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Liu M, Wu J, Yue M, Ning Y, Guan X, Gao S, Zhou J. YaliCMulti and YaliHMulti: Stable, efficient multi-copy integration tools for engineering Yarrowia lipolytica. Metab Eng 2024; 82:29-40. [PMID: 38224832 DOI: 10.1016/j.ymben.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/17/2024]
Abstract
Yarrowia lipolytica is widely used in biotechnology to produce recombinant proteins, food ingredients and diverse natural products. However, unstable expression of plasmids, difficult and time-consuming integration of single and low-copy-number plasmids hampers the construction of efficient production pathways and application to industrial production. Here, by exploiting sequence diversity in the long terminal repeats (LTRs) of retrotransposons and ribosomal DNA (rDNA) sequences, a set of vectors and methods that can recycle multiple and high-copy-number plasmids was developed that can achieve stable integration of long-pathway genes in Y. lipolytica. By combining these sequences, amino acids and antibiotic tags with the Cre-LoxP system, a series of multi-copy site integration recyclable vectors were constructed and assessed using the green fluorescent protein (HrGFP) reporter system. Furthermore, by combining the consensus sequence with the vector backbone of a rapidly degrading selective marker and a weak promoter, multiple integrated high-copy-number vectors were obtained and high levels of stable HrGFP expression were achieved. To validate the universality of the tools, simple integration of essential biosynthesis modules was explored, and 7.3 g/L of L-ergothioneine and 8.3 g/L of (2S)-naringenin were achieved in a 5 L fermenter, the highest titres reported to date for Y. lipolytica. These novel multi-copy genome integration strategies provide convenient and effective tools for further metabolic engineering of Y. lipolytica.
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Affiliation(s)
- Mengsu Liu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Junjun Wu
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Mingyu Yue
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Yang Ning
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Xin Guan
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Song Gao
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
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Bigey F, Pasteur E, Połomska X, Thomas S, Crutz-Le Coq AM, Devillers H, Neuvéglise C. Insights into the Genomic and Phenotypic Landscape of the Oleaginous Yeast Yarrowia lipolytica. J Fungi (Basel) 2023; 9:jof9010076. [PMID: 36675897 PMCID: PMC9865632 DOI: 10.3390/jof9010076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/30/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023] Open
Abstract
Although Yarrowia lipolytica is a model yeast for the study of lipid metabolism, its diversity is poorly known, as studies generally consider only a few standard laboratory strains. To extend our knowledge of this biotechnological workhorse, we investigated the genomic and phenotypic diversity of 56 natural isolates. Y. lipolytica is classified into five clades with no correlation between clade membership and geographic or ecological origin. A low genetic diversity (π = 0.0017) and a pan-genome (6528 genes) barely different from the core genome (6315 genes) suggest Y. lipolytica is a recently evolving species. Large segmental duplications were detected, totaling 892 genes. With three new LTR-retrotransposons of the Gypsy family (Tyl4, Tyl9, and Tyl10), the transposable element content of genomes appeared diversified but still low (from 0.36% to 3.62%). We quantified 34 traits with substantial phenotypic diversity, but genome-wide association studies failed to evidence any associations. Instead, we investigated known genes and found four mutational events leading to XPR2 protease inactivation. Regarding lipid metabolism, most high-impact mutations were found in family-belonging genes, such as ALK or LIP, and therefore had a low phenotypic impact, suggesting that the huge diversity of lipid synthesis and accumulation is multifactorial or due to complex regulations.
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Affiliation(s)
- Frédéric Bigey
- INRAE, Institut Agro, SPO, University Montpellier, 34060 Montpellier, France
| | - Emilie Pasteur
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Xymena Połomska
- Department of Biotechnology & Food Microbiology, Wroclaw University of Environmental and Life Sciences (WUELS), 50-375 Wroclaw, Poland
| | - Stéphane Thomas
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Anne-Marie Crutz-Le Coq
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
- IJPB, INRAE, 78000 Versailles, France
| | - Hugo Devillers
- INRAE, Institut Agro, SPO, University Montpellier, 34060 Montpellier, France
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Cécile Neuvéglise
- INRAE, Institut Agro, SPO, University Montpellier, 34060 Montpellier, France
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
- Correspondence:
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Yarrowia lipolytica Strains and Their Biotechnological Applications: How Natural Biodiversity and Metabolic Engineering Could Contribute to Cell Factories Improvement. J Fungi (Basel) 2021; 7:jof7070548. [PMID: 34356927 PMCID: PMC8307478 DOI: 10.3390/jof7070548] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 11/20/2022] Open
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 this gap by retracing the genealogy of the main Yarrowia lipolytica strains of industrial interest, by illustrating the search for new genetic backgrounds and by providing data about the main publicly available strains in yeast collections worldwide. At last, it will focus on exemplifying how advances in engineering tools can leverage a better biotechnological exploitation of the natural biodiversity of Yarrowia lipolytica and of other yeasts from the Yarrowia clade.
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Genome Sequence of the Oleaginous Yeast Yarrowia lipolytica H222. Microbiol Resour Announc 2019; 8:MRA01547-18. [PMID: 30701247 PMCID: PMC6346196 DOI: 10.1128/mra.01547-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 12/18/2018] [Indexed: 11/29/2022] Open
Abstract
Here, we report the genome sequence of the oleaginous yeast Yarrowia lipolytica H222. De novo genome assembly shows three main chromosomal rearrangements compared to that of strain E150/CLIB122. Here, we report the genome sequence of the oleaginous yeast Yarrowia lipolytica H222. De novo genome assembly shows three main chromosomal rearrangements compared to that of strain E150/CLIB122. This genomic resource will help integrate intraspecies diversity into synthetic biology projects that utilize Yarrowia as a biotechnological chassis for value-added chemical productions.
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Cheung S, Manhas S, Measday V. Retrotransposon targeting to RNA polymerase III-transcribed genes. Mob DNA 2018; 9:14. [PMID: 29713390 PMCID: PMC5911963 DOI: 10.1186/s13100-018-0119-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 04/16/2018] [Indexed: 12/20/2022] Open
Abstract
Retrotransposons are genetic elements that are similar in structure and life cycle to retroviruses by replicating via an RNA intermediate and inserting into a host genome. The Saccharomyces cerevisiae (S. cerevisiae) Ty1-5 elements are long terminal repeat (LTR) retrotransposons that are members of the Ty1-copia (Pseudoviridae) or Ty3-gypsy (Metaviridae) families. Four of the five S. cerevisiae Ty elements are inserted into the genome upstream of RNA Polymerase (Pol) III-transcribed genes such as transfer RNA (tRNA) genes. This particular genomic locus provides a safe environment for Ty element insertion without disruption of the host genome and is a targeting strategy used by retrotransposons that insert into compact genomes of hosts such as S. cerevisiae and the social amoeba Dictyostelium. The mechanism by which Ty1 targeting is achieved has been recently solved due to the discovery of an interaction between Ty1 Integrase (IN) and RNA Pol III subunits. We describe the methods used to identify the Ty1-IN interaction with Pol III and the Ty1 targeting consequences if the interaction is perturbed. The details of Ty1 targeting are just beginning to emerge and many unexplored areas remain including consideration of the 3-dimensional shape of genome. We present a variety of other retrotransposon families that insert adjacent to Pol III-transcribed genes and the mechanism by which the host machinery has been hijacked to accomplish this targeting strategy. Finally, we discuss why retrotransposons selected Pol III-transcribed genes as a target during evolution and how retrotransposons have shaped genome architecture.
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Affiliation(s)
- Stephanie Cheung
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Savrina Manhas
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Vivien Measday
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Food Science, Wine Research Centre, Faculty of Land and Food Systems, University of British Columbia, Room 325-2205 East Mall, Vancouver, British Columbia V6T 1Z4 Canada
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Magnan C, Yu J, Chang I, Jahn E, Kanomata Y, Wu J, Zeller M, Oakes M, Baldi P, Sandmeyer S. Sequence Assembly of Yarrowia lipolytica Strain W29/CLIB89 Shows Transposable Element Diversity. PLoS One 2016; 11:e0162363. [PMID: 27603307 PMCID: PMC5014426 DOI: 10.1371/journal.pone.0162363] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 08/22/2016] [Indexed: 12/27/2022] Open
Abstract
Yarrowia lipolytica, an oleaginous yeast, is capable of accumulating significant cellular mass in lipid making it an important source of biosustainable hydrocarbon-based chemicals. In spite of a similar number of protein-coding genes to that in other Hemiascomycetes, the Y. lipolytica genome is almost double that of model yeasts. Despite its economic importance and several distinct strains in common use, an independent genome assembly exists for only one strain. We report here a de novo annotated assembly of the chromosomal genome of an industrially-relevant strain, W29/CLIB89, determined by hybrid next-generation sequencing. For the first time, each Y. lipolytica chromosome is represented by a single contig. The telomeric rDNA repeats were localized by Irys long-range genome mapping and one complete copy of the rDNA sequence is reported. Two large structural variants and retroelement differences with reference strain CLIB122 including a full-length, novel Ty3/Gypsy long terminal repeat (LTR) retrotransposon and multiple LTR-like sequences are described. Strikingly, several of these are adjacent to RNA polymerase III-transcribed genes, which are almost double in number in Y. lipolytica compared to other Hemiascomycetes. In addition to previously-reported dimeric RNA polymerase III-transcribed genes, tRNA pseudogenes were identified. Multiple full-length and truncated LINE elements are also present. Therefore, although identified transposons do not constitute a significant fraction of the Y. lipolytica genome, they could have played an active role in its evolution. Differences between the sequence of this strain and of the existing reference strain underscore the utility of an additional independent genome assembly for this economically important organism.
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Affiliation(s)
- Christophe Magnan
- Department of Computer Science, School of Computer Sciences, University of California Irvine, Irvine, California, United States of America
- Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, California, United States of America
| | - James Yu
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Ivan Chang
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Ethan Jahn
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Yuzo Kanomata
- Department of Computer Science, School of Computer Sciences, University of California Irvine, Irvine, California, United States of America
- Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, California, United States of America
| | - Jenny Wu
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Michael Zeller
- Department of Computer Science, School of Computer Sciences, University of California Irvine, Irvine, California, United States of America
| | - Melanie Oakes
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Pierre Baldi
- Department of Computer Science, School of Computer Sciences, University of California Irvine, Irvine, California, United States of America
- Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, California, United States of America
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Suzanne Sandmeyer
- Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, California, United States of America
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America
- * E-mail:
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Identification and characterization of a LTR retrotransposon from the genome of Cyprinus carpio var. Jian. Genetica 2016; 144:325-33. [PMID: 27178280 DOI: 10.1007/s10709-016-9901-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 04/27/2016] [Indexed: 10/21/2022]
Abstract
A Ty3/gypsy-retrotransposon-type transposon was found in the genome of the Jian carp (Cyprinus carpio var. Jian) in a previous study (unpublished), and was designated a JRE retrotransposon (Jian retrotransposon). The full-length JRE retrotransposon is 5126 bp, which includes two long terminal repeats of 470 bp at the 5' end and 453 bp at the 3' end, and two open reading frames between them: 4203 bp encoding the group-specific antigen (GAG) and polyprotein (POL). The pol gene has a typical Ty3/gypsy retrotransposon structure, and the gene order is protease, reverse transcriptase, RNase H, and integrase (PR-RT-RH-IN). A phylogenetic analysis of the pol gene showed that it has similarities of 40.7, 40, and 32.8 %, to retrotransposons of Azumapecten farreri, Mizuhopecten yessoensis, and Xiphophorus maculatus, respectively. Therefore, JRE might belong to the JULE retrotransposon family. The copy number of the JRE transposon in the genome of the Jian carp is 124, determined with real-time quantitative PCR. The mRNA of the JRE retrotransposon is expressed in five Jian carp tissues, the liver, kidney, blood, muscle, and gonad, and slightly higher in the kidney and liver than in the other tissues.
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Kunze G, Gaillardin C, Czernicka M, Durrens P, Martin T, Böer E, Gabaldón T, Cruz JA, Talla E, Marck C, Goffeau A, Barbe V, Baret P, Baronian K, Beier S, Bleykasten C, Bode R, Casaregola S, Despons L, Fairhead C, Giersberg M, Gierski PP, Hähnel U, Hartmann A, Jankowska D, Jubin C, Jung P, Lafontaine I, Leh-Louis V, Lemaire M, Marcet-Houben M, Mascher M, Morel G, Richard GF, Riechen J, Sacerdot C, Sarkar A, Savel G, Schacherer J, Sherman DJ, Stein N, Straub ML, Thierry A, Trautwein-Schult A, Vacherie B, Westhof E, Worch S, Dujon B, Souciet JL, Wincker P, Scholz U, Neuvéglise C. The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:66. [PMID: 24834124 PMCID: PMC4022394 DOI: 10.1186/1754-6834-7-66] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 03/19/2014] [Indexed: 05/09/2023]
Abstract
BACKGROUND The industrially important yeast Blastobotrys (Arxula) adeninivorans is an asexual hemiascomycete phylogenetically very distant from Saccharomyces cerevisiae. Its unusual metabolic flexibility allows it to use a wide range of carbon and nitrogen sources, while being thermotolerant, xerotolerant and osmotolerant. RESULTS The sequencing of strain LS3 revealed that the nuclear genome of A. adeninivorans is 11.8 Mb long and consists of four chromosomes with regional centromeres. Its closest sequenced relative is Yarrowia lipolytica, although mean conservation of orthologs is low. With 914 introns within 6116 genes, A. adeninivorans is one of the most intron-rich hemiascomycetes sequenced to date. Several large species-specific families appear to result from multiple rounds of segmental duplications of tandem gene arrays, a novel mechanism not yet described in yeasts. An analysis of the genome and its transcriptome revealed enzymes with biotechnological potential, such as two extracellular tannases (Atan1p and Atan2p) of the tannic-acid catabolic route, and a new pathway for the assimilation of n-butanol via butyric aldehyde and butyric acid. CONCLUSIONS The high-quality genome of this species that diverged early in Saccharomycotina will allow further fundamental studies on comparative genomics, evolution and phylogenetics. Protein components of different pathways for carbon and nitrogen source utilization were identified, which so far has remained unexplored in yeast, offering clues for further biotechnological developments. In the course of identifying alternative microorganisms for biotechnological interest, A. adeninivorans has already proved its strengthened competitiveness as a promising cell factory for many more applications.
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Affiliation(s)
- Gotthard Kunze
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
- Yeast Genetics, Leibniz Institute of Plant Research (IPK), Corrensstrasse 3, Gatersleben 06466, Germany
| | - Claude Gaillardin
- AgroParisTech, Micalis UMR 1319, CBAI, Thiverval-Grignon, F-78850, France
- INRA French National Institute for Agricultural Research, Micalis UMR 1319, CBAI, Thiverval-Grignon F-78850, France
| | - Małgorzata Czernicka
- Institute of Plant Biology and Biotechnology, University of Agriculture in Krakow, Al. 29 Listopada 54, Krakow 31-425, Poland
| | - Pascal Durrens
- LaBRI (UMR 5800 CNRS) and project-team Magnome INRIA Bordeaux Sud-Ouest, Talence F-33405, France
| | - Tiphaine Martin
- LaBRI (UMR 5800 CNRS) and project-team Magnome INRIA Bordeaux Sud-Ouest, Talence F-33405, France
| | - Erik Böer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Jose A Cruz
- Université de Strasbourg, Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, F-67084 Strasbourg, France
| | - Emmanuel Talla
- Aix-Marseille Université, CNRS UMR 7283, Laboratoire de Chimie Bactérienne, F-13402 Marseille, Cedex 20, France
| | - Christian Marck
- CEA, Saclay Biology and Technologies Institute (iBiTec-S), Gif-sur-Yvette F-91191, France
| | - André Goffeau
- Université catholique de Louvain, Institut des Sciences de la Vie, Croix du Sud 5/15, Louvain-la-Neuve 1349, Belgium
| | - Valérie Barbe
- CEA, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, Évry F-91000, France
| | - Philippe Baret
- Université Catholique de Louvain, Earth and Life Institute (ELI), Louvain-la-Neuve 1348, Belgium
| | - Keith Baronian
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
| | | | - Rüdiger Bode
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorffstraße 4, Greifswald D-17487, Germany
| | - Serge Casaregola
- AgroParisTech, Micalis UMR 1319, CBAI, Thiverval-Grignon, F-78850, France
- INRA French National Institute for Agricultural Research, Micalis UMR 1319, CBAI, Thiverval-Grignon F-78850, France
| | - Laurence Despons
- Université de Strasbourg, CNRS UMR7156, Strasbourg F-67000, France
| | - Cécile Fairhead
- Institut de Génétique et Microbiologie, Université Paris-Sud, UMR CNRS 8621, F- Orsay CEDEX 91405, France
| | - Martin Giersberg
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
| | - Przemysław Piotr Gierski
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, Warsaw 02-109, Poland
| | - Urs Hähnel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
| | - Anja Hartmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
| | - Dagmara Jankowska
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
| | - Claire Jubin
- CEA, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, Évry F-91000, France
- CNRS UMR 8030, 2 Rue Gaston Crémieux, Évry F-91000, France
- Université d’Evry, Bd François Mitterand, Evry F-91025, France
| | - Paul Jung
- Université de Strasbourg, CNRS UMR7156, Strasbourg F-67000, France
| | - Ingrid Lafontaine
- Institut Pasteur, Université Pierre et Marie Curie UFR927, CNRS UMR 3525, F-75724 Paris-CEDEX 15, France
| | | | - Marc Lemaire
- Université Lyon 1, CNRS UMR 5240, Villeurbanne F-69621, France
| | - Marina Marcet-Houben
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
| | - Guillaume Morel
- AgroParisTech, Micalis UMR 1319, CBAI, Thiverval-Grignon, F-78850, France
- INRA French National Institute for Agricultural Research, Micalis UMR 1319, CBAI, Thiverval-Grignon F-78850, France
| | - Guy-Franck Richard
- Institut Pasteur, Université Pierre et Marie Curie UFR927, CNRS UMR 3525, F-75724 Paris-CEDEX 15, France
| | - Jan Riechen
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
| | - Christine Sacerdot
- Institut Pasteur, Université Pierre et Marie Curie UFR927, CNRS UMR 3525, F-75724 Paris-CEDEX 15, France
- Present address: École Normale Supérieure, Institut de Biologie de l’ENS (IBENS), 46 rue d’Ulm, Paris F-75005, France
| | - Anasua Sarkar
- LaBRI (UMR 5800 CNRS) and project-team Magnome INRIA Bordeaux Sud-Ouest, Talence F-33405, France
| | - Guilhem Savel
- LaBRI (UMR 5800 CNRS) and project-team Magnome INRIA Bordeaux Sud-Ouest, Talence F-33405, France
| | | | - David J Sherman
- LaBRI (UMR 5800 CNRS) and project-team Magnome INRIA Bordeaux Sud-Ouest, Talence F-33405, France
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
| | | | - Agnès Thierry
- Institut Pasteur, Université Pierre et Marie Curie UFR927, CNRS UMR 3525, F-75724 Paris-CEDEX 15, France
| | - Anke Trautwein-Schult
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
| | - Benoit Vacherie
- CEA, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, Évry F-91000, France
| | - Eric Westhof
- Université de Strasbourg, Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, F-67084 Strasbourg, France
| | - Sebastian Worch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
| | - Bernard Dujon
- Institut Pasteur, Université Pierre et Marie Curie UFR927, CNRS UMR 3525, F-75724 Paris-CEDEX 15, France
| | - Jean-Luc Souciet
- Université de Strasbourg, CNRS UMR7156, Strasbourg F-67000, France
| | - Patrick Wincker
- CEA, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, Évry F-91000, France
- CNRS UMR 8030, 2 Rue Gaston Crémieux, Évry F-91000, France
- Université d’Evry, Bd François Mitterand, Evry F-91025, France
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Gatersleben D-06466, Germany
| | - Cécile Neuvéglise
- AgroParisTech, Micalis UMR 1319, CBAI, Thiverval-Grignon, F-78850, France
- INRA French National Institute for Agricultural Research, Micalis UMR 1319, CBAI, Thiverval-Grignon F-78850, France
- INRA Institut Micalis UMR 1319, AgroParisTech, BIMLip, Avenue de Bretignières, Bât. CBAI, Thiverval-Grignon 78850, France
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9
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Groenewald M, Boekhout T, Neuvéglise C, Gaillardin C, van Dijck PWM, Wyss M. Yarrowia lipolytica: safety assessment of an oleaginous yeast with a great industrial potential. Crit Rev Microbiol 2013; 40:187-206. [PMID: 23488872 DOI: 10.3109/1040841x.2013.770386] [Citation(s) in RCA: 282] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Yarrowia lipolytica has been developed as a production host for a large variety of biotechnological applications. Efficacy and safety studies have demonstrated the safe use of Yarrowia-derived products containing significant proportions of Yarrowia biomass (as for DuPont's eicosapentaenoic acid-rich oil) or with the yeast itself as the final product (as for British Petroleum's single-cell protein product). The natural occurrence of the species in food, particularly cheese, other dairy products and meat, is a further argument supporting its safety. The species causes rare opportunistic infections in severely immunocompromised or otherwise seriously ill people with other underlying diseases or conditions. The infections can be treated effectively by the use of regular antifungal drugs, and in some cases even disappeared spontaneously. Based on our assessment, we conclude that Y. lipolytica is a "safe-to-use" organism.
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Affiliation(s)
- Marizeth Groenewald
- CBS-KNAW Fungal Biodiversity Centre, Institute of the Royal Netherlands Academy of Arts and Sciences , Utrecht , The Netherlands
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10
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Bleykasten-Grosshans C, Neuvéglise C. Transposable elements in yeasts. C R Biol 2011; 334:679-86. [PMID: 21819950 DOI: 10.1016/j.crvi.2011.05.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 03/31/2011] [Indexed: 11/19/2022]
Abstract
With the development of new sequencing technologies in the past decade, yeast genomes have been extensively sequenced and their structures investigated. Transposable elements (TEs) are ubiquitous in eukaryotes and constitute a limited part of yeast genomes. However, due to their ability to move in genomes and generate dispersed repeated sequences, they contribute to modeling yeast genomes and thereby induce plasticity. This review assesses the TE contents of yeast genomes investigated so far. Their diversity and abundance at the inter- and intraspecific levels are presented, and their effects on gene expression and genome stability is considered. Recent results concerning TE-host interactions are also analyzed.
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Affiliation(s)
- Claudine Bleykasten-Grosshans
- CNRS UMR 7156, Laboratoire Génétique Moléculaire Génomique Microbiologie, Université de Strasbourg, 28 rue Goethe, 67083 Strasbourg cedex, France.
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11
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Mekouar M, Blanc-Lenfle I, Ozanne C, Da Silva C, Cruaud C, Wincker P, Gaillardin C, Neuvéglise C. Detection and analysis of alternative splicing in Yarrowia lipolytica reveal structural constraints facilitating nonsense-mediated decay of intron-retaining transcripts. Genome Biol 2010; 11:R65. [PMID: 20573210 PMCID: PMC2911113 DOI: 10.1186/gb-2010-11-6-r65] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 06/15/2010] [Accepted: 06/23/2010] [Indexed: 11/10/2022] Open
Abstract
Background Hemiascomycetous yeasts have intron-poor genomes with very few cases of alternative splicing. Most of the reported examples result from intron retention in Saccharomyces cerevisiae and some have been shown to be functionally significant. Here we used transcriptome-wide approaches to evaluate the mechanisms underlying the generation of alternative transcripts in Yarrowia lipolytica, a yeast highly divergent from S. cerevisiae. Results Experimental investigation of Y. lipolytica gene models identified several cases of alternative splicing, mostly generated by intron retention, principally affecting the first intron of the gene. The retention of introns almost invariably creates a premature termination codon, as a direct consequence of the structure of intron boundaries. An analysis of Y. lipolytica introns revealed that introns of multiples of three nucleotides in length, particularly those without stop codons, were underrepresented. In other organisms, premature termination codon-containing transcripts are targeted for degradation by the nonsense-mediated mRNA decay (NMD) machinery. In Y. lipolytica, homologs of S. cerevisiae UPF1 and UPF2 genes were identified, but not UPF3. The inactivation of Y. lipolytica UPF1 and UPF2 resulted in the accumulation of unspliced transcripts of a test set of genes. Conclusions Y. lipolytica is the hemiascomycete with the most intron-rich genome sequenced to date, and it has several unusual genes with large introns or alternative transcription start sites, or introns in the 5' UTR. Our results suggest Y. lipolytica intron structure is subject to significant constraints, leading to the under-representation of stop-free introns. Consequently, intron-containing transcripts are degraded by a functional NMD pathway.
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Affiliation(s)
- Meryem Mekouar
- INRA UMR1319 Micalis - AgroParisTech, Biologie intégrative du métabolisme lipidique microbien, Bât, CBAI, 78850 Thiverval-Grignon, France
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12
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Sabot F, Schulman AH. Parasitism and the retrotransposon life cycle in plants: a hitchhiker's guide to the genome. Heredity (Edinb) 2006; 97:381-8. [PMID: 16985508 DOI: 10.1038/sj.hdy.6800903] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
LTR (long terminal repeat) retrotransposons are the main components of higher plant genomic DNA. They have shaped their host genomes through insertional mutagenesis and by effects on genome size, gene expression and recombination. These Class I transposable elements are closely related to retroviruses such as the HIV by their structure and presumptive life cycle. However, the retrotransposon life cycle has been closely investigated in few systems. For retroviruses and retrotransposons, individual defective copies can parasitize the activity of functional ones. However, some LTR retrotransposon groups as a whole, such as large retrotransposon derivatives and terminal repeats in miniature, are non-autonomous even though their genomic insertion patterns remain polymorphic between organismal accessions. Here, we examine what is known of the retrotransposon life cycle in plants, and in that context discuss the role of parasitism and complementation between and within retrotransposon groups.
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Affiliation(s)
- F Sabot
- MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
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13
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Current awareness on yeast. Yeast 2006. [DOI: 10.1002/yea.1172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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