9 elongases and their use in making polyunsaturated fatty acids - Google Patents

Delta-9 elongases and their use in making polyunsaturated fatty acids Download PDF

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US20070118929A1
US20070118929A1 US11/601,563 US60156306A US2007118929A1 US 20070118929 A1 US20070118929 A1 US 20070118929A1 US 60156306 A US60156306 A US 60156306A US 2007118929 A1 US2007118929 A1 US 2007118929A1
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delta
seq
elongase
desaturase
sequence
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Howard Damude
Brian McGonigle
Quinn Zhu
Zhixiong Xue
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EIDP Inc
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Assigned to E. I. DU PONT DE NEMOURS AND COMPANY reassignment E. I. DU PONT DE NEMOURS AND COMPANY ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: DAMUDE, HOWARD GLENN, XUE, ZHIXIONG, ZHU, QUINN QUN, MCGONIGLE, BRIAN
Publication of US20070118929A1 publication Critical patent/US20070118929A1/en
Priority to US12/725,482 priority patent/US8420892B2/en
Priority to US13/834,813 priority patent/US9150874B2/en
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8242—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits
    • C12N15/8243—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits involving biosynthetic or metabolic pathways, i.e. metabolic engineering, e.g. nicotine, caffeine
    • C12N15/8247—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits involving biosynthetic or metabolic pathways, i.e. metabolic engineering, e.g. nicotine, caffeine involving modified lipid metabolism, e.g. seed oil composition
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    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
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    • C11—ANIMAL OR VEGETABLE OILS, FATS, FATTY SUBSTANCES OR WAXES; FATTY ACIDS THEREFROM; DETERGENTS; CANDLES
    • C11B—PRODUCING, e.g. BY PRESSING RAW MATERIALS OR BY EXTRACTION FROM WASTE MATERIALS, REFINING OR PRESERVING FATS, FATTY SUBSTANCES, e.g. LANOLIN, FATTY OILS OR WAXES; ESSENTIAL OILS; PERFUMES
    • C11B1/00—Production of fats or fatty oils from raw materials
    • C11B1/02—Pretreatment
    • C11B1/025—Pretreatment by enzymes or microorganisms, living or dead
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/1025—Acyltransferases (2.3)
    • C12N9/1029—Acyltransferases (2.3) transferring groups other than amino-acyl groups (2.3.1)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P7/00—Preparation of oxygen-containing organic compounds
    • C12P7/64—Fats; Fatty oils; Ester-type waxes; Higher fatty acids, i.e. having at least seven carbon atoms in an unbroken chain bound to a carboxyl group; Oxidised oils or fats
    • C12P7/6409—Fatty acids
    • C12P7/6427—Polyunsaturated fatty acids [PUFA], i.e. having two or more double bonds in their backbone
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P7/00—Preparation of oxygen-containing organic compounds
    • C12P7/64—Fats; Fatty oils; Ester-type waxes; Higher fatty acids, i.e. having at least seven carbon atoms in an unbroken chain bound to a carboxyl group; Oxidised oils or fats
    • C12P7/6436—Fatty acid esters
    • C12P7/6445—Glycerides
    • C12P7/6458—Glycerides by transesterification, e.g. interesterification, ester interchange, alcoholysis or acidolysis
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    • C12P7/00—Preparation of oxygen-containing organic compounds
    • C12P7/64—Fats; Fatty oils; Ester-type waxes; Higher fatty acids, i.e. having at least seven carbon atoms in an unbroken chain bound to a carboxyl group; Oxidised oils or fats
    • C12P7/6436—Fatty acid esters
    • C12P7/6445—Glycerides
    • C12P7/6463—Glycerides obtained from glyceride producing microorganisms, e.g. single cell oil
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P7/00—Preparation of oxygen-containing organic compounds
    • C12P7/64—Fats; Fatty oils; Ester-type waxes; Higher fatty acids, i.e. having at least seven carbon atoms in an unbroken chain bound to a carboxyl group; Oxidised oils or fats
    • C12P7/6436—Fatty acid esters
    • C12P7/6445—Glycerides
    • C12P7/6472—Glycerides containing polyunsaturated fatty acid [PUFA] residues, i.e. having two or more double bonds in their backbone

Definitions

  • An alternate pathway for the biosynthesis of M and EPA operates in some organisms (i.e., the delta-9 elongase/delta-8 desaturase pathway).
  • Wherby LA and ALA are first elongated to eicosadienoic acid (EDA; 20:2, delta-11,14) and eicosatrienoic acid (EtrA; 20:3, delta-11,14,17), respectively, by a delta-9 elongase.
  • EDA eicosadienoic acid
  • EtrA eicosatrienoic acid
  • the delta-8 pathway is present inter alia, in euglenoid species where it is the dominant pathway for formation of 20-carbon PUFAs.
  • the invention concerns a method for producing a transformed plant comprising transforming a plant cell with a polynucleotide of the invention and regenerating a plant from the transformed plant cell.
  • a preferred plant is soybean.
  • the invention concerns a method for making long-chain polyunsaturated fatty acids in a plant cell comprising:
  • SEQ ID NO:25 is the sequence of pZUF17.
  • SEQ ID NO:59 is the sequence of pKR124.
  • SEQ ID NO:64 is the sequence of pKR270.
  • fragment that is functionally equivalent and “functionally equivalent subfragment” are used interchangeably herein. These terms refer to a portion 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 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 linking a nucleic acid fragment or subfragment thereof, whether or not it encodes an active enzyme, in the sense or antisense orientation relative to a plant promoter sequence.
  • 3′ non-coding sequences refer to DNA sequences located downstream of a coding sequence and include polyadenylation recognition sequences and other sequences encoding regulatory signals capable of affecting mRNA processing or gene expression.
  • the polyadenylation signal is usually characterized by affecting the addition of polyadenylic acid tracts to the 3′ end of the mRNA precursor.
  • the use of different 3′ non-coding sequences is exemplified by Ingelbrecht, I. L., et al. Plant Cell 1:671-680 (1989).
  • RNA refers to antisense RNA, ribozyme RNA, or other RNA that may not be translated but yet has an effect on cellular processes.
  • complement and “reverse complement” are used interchangeably herein with respect to mRNA transcripts, and are meant to define the antisense RNA of the message.
  • soybean seeds are cleaned, tempered, dehulled and flaked, thereby increasing the efficiency of oil extraction.
  • Oil extraction is usually accomplished by solvent (e.g., hexane) extraction but can also be achieved by a combination of physical pressure and/or solvent extraction.
  • the resulting oil is called crude oil.
  • the crude oil may be degummed by hydrating phospholipids and other polar and neutral lipid complexes that facilitate their separation from the nonhydrating, triglyceride fraction (soybean oil).
  • the resulting lecithin gums may be further processed to make commercially important lecithin products used in a variety of food and industrial products as emulsification and release (i.e., antisticking) agents.
  • delta-9 elongase/delta-8 desaturase pathway for the biosynthesis of long-chain PUFAs (e.g., AA and EPA) in these organisms
  • PUFAs long-chain PUFAs
  • codon-optimization techniques infra
  • a snack food product comprises any of the above or below described food products.
  • RNA STAT-60TM reagent TEL-TEST, Inc., Friendswood, Tex.
  • RNA STAT-60TM reagent TEL-TEST, Inc., Friendswood, Tex.
  • the mRNA was isolated from 1 mg of total RNA using the mRNA Purification Kit (Amersham Biosciences, Piscataway, N.J.) following the manufacturer's protocol provided. In this way, 85 ⁇ g of mRNA was obtained.
  • the BLASTX search using the nucleotide sequences from clone eeg1c.pk001.n5.f revealed similarity of the protein encoded by the cDNA to the long-chain PUFA elongation enzyme from Isochrysis galbana (SEQ ID NO:27) (NCBI Accession No. AAL37626 (GI 17226123), locus AAL37626, CDS AF390174; Qi et al., FEBS Lett. 510(3):159-165 (2002)).
  • SEQ ID NO:1 5′ end of cDNA insert.
  • E. coli was transformed separately with pT9(1-4) (SEQ ID NO:86) and pT9(5-8) (SEQ ID NO:87) and the plasmid DNA was isolated from ampicillin-resistant transformants. Plasmid DNA was purified and digested with the appropriate restriction endonucleases to liberate the 417 bp Ncol/PstI fragment of pT9(1-4) (SEQ ID NO:86) and the 377 bp PstI/Not1 fragment of pT9(5-8) (SEQ ID NO:87).
  • NcoI/SalI DNA fragment from pDMW263 (see construction in Example 5), containing the Yarrowia lipolytica FBAINm promoter, was cloned into the NcoI/SalI DNA fragment of pDMW237 (see construction in Example 4), containing 20 the synthetic delta-9 elongase gene (IgD9e), to produce pY 115 (SEQ ID NO:30; FIG. 1 ).
  • Either an intact plasmid or a DNA plasmid fragment containing the genes of interest and the selectable marker gene can be used for bombardment.
  • Fragments from plasmids such pKR274 (ATCC Accession No. PTA-4988) and pKR685 (ATCC Accession No. PTA-6047) or pKR681 (ATCC Accession No. PTA-6046) and/or other expression plasmids can be obtained by gel isolation of digested plasmids. In each case, 100 ⁇ g of plasmid DNA can be used in 0.5 mL of the specific enzyme mix described below.
  • pFBAIN-389Elo ( FIG. 28 ; SEQ ID NO:110) thereby contained the 15 following components: TABLE 10 Components of Plasmid pFBAIN-389Elo (SEQ ID NO: 110) RE Sites and Nucleotides Within SEQ Description of Fragment and Chimeric Gene ID NO: 110 Components BgIII-BsiWI FBAINm::E389D9e::Pex20, comprising: (6040-301) FBAINm: Yarrowia lipolytica FBAINm promoter (PCT Publication No. WO 2005/049805) E389D9e: Eutreptiella sp.

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US12/725,482 US8420892B2 (en) 2005-11-23 2010-03-17 Delta-9 elongases and their use in making polyunsaturated fatty acids
US13/834,813 US9150874B2 (en) 2005-11-23 2013-03-15 Delta-9 elongases and their use in making polyunsaturated fatty acids

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US11/992,899 Expired - Fee Related US8049062B2 (en) 2005-11-23 2006-11-16 Delta-9-elongases and their use in making polyunsaturated fatty acids
US11/601,564 Active 2027-10-19 US7645604B2 (en) 2005-11-23 2006-11-16 Delta-9 elongases and their use in making polyunsaturated fatty acids
US12/619,706 Active US8048653B2 (en) 2005-11-23 2009-11-17 Microbial oils produced in transformed host cells comprising delta-9 elongases
US12/725,482 Active 2027-04-26 US8420892B2 (en) 2005-11-23 2010-03-17 Delta-9 elongases and their use in making polyunsaturated fatty acids
US13/834,813 Expired - Fee Related US9150874B2 (en) 2005-11-23 2013-03-15 Delta-9 elongases and their use in making polyunsaturated fatty acids

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US11/601,564 Active 2027-10-19 US7645604B2 (en) 2005-11-23 2006-11-16 Delta-9 elongases and their use in making polyunsaturated fatty acids
US12/619,706 Active US8048653B2 (en) 2005-11-23 2009-11-17 Microbial oils produced in transformed host cells comprising delta-9 elongases
US12/725,482 Active 2027-04-26 US8420892B2 (en) 2005-11-23 2010-03-17 Delta-9 elongases and their use in making polyunsaturated fatty acids
US13/834,813 Expired - Fee Related US9150874B2 (en) 2005-11-23 2013-03-15 Delta-9 elongases and their use in making polyunsaturated fatty acids

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Cited By (21)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20080095915A1 (en) * 2006-10-23 2008-04-24 Howard Glenn Damude Delta-8 Desaturases And Their Use In Making Polyunsaturated Fatty Acids
US20080214667A1 (en) * 2006-11-17 2008-09-04 Tapas Das Elongase Gene and Uses Thereof
WO2008064096A3 (en) * 2006-11-17 2008-10-09 Abbott Lab Elongase gene and uses thereof
US20080254522A1 (en) * 2007-04-16 2008-10-16 Howard Glenn Damude Delta-9 elongases and their use in making polyunsaturated fatty acids
WO2009046231A1 (en) * 2007-10-03 2009-04-09 E. I. Du Pont De Nemours And Company Optimized strains of yarrowia lipolytica for high eicosapentaenoic acid production
WO2010118362A1 (en) * 2009-04-09 2010-10-14 The Regents Of The University Of Colorado, A Body Corporate Methods and compositions for inducing physiological hypertrophy
US20100297713A1 (en) * 2006-12-07 2010-11-25 E. I. Du Pont De Nemours And Company Mutant delta-8 desaturase genes engineered by targeted mutagenesis and their use in making polyunsaturated fatty acids
WO2011008510A2 (en) 2009-06-30 2011-01-20 E. I. Du Pont De Nemours And Company Plant seeds with altered storage compound levels, related constructs and methods involving genes encoding cytosolic pyrophosphatase
US20110015415A1 (en) * 2004-04-22 2011-01-20 Commonwealth Scientific And Industrial Research Organisation Synthesis of long-chain polyunsaturated fatty acids by recombinant cells
US20110054198A1 (en) * 2004-04-22 2011-03-03 Commonwealth Scientific And Industrial Research Organisation Synthesis of long-chain polyunsaturated fatty acids by recombinant cells
WO2011053898A2 (en) 2009-10-30 2011-05-05 E. I. Du Pont De Nemours And Company Plants and seeds with altered storage compound levels, related constructs and methods involving genes encoding proteins with similarity to bacterial 2,4-dihydroxy-hept-2-ene-1,7-dioic acid class ii-like aldolase proteins
US20110162104A1 (en) * 2009-12-24 2011-06-30 Howard Glenn Damude Plant Membrane Bound O-Acyl Transferase (MBOAT) Family Protein Sequences And Their Uses For Altering Fatty Acid Compositions
WO2011109618A2 (en) 2010-03-03 2011-09-09 E. I. Du Pont De Nemours And Company Plant seeds with altered storage compound levels, related constructs and methods involving genes encoding oxidoreductase motif polypeptides
WO2012003207A2 (en) 2010-07-01 2012-01-05 E. I. Du Pont De Nemours And Company Plant seeds with altered storage compound levels, related constructs and methods involving genes encoding pae and pae-like polypeptides
WO2012027676A1 (en) 2010-08-26 2012-03-01 E. I. Du Pont De Nemours And Company Mutant delta-9 elongases and their use in making polyunsaturated fatty acids
US8168858B2 (en) 2008-06-20 2012-05-01 E. I. Du Pont De Nemours And Company Delta-9 fatty acid elongase genes and their use in making polyunsaturated fatty acids
US8809559B2 (en) 2008-11-18 2014-08-19 Commonwelath Scientific And Industrial Research Organisation Enzymes and methods for producing omega-3 fatty acids
US8816111B2 (en) 2012-06-15 2014-08-26 Commonwealth Scientific And Industrial Research Organisation Lipid comprising polyunsaturated fatty acids
US8816106B2 (en) 2006-08-29 2014-08-26 Commonwealth Scientific And Industrial Research Organisation Synthesis of fatty acids
US9718759B2 (en) 2013-12-18 2017-08-01 Commonwealth Scientific And Industrial Research Organisation Lipid comprising docosapentaenoic acid
US10005713B2 (en) 2014-06-27 2018-06-26 Commonwealth Scientific And Industrial Research Organisation Lipid compositions comprising triacylglycerol with long-chain polyunsaturated fatty acids at the sn-2 position

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UA103595C2 (uk) * 2007-04-03 2013-11-11 Е. І. Дю Пон Де Немур Енд Компані Мультизими і їх застосування в отриманні поліненасичених жирних кислот
US7790156B2 (en) 2007-04-10 2010-09-07 E. I. Du Pont De Nemours And Company Δ-8 desaturases and their use in making polyunsaturated fatty acids
CA2695112A1 (en) 2007-07-31 2009-02-05 Basf Plant Science Gmbh Elongases and processes for the production of polyunsaturated fatty acids in transgenic organisms
CN101883843B (zh) * 2007-10-03 2016-03-02 纳幕尔杜邦公司 破坏过氧化物酶体生物合成因子蛋白(pex)以改变含油真核生物中多不饱和脂肪酸和总脂质含量
US9175318B2 (en) 2008-12-18 2015-11-03 E. I. Dupont De Nemours And Company Reducing byproduction of malonates by yeast in a fermentation process
CA2755027C (en) 2009-04-01 2018-09-18 E. I. Du Pont De Nemours And Company Use of a seed specific promoter to drive odp1 expression in cruciferous oilseed plants to increase oil content while maintaining normal germination
CN102595917A (zh) 2009-06-16 2012-07-18 纳幕尔杜邦公司 来自改善的优化的解脂耶氏酵母菌株的高二十碳五烯酸油
EP2475679B1 (en) 2009-06-16 2016-02-10 E. I. du Pont de Nemours and Company Improved optimized strains of yarrowia lipolytica for high eicosapentaenoic acid production
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