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
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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)
    • 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
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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
    • C12P7/6409—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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US11/601,563 2005-11-23 2006-11-16 Delta-9 elongases and their use in making polyunsaturated fatty acids Abandoned US20070118929A1 (en)

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US11/601,563 US20070118929A1 (en) 2005-11-23 2006-11-16 Delta-9 elongases and their use in making polyunsaturated fatty acids
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)

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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
WO2011079005A1 (en) 2009-12-24 2011-06-30 E.I. Dupont De Nemours And Company 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
US8816106B2 (en) 2006-08-29 2014-08-26 Commonwealth Scientific And Industrial Research Organisation Synthesis of fatty acids
US8816111B2 (en) 2012-06-15 2014-08-26 Commonwealth Scientific And Industrial Research Organisation Lipid comprising polyunsaturated 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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US8188338B2 (en) 2007-04-10 2012-05-29 E. I. Du Pont De Nemours And Company Delta-8 desaturases and their use in making polyunsaturated fatty acids
WO2009016208A2 (de) 2007-07-31 2009-02-05 Basf Plant Science Gmbh Elongasen und verfahren zur herstellung mehrfach ungesättigter fettsäuren in transgenen organismen
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BRPI1009690A2 (pt) 2009-06-16 2015-08-25 Du Pont "célula hospedeira microbiana oleaginosa, óleo, método de elaboração de um óleo, método de aumento da eficiência de conversão de alongamento de c18 para c20 em uma célula hospedeira recombinante microbiana oleaginosa e método de aumento da eficiência de conversão de dessaturação (delta) 4 em uma célula hospedeira recombinante microbiana oleaginosa produtora de ácidos graxos póli-insaturados de cadeia longa"
US8188335B2 (en) * 2009-07-17 2012-05-29 Abbott Laboratories Δ9-elongase for production of polyunsaturated fatty acid-enriched oils
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