DOCSLIB.ORG

WO 2017/015368 Al 2 6 January 2017 (26.01.2017) P O P C T

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
WO 2017/015368 Al 2 6 January 2017 (26.01.2017) P O P C T (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization II International Bureau (10) International Publication Number (43) International Publication Date WO 2017/015368 Al 2 6 January 2017 (26.01.2017) P O P C T (51) International Patent Classification: Plaza 721/2340, 974 Centre Road, PO Box 291 5 Wilming C12N 1/19 (2006.01) C12N 9/00 (2006.01) ton, US 19805 (US). C12P 7/64 (2006.01) (81) Designated States (unless otherwise indicated, for every (21) International Application Number: kind of national protection available): AE, AG, AL, AM, PCT/US20 16/043 133 AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (22) International Filing Date: DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, 20 July 20 16 (20.07.2016) HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (25) Filing Language: English KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (26) Publication Language: English PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, (30) Priority Data: SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 62/195,340 22 July 2015 (22.07.2015) US TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. 62/195,338 22 July 2015 (22.07.2015) US (84) Designated States (unless otherwise indicated, for every (71) Applicant: E I DU PONT DE NEMOURS AND COM¬ kind of regional protection available): ARIPO (BW, GH, PANY [US/US]; Chestnut Run Plaza, 974 Centre Road, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, P.O. Box 2915, Wilmington, Delaware 19805 (US). TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, (72) Inventors: ZHU, Quinn Qun; 544 Revere Road, West DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, Chester, Pennsylvania 19382 (US). FAN, Xiaochun; 175 LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, Pratt Lane, West Chester, Pennsylvania 19382 (US). SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, HONG, Seung-PYO; 9 Pierson's Ridge, Hockessin, GW, KM, ML, MR, NE, SN, TD, TG). Delaware 19707 (US). BOUGIOUKOU, Despina; 230 Published: Presidential Drive, Wilmington, Delaware 19807 (US). XIE, Dongming; 33 Renee Lane, Newark, Delaware — with international search report (Art. 21(3)) 1971 1 (US). DHAMANKAR, Himanshu H.; 258 Presid — with sequence listing part of description (Rule 5.2(a)) ential Drive, Apt. D, Greenville, Delaware 19807 (US). (74) Agent: CHESIRE, Dennis; E.I. du Pont de Nemours and Company, Legal Patent Records Center, Chestnut Run (54) Title: HIGH LEVEL PRODUCTION OF LONG-CHAIN DICARBOXYLIC ACIDS WITH MICROBES FIG. 1 © (57) Abstract: Recombinant microbial cells comprising an engineered LCDA production pathway that comprises at least one up- o regulated long-chain acyl-CoA synthetase (ACoS) are disclosed. These recombinant microbial cells are capable of producing one or more long-chain dicarboxylic acid (LCDA) products from a long-chain fatty acid-comprising substrate. Methods of using recombin ant microbial cells to produce LCDAs are also disclosed. TITLE HIGH LEVEL PRODUCTION OF LONG-CHAIN DICARBOXYLIC ACIDS WITH MICROBES This application claims the benefit of U.S. Provisional Application Nos. 62/1 95,340 (filed July 22, 201 6) and 62/1 95,338 (filed July 22, 201 6), which are both incorporated herein by reference in their entirety. FIELD OF INVENTION The present disclosure is in the field of molecular biology. For example, the disclosure pertains to microbes, such as yeast, genetically engineered to produce long- chain dicarboxylic acids (LCDA) from fatty acid-comprising substrates. REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY The official copy of the sequence listing is submitted electronically via EFS-Web as an ASCII formatted sequence listing with a file named CL6467WOPCT_SequenceListing_ST25 created on July 18 , 2016, and having a size of 480 kilobytes and is filed concurrently with the specification. The sequence listing contained in this ASCII-formatted document is part of the specification and is herein incorporated by reference in its entirety. BACKGROUND Dicarboxylic acids comprising ten or more carbon atoms can be referred to as long-chain dicarboxylic acids (LCDAs). LCDAs are useful as constituent monomers for various synthetic materials such as polyamides (nylons), polyurethanes, and polyesters. Other uses of LCDAs include, for example, production of certain polycarbonates, powder coatings, fragrances, personal care items, food additives, solvents, cleaning additives, hot-melt adhesives, lubricants, insecticides and fungicides. LCDAs can also be used as plasticizers for engineering plastics and as corrosion inhibitors in metal processing technology, for example. Quantities of LCDAs suitable for carrying out commercial applications such as described above are generally not found in nature. Certain LCDAs, such as dodecanedioic acid (DDDA), can be prepared via various synthetic processes. However, biological processes such as microbial fermentation could also be useful for producing LCDAs. Feedstocks containing oil or free fatty acids, for example, may be suitable as substrates for fermenting LCDA products. Efforts to ferment LCDAs with yeast biocatalysts have been undertaken (U.S. Pat. Appl. Publ. Nos. 2004/0146999, 2010/0041 5 , 201 3/0267012, 2014/0228586). Fatty acids can be activated in yeast for use in beta-oxidation and other downstream pathways, thereby drawing fatty acids away from pathways of omega- oxidation. Thus, some yeast biocatalysts have been modified to exhibit reduced fatty acid activation, such as by down-regulating expression of long-chain fatty acyl-CoA synthetase, to augment fermentation of LCDA products via omega-oxidation (e.g., see U.S. Pat. Appl. Publ. Nos. 2014/0228586 and 2013/0267012). The above disclosures notwithstanding, it has now surprisingly been found that increasing fatty acid activation in yeast by up-regulating long-chain fatty acyl-CoA synthetase allows for high LCDA production. Thus, microbial biocatalysts engineered for high levels of LCDA production are disclosed herein. SUMMARY OF INVENTION In one embodiment, the disclosure concerns a recombinant microbial cell comprising an engineered LCDA production pathway that comprises up-regulation of a polynucleotide sequence encoding a long-chain acyl-CoA synthetase (ACoS enzyme), wherein the microbial cell is capable of producing one or more long-chain dicarboxylic acid (LCDA) products from a long-chain fatty acid-comprising substrate. Another embodiment concerns a recombinant microbial cell, comprising: (i) up-regulation of a polynucleotide sequence encoding a cytochrome P450 monooxygenase (CYP enzyme) and/or up-regulation of a polynucleotide sequence encoding a cytochrome P450 reductase (CPR enzyme), (ii) up-regulation of a polynucleotide sequence encoding a long-chain acyl- CoA synthetase (ACoS enzyme), and (iii) down-regulation of an endogenous polynucleotide sequence encoding a peroxisome biogenesis factor-3, wherein the microbial cell is capable of producing one or more long-chain dicarboxylic acid (LCDA) products from a long-chain fatty acid-comprising substrate. Another embodiment concerns a method of producing a long-chain dicarboxylic acid (LCDA). This method comprises: a) contacting a recombinant microbial cell as disclosed herein with a long-chain fatty acid-comprising substrate, wherein the microbial cell synthesizes an LCDA from the substrate; and b) optionally recovering the LCDA of step (a). BRIEF DESCRIPTION OF THE DRAWINGS AND SEQUENCES FIG. 1: Lipid metabolic pathways, including fatty acid beta-oxidation and omega- oxidation aspects of lipid metabolism, are depicted. Dashed lines/arrows indicate low or weak activity in Y. lipolytica. FIG. 2 : Strategies are shown for engineering . lipolytica to produce LCDA from oil, oil-derived fatty acids, and/or fatty acid esters. FIG. 3 : Phylogenetic tree of candidate acyl-CoA synthetases from S. cerevisiae, Y. lipolytica and C. tropicalis. Certain abbreviations used in this figure: FAA1 and FAA2 denote S. cerevisiae Faal p and Faa2p, respectively. YA-1 denotes YIFaal p. Α -" denotes "YIACoS-". Refer to Example 1. FIG. 4 : LCDA production by strain D0145 in flask assay. DCA, dicarboxylic acid. Refer to Example 2 . FIG. 5A: Plasmid construct pZP2-YIACoS-3Ps (SEQ ID NO:63). FIG. 5B: Plasmid construct pZP2-YIACoS-5Ps (SEQ ID NO:64). FIG. 5C: Plasmid construct pZP2-YIACoS-6Ps (SEQ ID NO:65). FIG. 5D: Plasmid construct pZP2-YIACoS-1 0Ps (SEQ ID NO:66). FIG. 5E: Plasmid construct pZKL7A-FYIFAAs (SEQ ID NO:67). FIG. 5F: Plasmid construct pZP2-YIACoS-5PS3s (SEQ ID NO:68). FIG. 6A: SDS-PAGE analysis of soluble and insoluble fractions of E . coli cells transformed to over-express putative fatty acyl CoA synthetases. Lanes 1, 2 , 3 , 4 , 5 , 6 : samples from E . coli cells over-expressing YIACoS-3P (SEQ ID NO:39), YIACoS-5P (SEQ ID NO:42), YIAC0S-6P (SEQ ID NO:44), YIACoS-10P (SEQ ID NO:49), YIFAA (SEQ ID NO:36), or YIACoS-5PS3 (SEQ ID NO:56), respectively. Lane C : sample from E . coli cells transformed with the pET23d vector alone (negative control). Lane M : protein markers. Refer to Example 5 . FIG. 6B: SDS-PAGE of lysates of E . coli cells before and after IPTG-induced over-expression of putative fatty acyl CoA synthetases. Lanes 1, 2 , 3 , 4 : samples from E . coli cells over-expressing YIACoS-3P (SEQ ID NO:39), YIACoS-5P (SEQ ID NO:42), YIAC0S-6P (SEQ ID NO:44), or YIACoS-1 0P (SEQ ID NO:49), respectively. Lane C : sample from E . coli cells transformed with the pET23d vector alone (negative control). Lane M : protein markers. Refer to Example 5 . FIG. 7A: A diagram is shown depicting the lineage of certain strains listed in Table 7 .
Load more

Recommended publications
  • A 37-Amino Acid Loop in the Yarrowia Lipolytica Hexokinase Impacts Its Activity and Affinity and Modulates Gene Expression
    www.nature.com/scientificreports OPEN A 37‑amino acid loop in the Yarrowia lipolytica hexokinase impacts its activity and afnity and modulates gene expression Piotr Hapeta1, Patrycja Szczepańska1, Cécile Neuvéglise2 & Zbigniew Lazar1* The oleaginous yeast Yarrowia lipolytica is a potent cell factory as it is able to use a wide variety of carbon sources to convert waste materials into value‑added products. Nonetheless, there are still gaps in our understanding of its central carbon metabolism. Here we present an in‑depth study of Y. lipolytica hexokinase (YlHxk1), a structurally unique protein. The greatest peculiarity of YlHxk1 is a 37‑amino acid loop region, a structure not found in any other known hexokinases. By combining bioinformatic and experimental methods we showed that the loop in YlHxk1 is essential for activity of this protein and through that on growth of Y. lipolytica on glucose and fructose. We further proved that the loop in YlHxk1 hinders binding with trehalose 6‑phosphate (T6P), a glycolysis inhibitor, as hexokinase with partial deletion of this region is 4.7‑fold less sensitive to this molecule. We also found that YlHxk1 devoid of the loop causes strong repressive efect on lipase‑encoding genes LIP2 and LIP8 and that the hexokinase overexpression in Y. lipolytica changes glycerol over glucose preference when cultivated in media containing both substrates. Yarrowia lipolytica is an oleaginous yeast that has become a biotechnological workhorse due to its industrially- relevant abilities. Tis yeast synthesize high concentration of intracellular lipids and secrete high amount of proteins as well as organic acids and polyols 1–6.
    [Show full text]
  • Fungal Evolution: Major Ecological Adaptations and Evolutionary Transitions
    Biol. Rev. (2019), pp. 000–000. 1 doi: 10.1111/brv.12510 Fungal evolution: major ecological adaptations and evolutionary transitions Miguel A. Naranjo-Ortiz1 and Toni Gabaldon´ 1,2,3∗ 1Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain 2 Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain 3ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain ABSTRACT Fungi are a highly diverse group of heterotrophic eukaryotes characterized by the absence of phagotrophy and the presence of a chitinous cell wall. While unicellular fungi are far from rare, part of the evolutionary success of the group resides in their ability to grow indefinitely as a cylindrical multinucleated cell (hypha). Armed with these morphological traits and with an extremely high metabolical diversity, fungi have conquered numerous ecological niches and have shaped a whole world of interactions with other living organisms. Herein we survey the main evolutionary and ecological processes that have guided fungal diversity. We will first review the ecology and evolution of the zoosporic lineages and the process of terrestrialization, as one of the major evolutionary transitions in this kingdom. Several plausible scenarios have been proposed for fungal terrestralization and we here propose a new scenario, which considers icy environments as a transitory niche between water and emerged land. We then focus on exploring the main ecological relationships of Fungi with other organisms (other fungi, protozoans, animals and plants), as well as the origin of adaptations to certain specialized ecological niches within the group (lichens, black fungi and yeasts).
    [Show full text]
  • BIODEGRADAÇÃO DE QUEROSENE POR Candida Lipolytica EM ÁGUA DO MAR
    UNIVERSIDADE CATÓLICA DE PERNAMBUCO PRÓ-REITORIA ACADÊMICA COORDENAÇÃO GERAL DE PÓS-GRADUAÇÃO MESTRADO EM DESENVOLVIMENTO DE PROCESSOS AMBIENTAIS Jupiranan Ferreira da Silva BIODEGRADAÇÃO DE QUEROSENE POR Candida lipolytica UCP EM ÁGUA DO MAR Recife 2012 Jupiranan Ferreira da Silva BIODEGRADAÇÃO DE QUEROSENE POR Candida lipolytica EM ÁGUA DO MAR Dissertação apresentada ao Programa de Pós-Graduação em Desenvolvimento em Processos Ambientais Universidade Católica de Pernambuco como pré-requisito para obtenção do título de Mestre em Desenvolvimento de Processos Ambientais. Área de Concentração: Desenvolvimento em Processos Ambientais Linha de Pesquisa: Biotecnologia e Meio Ambiente/ Informática, Modelagem e Controle de Processo Orientadora: Prof. Dra. Clarissa Daisy da Costa Albuquerque Recife/ 2012 i Silva, Jupiranan Ferreira da Biodegradação de Querosene por Candida lipolytica em Água do Mar./ Jupiranan Ferreira da Silva; orientadora Clarissa Daisy da Costa Albuquerque, 2012. Dissertação (Mestrado) – Universidade Católica de Pernambuco. Programa de Pós-Graduação em Desenvolvimento de Processos Ambientais. 1. Biodegradação. 2. Querosene. 3. Água do mar. 4. Candida lipolytica. 5. Biossurfactante. I. Programa de Pós-Graduação em Desenvolvimento de Processos Ambientais. Centro de Ciências e Tecnologia. ii BIODEGRADAÇÃO DE QUEROSENE POR Candida lipolytica EM ÁGUA DO MAR JUPIRANAN FERREIRA DA SILVA Examinadores: ________________________________________________________ Profª. Drª Clarissa Daisy da Costa Albuquerque - Orientadora Universidade Católica de Pernambuco – UNICAP ____________________________________ Profª Drª Kaoru Okada Universidade Católica de Pernambuco – UNICAP _______________________________________ Profª Drª Norma Buarque de Gusmão Universidade Federal de Pernambuco iii A Meus pais Neuma e Ferreira Cada gesto, pensamento ou palavra aqui contido... As alegrias que pude sentir... Todo empenho, esforço e superação... Os sonhos que almejei e realizei... iv Conheces-me bem..
    [Show full text]
  • Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity
    Journal of Fungi Article Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity Daniel Peterson 1, Tang Li 2, Ana M. Calvo 1,* and Yanbin Yin 2,* 1 Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA; [email protected] 2 Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska–Lincoln, Lincoln, NE 68588, USA; [email protected] * Correspondence: [email protected] (A.M.C.); [email protected] (Y.Y.); Tel.: +1-(815)-753-0451 (A.M.C.); +1-(402)-472-4303 (Y.Y.) Abstract: Phytopathogenic Ascomycota are responsible for substantial economic losses each year, destroying valuable crops. The present study aims to provide new insights into phytopathogenicity in Ascomycota from a comparative genomic perspective. This has been achieved by categorizing orthologous gene groups (orthogroups) from 68 phytopathogenic and 24 non-phytopathogenic Ascomycota genomes into three classes: Core, (pathogen or non-pathogen) group-specific, and genome-specific accessory orthogroups. We found that (i) ~20% orthogroups are group-specific and accessory in the 92 Ascomycota genomes, (ii) phytopathogenicity is not phylogenetically determined, (iii) group-specific orthogroups have more enriched functional terms than accessory orthogroups and this trend is particularly evident in phytopathogenic fungi, (iv) secreted proteins with signal peptides and horizontal gene transfers (HGTs) are the two functional terms that show the highest Citation: Peterson, D.; Li, T.; Calvo, occurrence and significance in group-specific orthogroups, (v) a number of other functional terms are A.M.; Yin, Y. Categorization of Orthologous Gene Clusters in 92 also identified to have higher significance and occurrence in group-specific orthogroups.
    [Show full text]
  • Studies on Upgradation of Waste Fish Oil to Lipid-Rich Yeast Biomass in Yarrowia Lipolytica Batch Cultures
    foods Article Studies on Upgradation of Waste Fish Oil to Lipid-Rich Yeast Biomass in Yarrowia lipolytica Batch Cultures Agata Urszula Fabiszewska 1,* , Bartłomiej Zieniuk 1 , Mariola Kozłowska 1 , Patrycja Maria Mazurczak-Zieniuk 1, Małgorzata Wołoszynowska 2, Paulina Misiukiewicz-St˛epie´n 3 and Dorota Nowak 4 1 Department of Chemistry, Institute of Food Sciences, Warsaw University of Life Sciences-SGGW, 159c Nowoursynowska Street, 02-776 Warsaw, Poland; [email protected] (B.Z.); [email protected] (M.K.); [email protected] (P.M.M.-Z.) 2 Łukasiewicz Research Network—Institute of Industrial Organic Chemistry, 6 Annopol Street, 03-236 Warsaw, Poland; [email protected] 3 Postgraduate School of Molecular Medicine, Medical University of Warsaw, 2a Trojdena Street, 02-091 Warsaw, Poland; [email protected] 4 Department of Food Engineering and Process Management, Institute of Food Sciences, Warsaw University of Life Sciences-SGGW, Nowoursynowska Street 159c, 02-776 Warsaw, Poland; [email protected] * Correspondence: [email protected]; Tel.: +48-22-59-37-621 Abstract: The aim of the study was to evaluate the possibility to utilize a fish waste oil issued from Citation: Fabiszewska, A.U.; the industrial smoking process in nitrogen-limited Yarrowia lipolytica yeast batch cultures. The waste Zieniuk, B.; Kozłowska, M.; Mazurczak-Zieniuk, P.M.; carbon source was utilized by the yeast and stimulated the single cell oil production via an ex novo Wołoszynowska, M.; pathway. The yeast biomass contained lipids up to 0.227 g/g d.m.. Independently from culture Misiukiewicz-St˛epie´n,P.; Nowak, D.
    [Show full text]
  • Engineering of Metabolic Pathways and Global Regulators of Yarrowia Lipolytica to Produce High Value Commercial Products Ethal Jackson Du Pont
    Engineering Conferences International ECI Digital Archives Metabolic Engineering IX Proceedings Summer 6-7-2012 Engineering of Metabolic Pathways and Global Regulators of Yarrowia lipolytica to Produce High Value Commercial Products Ethal Jackson Du Pont Follow this and additional works at: http://dc.engconfintl.org/metabolic_ix Part of the Biomedical Engineering and Bioengineering Commons Recommended Citation Ethal Jackson, "Engineering of Metabolic Pathways and Global Regulators of Yarrowia lipolytica to Produce High Value Commercial Products" in "Metabolic Engineering IX", E. Heinzle, Saarland Univ.; P. Soucaille, INSA; G. Whited, Danisco Eds, ECI Symposium Series, (2013). http://dc.engconfintl.org/metabolic_ix/18 This Conference Proceeding is brought to you for free and open access by the Proceedings at ECI Digital Archives. It has been accepted for inclusion in Metabolic Engineering IX by an authorized administrator of ECI Digital Archives. For more information, please contact [email protected]. Engineering of Metabolic Pathways and Global Regulators of Yarrowia lipolytica to Produce High Value Commercial Products Ethel Jackson CR&D, E.I. du Pont de Nemours and Company, USA Metabolic Engineering IX, Biarritz, France 2012 2 Metabolic Engineering of Yarrowia : LandLand--basedbased Renewable Source of OmegaOmega--33 Current Wild Harvest of Ocean Fish Unsustainable Future Renewable LandLand--basedbased Fermentation 3 Essential OmegaOmega--33 Fatty Acids: EPA and DHA • EPA & DHA required in diet of humans & animals Total Omega-3 market
    [Show full text]
  • Supplementary Materials For
    Electronic Supplementary Material (ESI) for RSC Advances. This journal is © The Royal Society of Chemistry 2019 Supplementary materials for: Fungal community analysis in the seawater of the Mariana Trench as estimated by Illumina HiSeq Zhi-Peng Wang b, †, Zeng-Zhi Liu c, †, Yi-Lin Wang d, Wang-Hua Bi c, Lu Liu c, Hai-Ying Wang b, Yuan Zheng b, Lin-Lin Zhang e, Shu-Gang Hu e, Shan-Shan Xu c, *, Peng Zhang a, * 1 Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China 2 Key Laboratory of Sustainable Development of Polar Fishery, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China 3 School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China. 4 College of Science, China University of Petroleum, Qingdao, Shandong 266580, China. 5 College of Chemistry & Environmental Engineering, Shandong University of Science & Technology, Qingdao, 266510, China. a These authors contributed equally to this work *Authors to whom correspondence should be addressed Supplementary Table S1. Read counts of OTUs in different sampled sites. OTUs M1.1 M1.2 M1.3 M1.4 M3.1 M3.2 M3.4 M4.2 M4.3 M4.4 M7.1 M7.2 M7.3 Total number OTU1 13714 398 5405 671 11604 3286 3452 349 3560 2537 383 2629 3203 51204 OTU2 6477 2203 2188 1048 2225 1722 235 1270 2564 5258 7149 7131 3606 43089 OTU3 165 39 13084 37 81 7 11 11 2 176 289 4 2102 16021 OTU4 642 4347 439 514 638 191 170 179 0 1969 570 678 0 10348 OTU5 28 13 4806 7 44 151 10 620 3
    [Show full text]
  • Yarrowia Lipolytica: a Beneficious Yeast in Biotechnology As a Rare Opportunistic Fungal Pathogen: a Minireview
    World Journal of Microbiology and Biotechnology (2019) 35:10 https://doi.org/10.1007/s11274-018-2583-8 REVIEW Yarrowia lipolytica: a beneficious yeast in biotechnology as a rare opportunistic fungal pathogen: a minireview Bartłomiej Zieniuk1 · Agata Fabiszewska1 Received: 16 September 2018 / Accepted: 17 December 2018 / Published online: 21 December 2018 © The Author(s) 2018 Abstract Yarrowia lipolytica is one of the most studied “non-conventional” yeast species capable of synthesizing a wide group of valu- able metabolites, in particular lipases and other hydrolytic enzymes, microbial oil, citric acid, erythritol and γ-decalactone. Processes based on the yeast have GRAS status (“generally recognized as safe”) given by Food and Drug Administration. The majority of research communications regarding to Y. lipolytica claim that the yeast species is non-pathogenic. In spite of that, Y. lipolytica, like other fungal species, can cause infections in immunocompromised and critically ill patients. The yeast possess features that facilitate invasion of the host cell (particularly production of hydrolytic enzymes), as well as the protection of the own cells, such as biofilm formation. The aim of this study was to present well-known yeast species Y. lipolytica as a rare opportunistic fungal pathogen. Possible pathogenicity and epidemiology of this yeast species were discussed. Antifungal drugs susceptibility and increasing resistance to azoles in Y. lipolytica yeasts were also presented. Keywords Drug susceptibility · Fungemia · Opportunistic pathogen · Virulence factors · Yarrowia lipolytica Introduction of usage in food industry and an expanding biotechnologi- cal potential, the yeast species could be an example of a One of the latest World Health Organization (WHO) report rare opportunistic fungal pathogen, which cause infections in shows a growing threat from antibiotic-resistant microorgan- premature newborns, immunocompromised and critically ill isms (WHO report 2017).
    [Show full text]
  • Yarrowia Lipolytica Strains and Their Biotechnological Applications: How Natural Biodiversity and Metabolic Engineering Could Contribute to Cell Factories Improvement
    Journal of Fungi Review Yarrowia lipolytica Strains and Their Biotechnological Applications: How Natural Biodiversity and Metabolic Engineering Could Contribute to Cell Factories Improvement Catherine Madzak † Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, F-78850 Thiverval-Grignon, France; [email protected] † INRAE Is France’s New National Research Institute for Agriculture, Food and Environment, Created on 1 January 2020 by the Merger of INRA, the National Institute for Agricultural Research, and IRSTEA, the National Research Institute of Science and Technology for the Environment and Agriculture. Abstract: Among non-conventional yeasts of industrial interest, the dimorphic oleaginous yeast Yarrowia lipolytica appears as one of the most attractive for a large range of white biotechnology applications, from heterologous proteins secretion to cell factories process development. The past, present and potential applications of wild-type, traditionally improved or genetically modified Yarrowia lipolytica strains will be resumed, together with the wide array of molecular tools now available to genetically engineer and metabolically remodel this yeast. The present review will also provide a detailed description of Yarrowia lipolytica strains and highlight the natural biodiversity of this yeast, a subject little touched upon in most previous reviews. This work intends to fill Citation: Madzak, C. Yarrowia this gap by retracing the genealogy of the main Yarrowia lipolytica strains of industrial interest, by lipolytica Strains and Their illustrating the search for new genetic backgrounds and by providing data about the main publicly Biotechnological Applications: How available strains in yeast collections worldwide. At last, it will focus on exemplifying how advances Natural Biodiversity and Metabolic in engineering tools can leverage a better biotechnological exploitation of the natural biodiversity of Engineering Could Contribute to Cell Yarrowia lipolytica and of other yeasts from the Yarrowia clade.
    [Show full text]
  • Metabolic Engineering of the Yeast Yarrowia Lipolytica for the Production of Even- and Odd-Chain Fatty Acids Young Kyoung Park
    Metabolic engineering of the yeast Yarrowia lipolytica for the production of even- and odd-chain fatty acids Young Kyoung Park To cite this version: Young Kyoung Park. Metabolic engineering of the yeast Yarrowia lipolytica for the production of even- and odd-chain fatty acids. Biotechnology. Université Paris-Saclay, 2020. English. NNT : 2020UPASB010. tel-03191617 HAL Id: tel-03191617 https://pastel.archives-ouvertes.fr/tel-03191617 Submitted on 7 Apr 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Metabolic engineering of the yeast Yarrowia lipolytica for the production of even- and odd-chain fatty acids Thèse de doctorat de l'université Paris-Saclay École doctorale n° 581 : agriculture, alimentation, biologie, environnement et santé (ABIES) Spécialité de doctorat : Biotechnologies Unité de recherche : Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas 78352 France Référent : AgroParisTech Thèse présentée et soutenue à Paris-Saclay, le 1er Octobre 2020, par Young-Kyoung PARK Composition du Jury Marie-Joëlle VIROLLE Presidente Directrice de recherche, CNRS, Gif-sur-Yvette Fayza DABOUSSI Rapporteur & Examinatrice Directrice de recherche, INRAE, Toulouse Frédéric DOMERGUE Rapporteur & Examinateur Chargé de recherche (HDR), CNRS, Bordeaux Sébastien BAUD Examinateur Directeur de recherche, CNRS, Versailles Ioana POPESCU Examinatrice Maître de conférences, Université d'Evry-Val-Essonne B010 Michael SAUER Examinateur Professeur, BOKU University Vasiliki TSAKRAKLIDES Examinatrice Responsable, Novogy Inc.
    [Show full text]
  • Genomic Analysis of Novel Yarrowia-Like Yeast Symbionts Associated with the Carrion-Feeding Burying Beetle Nicrophorus Vespilloides
    Brinkrolf et al. BMC Genomics (2021) 22:323 https://doi.org/10.1186/s12864-021-07597-z RESEARCH ARTICLE Open Access Genomic analysis of novel Yarrowia-like yeast symbionts associated with the carrion-feeding burying beetle Nicrophorus vespilloides Karina Brinkrolf1,2*, Shantanu P. Shukla3, Sven Griep2, Oliver Rupp2, Philipp Heise1, Alexander Goesmann2, David G. Heckel3, Heiko Vogel3 and Andreas Vilcinskas1,4 Abstract Background: Mutualistic interactions with microbes can help insects adapt to extreme environments and unusual diets. An intriguing example is the burying beetle Nicrophorus vespilloides, which feeds and reproduces on small vertebrate carcasses. Its fungal microbiome is dominated by yeasts that potentially facilitate carcass utilization by producing digestive enzymes, eliminating cadaver-associated toxic volatiles (that would otherwise attract competitors), and releasing antimicrobials to sanitize the microenvironment. Some of these yeasts are closely related to the biotechnologically important species Yarrowia lipolytica. Results: To investigate the roles of these Yarrowia-like yeast (YLY) strains in more detail, we selected five strains from two different phylogenetic clades for third-generation sequencing and genome analysis. The first clade, represented by strain B02, has a 20-Mb genome containing ~ 6400 predicted protein-coding genes. The second clade, represented by strain C11, has a 25-Mb genome containing ~ 6300 predicted protein-coding genes, and extensive intraspecific variability within the ITS–D1/D2 rDNA region commonly used for species assignments. Phenotypic microarray analysis revealed that both YLY strains were able to utilize a diverse range of carbon and nitrogen sources (including microbial metabolites associated with putrefaction), and can grow in environments with extreme pH and salt concentrations.
    [Show full text]
  • Yarrowia Lipolytica As a Biotechnological Chassis to Produce Usual and Unusual Fatty Acids
    CORE Metadata, citation and similar papers at core.ac.uk Provided by Elsevier - Publisher Connector Progress in Lipid Research 61 (2016) 40–50 Contents lists available at ScienceDirect Progress in Lipid Research journal homepage: www.elsevier.com/locate/plipres Review Yarrowia lipolytica as a biotechnological chassis to produce usual and unusual fatty acids Rodrigo Ledesma-Amaro ⁎, Jean-Marc Nicaud ⁎ a INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France b AgroParisTech, UMR Micalis, Jouy-en-Josas, France article info abstract Article history: One of the most promising alternatives to petroleum for the production of fuels and chemicals is bio-oil based Received 24 September 2015 chemistry. Microbial oils are gaining importance because they can be engineered to accumulate lipids enriched Received in revised form 2 December 2015 in desired fatty acids. These specific lipids are closer to the commercialized product, therefore reducing pollutants Accepted 8 December 2015 and costly chemical steps. Yarrowia lipolytica is the most widely studied and engineered oleaginous yeast. Differ- Available online 15 December 2015 ent molecular and bioinformatics tools permit systems metabolic engineering strategies in this yeast, which can Keywords: produce usual and unusual fatty acids. Usual fatty acids, those usually found in triacylglycerol, accumulate Yarrowia lipolytica through the action of several pathways, such as fatty acid/triacylglycerol synthesis, transport and degradation. Lipid metabolism Unusual fatty acids are enzymatic modifications of usual fatty acids to produce compounds that are not naturally Oleaginous yeasts synthetized in the host. Recently, the metabolic engineering of microorganisms has produced different unusual Unusual fatty acids fatty acids, such as building block ricinoleic acid and nutraceuticals such as conjugated linoleic acid or polyunsat- Systems metabolic engineering urated fatty acids.
    [Show full text]