WO2006052871A2 - Docosahexaenoic acid producing strains of yarrowia lipolytica - Google Patents

Docosahexaenoic acid producing strains of yarrowia lipolytica Download PDF

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WO2006052871A2
WO2006052871A2 PCT/US2005/040256 US2005040256W WO2006052871A2 WO 2006052871 A2 WO2006052871 A2 WO 2006052871A2 US 2005040256 W US2005040256 W US 2005040256W WO 2006052871 A2 WO2006052871 A2 WO 2006052871A2
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Prior art keywords
desaturase
gene encoding
elongase
gene
seq
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French (fr)
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WO2006052871A3 (en
Inventor
Howard G. Damude
Peter John Gillies
Daniel Joseph Macool
Stephen K. Picataggio
James John Ragghianti
Zhixiong Xue
Narendra S. Yadav
Hongxiang Zhang
Quinn Qun Zhu
John E. Seip
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EIDP Inc
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EI Du Pont de Nemours and Co
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Priority to EP05818385.6A priority Critical patent/EP1809756B1/en
Priority to CA2585235A priority patent/CA2585235C/en
Priority to JP2007540127A priority patent/JP5080979B2/ja
Priority to DK05818385.6T priority patent/DK1809756T3/en
Publication of WO2006052871A2 publication Critical patent/WO2006052871A2/en
Anticipated expiration legal-status Critical
Priority to NO20072516A priority patent/NO20072516L/no
Publication of WO2006052871A3 publication Critical patent/WO2006052871A3/en
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Definitions

  • DHA is naturally found in different types of fish oil and marine plankton, it is expected that the supply of this ⁇ -3 fatty acid will not be sufficient to meet growing demands.
  • Fish oils have highly heterogeneous compositions (thereby requiring extensive purification to enrich for DHA), unpleasant tastes and odors (making removal economically difficult and rendering the oils unacceptable as food ingredients), and are subject to environmental bioaccumulation of heavy metal contaminants and fluctuations in availability (due to weather, disease and/or over-fishing).
  • LA and ALA are converted to EDA and ETrA, respectively, by a ⁇ 9 elongase; 2.) EDA and ETrA are converted to DGLA and ETA, respectively, by a ⁇ 8 desaturase; and 3.) DGLA and ETA are ultimately converted to EPA, as described above.
  • EPA Upon synthesis of EPA, a C-20/22 elongase is responsible for conversion of the substrate to DPA, followed by desaturation by a ⁇ 4 desaturase to yield DHA.
  • SEQ ID NOs:385-388 correspond to primers 475, 477, 478 and 476, respectively, used to clone a bifunctional ⁇ 5/ ⁇ 6 desaturase.
  • SEQ ID NOs:403 and 404 correspond to primers pzuf-mod1 and pzuf-mod2, respectively, used for creating "control" plasmid pZUF-MOD-1.
  • SEQ ID NOs:405 and 406 correspond to primers MACAT-F1 and MACAT-R, respectively, used for cloning of the M. alpina DGAT1 ORF.
  • SEQ ID NOs:407 and 408 correspond to primers MDGAT-F and MDGAT-R1 , respectively, used for cloning of the M. alpina DGAT2 ORF.
  • SEQ ID NOs:409 and 410 correspond to primers MGPAT-N1 and
  • SEQ ID NOs:416-419 correspond to the PCR primers used in genome-walking: MGPAT-5-1A, Adaptor-1 (AP1), MGPAT-3N1 and Nested Adaptor Primer 2 (AP2), respectively.
  • SEQ ID NOs:430 and 431 correspond to primers YL325 and YL326, respectively, used to amplify a Notl/Pacl fragment containing the Aco 3 1 terminator.
  • SEQ ID NOs:432-435 correspond to primers YL567, YL568, YL569 and YL570, respectively, used for amplifying the coding region of Y. lipolytics YE 1.
  • a food is a "medical food" only if: (i) It is a specially formulated and processed product (as opposed to a naturally occurring foodstuff used in its natural state) for the partial or exclusive feeding of a patient by means of oral intake or enteral feeding by tube; (ii) It is intended for the dietary management of a patient who, because of therapeutic or chronic medical needs, has limited or impaired capacity to ingest, digest, absorb, or metabolize ordinary foodstuffs or certain nutrients, or who has other special medically determined nutrient requirements, the dietary management of which cannot be achieved by the modification of the normal diet alone; (iii) It provides nutritional support specifically modified for the management of the unique nutrient needs that result from the specific disease or condition, as determined by medical evaluation; (iv) It is intended to be used under medical supervision; and (v) It is intended only for a patient receiving active and ongoing medical supervision wherein the patient requires medical care on a recurring basis for, among other things, instructions on the use of the medical food.
  • essential fatty acid refers to a particular PUFA that an organism must ingest in order to survive, being unable to synthesize the particular essential fatty acid de novo.
  • mammals can not synthesize the essential fatty acids LA (18:2, ⁇ -6) and ALA (18:3, co-3).
  • Other essential fatty acids include GLA ( ⁇ -6), DGLA ( ⁇ -6), ARA ( ⁇ -6), EPA ( ⁇ -3) and DHA ( ⁇ -3).
  • the former family shares homology with the acyl-CoA:cholesterol acyltransferase (ACAT) gene family, while the latter family is unrelated (Lardizabal et al., J. Biol. Chem. 276(42):38862-38869 (2001)).
  • ACAT acyl-CoA:cholesterol acyltransferase
  • PDAT refers to a phospholipid:diacylglycerol acyltransferase enzyme (EC 2.3.1.158). This enzyme is responsible for the transfer of an acyl group from the sn-2 position of a phospholipid to the sn-3 position of 1 ,2-diacylglycerol, thus resulting in lysophospholipid and TAG (thereby involved in the terminal step of TAG biosynthesis). This enzyme differs from DGAT (EC 2.3.1.20) by synthesizing TAG via an acyl- CoA-independent mechanism.
  • omega-reference system refers to a polypeptide that can desaturate, i.e., introduce a double bond, in one or more fatty acids to produce a fatty acid or precursor of interest.
  • Enhancer refers to a c/s-regulatory sequence that can elevate levels of transcription from an adjacent eukaryotic promoter, thereby increasing transcription of the gene. Enhancers can act on promoters over many tens of kilobases of DNA and can be 5' or 3' to the promoter they regulate. Enhancers can also be located within introns.
  • Yarrowia lipolytica was selected as the preferred microbial host for the purposes herein. This selection was based on the knowledge that oleaginous strains were available that were capable of incorporating ⁇ -3 fatty acids into the TAG fraction, the organism was amenable to genetic manipulation, and previous use of the species as a Generally Recognized As Safe (“GRAS", according to the U.S. Food and Drug Administration) source of food-grade citric acid. In a further embodiment, most preferred are the Y.
  • LA is converted to EDA by the action of a ⁇ 9 elongase; then, a ⁇ 8 desaturase converts EDA to DGLA.
  • a ⁇ 5 desaturase yields ARA, as described above, wherein ARA can be converted directly to EPA by the action of a ⁇ 17 desaturase.
  • the Applicants have performed considerable analysis of various elongases, to either determine or confirm each enzyme's substrate specificity and/or substrate selectivity when expressed in Yarrowia lipolytica.
  • the coding sequences of the two Y. lipolytica elongases were publically available and each protein was annotated as a putative long-chain fatty-acyl elongase or shared significant homology to other fatty acid elongases, the substrate specificity of these enzymes had never been determined.
  • Saccharomyces kluyveri ⁇ 12 desaturase (GenBank Accession No. BAD08375) was described in Watanabe et al. (Biosci. Biotech. Biocheml. 68(3):721-727 (2004)), while that from Mortierella alpina (GenBank Accession No. AB182163) was described by Sakuradani et al. (Eur. J. Biochem. 261 (3):812-820 (1999)).
  • PDAT removes an acyl group from the sn-2 position of a phosphatidylcholine substrate for transfer to DAG to produce TAG.
  • This enzyme is structurally related to the LCAT family; and although the function of PDAT is not as well characterized as DGAT2, PDAT has been postulated to play a major role in removing "unusual" fatty acids from phospholipids in some oilseed plants (Banas, A. et al., Biochem. Soc. Trans. 28(6):703-705 (2000)).
  • acyl-CoA:sterol-acyltransferases encoded by the ARE1 and ARE2 genes
  • ARE1 and ARE2 genes are known that utilize acyl-CoAs and sterols to produce sterol esters (and TAGs in low quantities; see Sandager et al., Biochem. Soc. Trans. 28(6):700-702 (2000)).
  • PDAT and DGAT2 are responsible for approximately 95% of oil biosynthesis in S. cerevisiae.
  • LPCAT allowed efficient and continuous exchange of the newly synthesized fatty acids between phospholipids and the acyl-CoA pool, since desaturases catalyze the introduction of double bonds in lipid-coupled fatty acids (sn-2 acyl PC) while elongases exclusively catalyze the elongation of CoA esterified fatty acids (acyl-CoAs).
  • 18:2 fatty acids (and less commonly, 18:3 fatty acids), it would be likely that the host organism's native genes encoding GPAT, LPAAT (i.e., LPAAT1 or LPAAT2), DGAT1 , DGAT2, PDAT and LPCAT could have difficulty efficiently synthesizing TAGs comprising fatty acids that were 18:3 and greater in length (e.g., DHA).
  • LPAAT i.e., LPAAT1 or LPAAT2
  • DGAT1 , DGAT2, PDAT and LPCAT could have difficulty efficiently synthesizing TAGs comprising fatty acids that were 18:3 and greater in length (e.g., DHA).
  • a heterologous (or "foreign") acyltransferase could be preferred over a native enzyme.
  • the Applicants identified the genes encoding GPAT, LPAAT, DGAT1 and DGAT2 in M. alpina and expressed these genes in engineered Yarrowia hosts producing EPA, resulting in increased PUFA biosynthesis (Examples 17-20 herein). Subsequently, the activity of several of the native acyltransferases (e.g., DGAT1 and DGAT2) in Y. lipolytica were diminished or knocked-out, as a means to reduce substrate competition between the native and heterologous acyltransferase. Similar results would be expected in an engineered Yarrowia host producing DHA. One must also consider manipulation of pathways and global regulators that affect DHA production.
  • the transformed microbial host cell is grown under conditions that optimize expression of chimeric genes (e.g., encoding desaturases, elongases, acyltransferases, etc.) and produce the greatest and the most economical yield of DHA.
  • media conditions that may be optimized include the type and amount of carbon source, the type and amount of nitrogen source, the carbon-to-nitrogen ratio, the oxygen level, growth temperature, pH, length of the biomass production phase, length of the oil accumulation phase and the time of cell harvest.
  • ⁇ -glucans convey enhanced protection against viral, bacterial, fungal and parasitic infections; exert an adjuvant effect when used in conjunction with antibiotics and vaccines; enhance wound healing; counter damage resulting from free radicals; enhance tumor regression; modulate toxicity of bacterial endotoxins; and strengthen mucosal immunity (reviewed in Raa, J. et al., Norwegian Beta Glucan Research, Clinical Applications of Natural Medicine. Immune: Depressions Dysfunction & Deficiency (1990)).
  • a sample of current literature documenting the utility of yeast ⁇ -glucans, mannans and chitins in both traditional animal husbandry and within the aquacultural sector include: L.A. White et al. (J. Anim.
  • PCR buffer containing 10 mM KCI, 10 mM (NH 4 ) 2 SO 4 , 20 mM Tris-HCI (pH 8.75), 2 mM MgSO 4 , 0.1 % Triton X-100), 100 ⁇ g/mL BSA (final concentration), 200 ⁇ M each deoxyribonucleotide triphosphate, 10 pmole of each primer and 1 ⁇ l of Pfu DNA polymerase (Stratagene, San Diego, CA), unless otherwise specified.
  • the amino acid sequence of the synthetic D8S-3 gene in pDMW261 was corrected according to the amino acid sequence of the functional Euglena ⁇ 8 desaturase (SEQ ID NOs:77 and 78).
  • pDMW261 as a template and oligonucleotides ODMW404 (SEQ ID NO:364) and D8-13R (SEQ ID NO:347)
  • the DNA fragment encoding the synthetic D8S-3 desaturase gene was amplified.
  • the resulting PCR fragment was purified with Biol 01 's Geneclean kit and subsequently digested with Kpn1 and ⁇ /ofl (primer ODMW404 introduced a Kpn ⁇ site while primer D8-13R introduced a Not ⁇ site).
  • Plasmid pZKUGPEIS was digested with Pstl/Pacl, and then used to transform strain Y2089 according to the General Methods. Following transformation, cells were plated onto MM + 5-FOA selection plates and maintained at 30 C for 3 to 4 days.
  • a Clontech Universal GenomeWalkerTM kit was used to obtain a piece of genomic DNA corresponding to the 5'-end region of the M. alpina GPAT. Briefly, 2.5 ⁇ g each of M. alpina genomic DNA was digested with Dral, EcoRV, Pvull or Stul individually, the digested DNA samples were purified using Qiagen Qiaquick PCR purification kits and eluted with 30 ⁇ l each of kit buffer EB, and the purified samples were then ligated with Genome Walker adaptor (SEQ ID NOs:414 [top strand] and 415 [bottom strand]), as shown below:
  • a DNA fragment was obtained from the second round of PCR. This fragment was purified and cloned into pCR2.1-TOPO and sequenced. Sequence analysis showed that the 1908 bp fragment (SEQ ID NO:143) was the 5'-end of the M. alpina GPAT gene. Similarly, a 966 bp fragment (SEQ ID NO:144) was obtained by two rounds of genome walking as described above, except using primer MGPAT- 5N1 as the gene specific primer for the first round of PCR and primer MGPAT- 5N2 as the gene specific primer for the second round. This fragment was also purified, cloned into pCR2.1-TOPO and sequenced.

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