Transcriptomic analyses during the transition from biomass production to lipid accumulation in the oleaginous yeast Yarrowia lipolytica
We previously developed a fermentation protocol for lipid accumulation in the oleaginous yeast Y. lipolytica. This process was used to perform transcriptomic time-course analyses to explore gene expression in Y. lipolytica during the transition from biomass production to lipid accumulation. In this...
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| description | We previously developed a fermentation protocol for lipid accumulation in the oleaginous yeast Y. lipolytica. This process was used to perform transcriptomic time-course analyses to explore gene expression in Y. lipolytica during the transition from biomass production to lipid accumulation. In this experiment, a biomass concentration of 54.6 g(CDW)/l, with 0.18 g/g(CDW) lipid was obtained in ca. 32 h, with low citric acid production. A transcriptomic profiling was performed on 11 samples throughout the fermentation. Through statistical analyses, 569 genes were highlighted as differentially expressed at one point during the time course of the experiment. These genes were classified into 9 clusters, according to their expression profiles. The combination of macroscopic and transcriptomic profiles highlighted 4 major steps in the culture: (i) a growth phase, (ii) a transition phase, (iii) an early lipid accumulation phase, characterized by an increase in nitrogen metabolism, together with strong repression of protein production and activity; (iv) a late lipid accumulation phase, characterized by the rerouting of carbon fluxes within cells. This study explores the potential of Y. lipolytica as an alternative oil producer, by identifying, at the transcriptomic level, the genes potentially involved in the metabolism of oleaginous species. |
| doi_str_mv | 10.1371/journal.pone.0027966 |
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This process was used to perform transcriptomic time-course analyses to explore gene expression in Y. lipolytica during the transition from biomass production to lipid accumulation. In this experiment, a biomass concentration of 54.6 g(CDW)/l, with 0.18 g/g(CDW) lipid was obtained in ca. 32 h, with low citric acid production. A transcriptomic profiling was performed on 11 samples throughout the fermentation. Through statistical analyses, 569 genes were highlighted as differentially expressed at one point during the time course of the experiment. These genes were classified into 9 clusters, according to their expression profiles. The combination of macroscopic and transcriptomic profiles highlighted 4 major steps in the culture: (i) a growth phase, (ii) a transition phase, (iii) an early lipid accumulation phase, characterized by an increase in nitrogen metabolism, together with strong repression of protein production and activity; (iv) a late lipid accumulation phase, characterized by the rerouting of carbon fluxes within cells. This study explores the potential of Y. lipolytica as an alternative oil producer, by identifying, at the transcriptomic level, the genes potentially involved in the metabolism of oleaginous species.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0027966</identifier><identifier>PMID: 22132183</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Accumulation ; Acid production ; Analysis ; Baking yeast ; Batch Cell Culture Techniques ; Biodiesel fuels ; Biology ; Biomass ; Cell culture ; Citric acid ; Cluster Analysis ; Down-Regulation - genetics ; Energy Metabolism - genetics ; Fermentation ; Fluxes ; Fungal Proteins - genetics ; Fungal Proteins - metabolism ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation, Fungal ; Genes ; Genes, Fungal - genetics ; Kinetics ; Life Sciences ; Lipid Metabolism - genetics ; Lipids ; Lipids - genetics ; Metabolism ; Nitrogen metabolism ; Oils & fats ; Organic acids ; Phase transitions ; Physiological aspects ; Protein turnover ; Saccharomyces cerevisiae ; Statistical analysis ; Statistical methods ; Transcription Factors - genetics ; Transcription Factors - metabolism ; Transcriptome - genetics ; Up-Regulation - genetics ; Yarrowia - genetics ; Yarrowia - metabolism ; Yarrowia lipolytica ; Yeast</subject><ispartof>PloS one, 2011-11, Vol.6 (11), p.e27966-e27966</ispartof><rights>COPYRIGHT 2011 Public Library of Science</rights><rights>2011 Morin et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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This process was used to perform transcriptomic time-course analyses to explore gene expression in Y. lipolytica during the transition from biomass production to lipid accumulation. In this experiment, a biomass concentration of 54.6 g(CDW)/l, with 0.18 g/g(CDW) lipid was obtained in ca. 32 h, with low citric acid production. A transcriptomic profiling was performed on 11 samples throughout the fermentation. Through statistical analyses, 569 genes were highlighted as differentially expressed at one point during the time course of the experiment. These genes were classified into 9 clusters, according to their expression profiles. 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This study explores the potential of Y. lipolytica as an alternative oil producer, by identifying, at the transcriptomic level, the genes potentially involved in the metabolism of oleaginous species.</description><subject>Accumulation</subject><subject>Acid production</subject><subject>Analysis</subject><subject>Baking yeast</subject><subject>Batch Cell Culture Techniques</subject><subject>Biodiesel fuels</subject><subject>Biology</subject><subject>Biomass</subject><subject>Cell culture</subject><subject>Citric acid</subject><subject>Cluster Analysis</subject><subject>Down-Regulation - genetics</subject><subject>Energy Metabolism - genetics</subject><subject>Fermentation</subject><subject>Fluxes</subject><subject>Fungal Proteins - genetics</subject><subject>Fungal Proteins - metabolism</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Fungal</subject><subject>Genes</subject><subject>Genes, Fungal - 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analyses during the transition from biomass production to lipid accumulation in the oleaginous yeast Yarrowia lipolytica</title><author>Morin, Nicolas ; Cescut, Julien ; Beopoulos, Athanasios ; Lelandais, Gaëlle ; Le Berre, Veronique ; Uribelarrea, Jean-Louis ; Molina-Jouve, Carole ; Nicaud, Jean-Marc</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c725t-6c86d0366421b79484762bf93f6ede4a63239ec1f278c31f27684509d24d35ab3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Accumulation</topic><topic>Acid production</topic><topic>Analysis</topic><topic>Baking yeast</topic><topic>Batch Cell Culture Techniques</topic><topic>Biodiesel fuels</topic><topic>Biology</topic><topic>Biomass</topic><topic>Cell culture</topic><topic>Citric acid</topic><topic>Cluster Analysis</topic><topic>Down-Regulation - genetics</topic><topic>Energy Metabolism - 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one</jtitle><addtitle>PLoS One</addtitle><date>2011-11-22</date><risdate>2011</risdate><volume>6</volume><issue>11</issue><spage>e27966</spage><epage>e27966</epage><pages>e27966-e27966</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>We previously developed a fermentation protocol for lipid accumulation in the oleaginous yeast Y. lipolytica. This process was used to perform transcriptomic time-course analyses to explore gene expression in Y. lipolytica during the transition from biomass production to lipid accumulation. In this experiment, a biomass concentration of 54.6 g(CDW)/l, with 0.18 g/g(CDW) lipid was obtained in ca. 32 h, with low citric acid production. A transcriptomic profiling was performed on 11 samples throughout the fermentation. Through statistical analyses, 569 genes were highlighted as differentially expressed at one point during the time course of the experiment. These genes were classified into 9 clusters, according to their expression profiles. The combination of macroscopic and transcriptomic profiles highlighted 4 major steps in the culture: (i) a growth phase, (ii) a transition phase, (iii) an early lipid accumulation phase, characterized by an increase in nitrogen metabolism, together with strong repression of protein production and activity; (iv) a late lipid accumulation phase, characterized by the rerouting of carbon fluxes within cells. This study explores the potential of Y. lipolytica as an alternative oil producer, by identifying, at the transcriptomic level, the genes potentially involved in the metabolism of oleaginous species.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>22132183</pmid><doi>10.1371/journal.pone.0027966</doi><tpages>e27966</tpages><orcidid>https://orcid.org/0000-0002-8022-4295</orcidid><orcidid>https://orcid.org/0000-0003-2097-4120</orcidid><orcidid>https://orcid.org/0000-0003-4541-6547</orcidid><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2011-11, Vol.6 (11), p.e27966-e27966 |
| issn | 1932-6203 1932-6203 |
| language | eng |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Accumulation Acid production Analysis Baking yeast Batch Cell Culture Techniques Biodiesel fuels Biology Biomass Cell culture Citric acid Cluster Analysis Down-Regulation - genetics Energy Metabolism - genetics Fermentation Fluxes Fungal Proteins - genetics Fungal Proteins - metabolism Gene expression Gene Expression Profiling Gene Expression Regulation, Fungal Genes Genes, Fungal - genetics Kinetics Life Sciences Lipid Metabolism - genetics Lipids Lipids - genetics Metabolism Nitrogen metabolism Oils & fats Organic acids Phase transitions Physiological aspects Protein turnover Saccharomyces cerevisiae Statistical analysis Statistical methods Transcription Factors - genetics Transcription Factors - metabolism Transcriptome - genetics Up-Regulation - genetics Yarrowia - genetics Yarrowia - metabolism Yarrowia lipolytica Yeast |
| title | Transcriptomic analyses during the transition from biomass production to lipid accumulation in the oleaginous yeast Yarrowia lipolytica |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-08T01%3A34%3A44IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Transcriptomic%20analyses%20during%20the%20transition%20from%20biomass%20production%20to%20lipid%20accumulation%20in%20the%20oleaginous%20yeast%20Yarrowia%20lipolytica&rft.jtitle=PloS%20one&rft.au=Morin,%20Nicolas&rft.date=2011-11-22&rft.volume=6&rft.issue=11&rft.spage=e27966&rft.epage=e27966&rft.pages=e27966-e27966&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0027966&rft_dat=%3Cgale_plos_%3EA476861935%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1310230860&rft_id=info:pmid/22132183&rft_galeid=A476861935&rft_doaj_id=oai_doaj_org_article_9f3561994b6a4999a4fe6748f2c2ebfa&rfr_iscdi=true |