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Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides
The basidiomycete yeast (also known as ) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB...
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| Published in: | eLife 2018-03, Vol.7 |
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| creator | Coradetti, Samuel T Pinel, Dominic Geiselman, Gina M Ito, Masakazu Mondo, Stephen J Reilly, Morgann C Cheng, Ya-Fang Bauer, Stefan Grigoriev, Igor V Gladden, John M Simmons, Blake A Brem, Rachel B Arkin, Adam P Skerker, Jeffrey M |
| description | The basidiomycete yeast
(also known as
) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcoded
T-DNA insertions. We identified 1,337 putative essential genes with low T-DNA insertion rates. We functionally profiled genes required for fatty acid catabolism and lipid accumulation, validating results with 35 targeted deletion strains. We identified a high-confidence set of 150 genes affecting lipid accumulation, including genes with predicted function in signaling cascades, gene expression, protein modification and vesicular trafficking, autophagy, amino acid synthesis and tRNA modification, and genes of unknown function. These results greatly advance our understanding of lipid metabolism in this oleaginous species and demonstrate a general approach for barcoded mutagenesis that should enable functional genomics in diverse fungi. |
| doi_str_mv | 10.7554/eLife.32110 |
| format | article |
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(also known as
) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcoded
T-DNA insertions. We identified 1,337 putative essential genes with low T-DNA insertion rates. We functionally profiled genes required for fatty acid catabolism and lipid accumulation, validating results with 35 targeted deletion strains. We identified a high-confidence set of 150 genes affecting lipid accumulation, including genes with predicted function in signaling cascades, gene expression, protein modification and vesicular trafficking, autophagy, amino acid synthesis and tRNA modification, and genes of unknown function. These results greatly advance our understanding of lipid metabolism in this oleaginous species and demonstrate a general approach for barcoded mutagenesis that should enable functional genomics in diverse fungi.</description><identifier>ISSN: 2050-084X</identifier><identifier>EISSN: 2050-084X</identifier><identifier>DOI: 10.7554/eLife.32110</identifier><identifier>PMID: 29521624</identifier><language>eng</language><publisher>England: eLife Sciences Publications Ltd</publisher><subject>Agrobacterium tumefaciens ; Amino acids ; Autophagy ; BASIC BIOLOGICAL SCIENCES ; Bioengineering ; Biomass ; Carbon sources ; Carotenoids ; Carotenoids - biosynthesis ; Carotenoids - genetics ; Cellular biology ; Clonal deletion ; Computational and Systems Biology ; Deoxyribonucleic acid ; DNA ; Experiments ; Fatty acids ; functional genomics ; Fungi ; Gene deletion ; Gene expression ; Gene Expression Regulation, Fungal - genetics ; Genes ; Genomics ; Insertion ; Laboratories ; lipid droplet ; Lipid metabolism ; Lipid Metabolism - genetics ; Lipids ; Lipids - biosynthesis ; Metabolic Engineering ; Metabolism ; Microbiology and Infectious Disease ; Microscopy ; Mutagenesis ; Mutagenesis, Insertional ; Nitrogen ; Nucleotide sequence ; oleaginous yeast ; Phagocytosis ; Phenotype ; Protein transport ; Proteins ; Rhodosporidium toruloides ; Rhodotorula - genetics ; Rhodotorula - metabolism ; Rhodotorula toruloides ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae - genetics ; T-DNA ; TnSeq ; Transformation, Genetic ; tRNA ; tRNA Ala</subject><ispartof>eLife, 2018-03, Vol.7</ispartof><rights>2018. This work is licensed under the Creative Commons Public Domain Dedication ( https://creativecommons.org/publicdomain/zero/1.0/ ) (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c568t-824c139eec137bf2359a41912305d3b1ba6c5c58d62448dab8c121681ad5c7a63</citedby><cites>FETCH-LOGICAL-c568t-824c139eec137bf2359a41912305d3b1ba6c5c58d62448dab8c121681ad5c7a63</cites><orcidid>0000-0003-0173-0403 ; 0000-0003-2653-1566 ; 0000-0002-4999-2931 ; 0000-0001-5797-0647 ; 0000-0002-6985-2485 ; 0000000157970647 ; 0000000326531566 ; 0000000301730403 ; 0000000269852485 ; 0000000249992931</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/2032699554/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2032699554?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,724,777,781,882,25734,27905,27906,36993,44571,53772,53774,74875</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29521624$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/biblio/1466439$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Coradetti, Samuel T</creatorcontrib><creatorcontrib>Pinel, Dominic</creatorcontrib><creatorcontrib>Geiselman, Gina M</creatorcontrib><creatorcontrib>Ito, Masakazu</creatorcontrib><creatorcontrib>Mondo, Stephen J</creatorcontrib><creatorcontrib>Reilly, Morgann C</creatorcontrib><creatorcontrib>Cheng, Ya-Fang</creatorcontrib><creatorcontrib>Bauer, Stefan</creatorcontrib><creatorcontrib>Grigoriev, Igor V</creatorcontrib><creatorcontrib>Gladden, John M</creatorcontrib><creatorcontrib>Simmons, Blake A</creatorcontrib><creatorcontrib>Brem, Rachel B</creatorcontrib><creatorcontrib>Arkin, Adam P</creatorcontrib><creatorcontrib>Skerker, Jeffrey M</creatorcontrib><creatorcontrib>Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)</creatorcontrib><creatorcontrib>Pacific Northwest National Lab. (PNNL), Richland, WA (United States)</creatorcontrib><title>Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides</title><title>eLife</title><addtitle>Elife</addtitle><description>The basidiomycete yeast
(also known as
) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcoded
T-DNA insertions. We identified 1,337 putative essential genes with low T-DNA insertion rates. We functionally profiled genes required for fatty acid catabolism and lipid accumulation, validating results with 35 targeted deletion strains. We identified a high-confidence set of 150 genes affecting lipid accumulation, including genes with predicted function in signaling cascades, gene expression, protein modification and vesicular trafficking, autophagy, amino acid synthesis and tRNA modification, and genes of unknown function. These results greatly advance our understanding of lipid metabolism in this oleaginous species and demonstrate a general approach for barcoded mutagenesis that should enable functional genomics in diverse fungi.</description><subject>Agrobacterium tumefaciens</subject><subject>Amino acids</subject><subject>Autophagy</subject><subject>BASIC BIOLOGICAL SCIENCES</subject><subject>Bioengineering</subject><subject>Biomass</subject><subject>Carbon sources</subject><subject>Carotenoids</subject><subject>Carotenoids - biosynthesis</subject><subject>Carotenoids - genetics</subject><subject>Cellular biology</subject><subject>Clonal deletion</subject><subject>Computational and Systems Biology</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Experiments</subject><subject>Fatty acids</subject><subject>functional genomics</subject><subject>Fungi</subject><subject>Gene deletion</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Fungal - genetics</subject><subject>Genes</subject><subject>Genomics</subject><subject>Insertion</subject><subject>Laboratories</subject><subject>lipid droplet</subject><subject>Lipid metabolism</subject><subject>Lipid Metabolism - genetics</subject><subject>Lipids</subject><subject>Lipids - biosynthesis</subject><subject>Metabolic Engineering</subject><subject>Metabolism</subject><subject>Microbiology and Infectious Disease</subject><subject>Microscopy</subject><subject>Mutagenesis</subject><subject>Mutagenesis, Insertional</subject><subject>Nitrogen</subject><subject>Nucleotide sequence</subject><subject>oleaginous yeast</subject><subject>Phagocytosis</subject><subject>Phenotype</subject><subject>Protein transport</subject><subject>Proteins</subject><subject>Rhodosporidium toruloides</subject><subject>Rhodotorula - genetics</subject><subject>Rhodotorula - metabolism</subject><subject>Rhodotorula toruloides</subject><subject>Saccharomyces cerevisiae</subject><subject>Saccharomyces cerevisiae - genetics</subject><subject>T-DNA</subject><subject>TnSeq</subject><subject>Transformation, Genetic</subject><subject>tRNA</subject><subject>tRNA Ala</subject><issn>2050-084X</issn><issn>2050-084X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNpVkV1rFDEUhgdRbKm98l6CXsrWfM4kN4IU-wELgijoVcicnNnNMjNZk0yh_964W0ubiyQkL8954Wmat4xedErJT7gOA14Izhh90ZxyquiKavnr5ZP7SXOe847W1UmtmXndnHCjOGu5PG1-Xy0zlBBnN5INznEKkEkcyBj2wZMJi-vjGPJEwkzKFkkc0W3CHJdM7tHlQr5vo495H1PwYZlIiWkZY_CY3zSvBjdmPH84z5qfV19_XN6s1t-uby-_rFegWl1WmktgwiDWvesHLpRxkhnGBVVe9Kx3LShQ2te6UnvXa2C1u2bOK-hcK86a2yPXR7ez-xQml-5tdMEeHmLaWJdKgBGt8mikVADQ9lKgNNQB76WXPQMN2FXW5yNrv_QTesC5JDc-gz7_mcPWbuKdVYZz08kKeH8ExFyCzRAKwhbiPCMUy2TbSmFq6MPDlBT_LJiL3cUlVQPZcip4a0w1W1MfjylIMeeEw2MNRu0_9_bg3h7c1_S7p80fs_9Ni792rqvb</recordid><startdate>20180309</startdate><enddate>20180309</enddate><creator>Coradetti, Samuel T</creator><creator>Pinel, Dominic</creator><creator>Geiselman, Gina M</creator><creator>Ito, Masakazu</creator><creator>Mondo, Stephen J</creator><creator>Reilly, Morgann C</creator><creator>Cheng, Ya-Fang</creator><creator>Bauer, Stefan</creator><creator>Grigoriev, Igor V</creator><creator>Gladden, John M</creator><creator>Simmons, Blake A</creator><creator>Brem, Rachel B</creator><creator>Arkin, Adam P</creator><creator>Skerker, Jeffrey M</creator><general>eLife Sciences Publications Ltd</general><general>eLife Sciences Publications, Ltd</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>88I</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>OTOTI</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0003-0173-0403</orcidid><orcidid>https://orcid.org/0000-0003-2653-1566</orcidid><orcidid>https://orcid.org/0000-0002-4999-2931</orcidid><orcidid>https://orcid.org/0000-0001-5797-0647</orcidid><orcidid>https://orcid.org/0000-0002-6985-2485</orcidid><orcidid>https://orcid.org/0000000157970647</orcidid><orcidid>https://orcid.org/0000000326531566</orcidid><orcidid>https://orcid.org/0000000301730403</orcidid><orcidid>https://orcid.org/0000000269852485</orcidid><orcidid>https://orcid.org/0000000249992931</orcidid></search><sort><creationdate>20180309</creationdate><title>Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides</title><author>Coradetti, Samuel T ; Pinel, Dominic ; Geiselman, Gina M ; Ito, Masakazu ; Mondo, Stephen J ; Reilly, Morgann C ; Cheng, Ya-Fang ; Bauer, Stefan ; Grigoriev, Igor V ; Gladden, John M ; Simmons, Blake A ; Brem, Rachel B ; Arkin, Adam P ; Skerker, Jeffrey M</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c568t-824c139eec137bf2359a41912305d3b1ba6c5c58d62448dab8c121681ad5c7a63</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Agrobacterium tumefaciens</topic><topic>Amino acids</topic><topic>Autophagy</topic><topic>BASIC BIOLOGICAL SCIENCES</topic><topic>Bioengineering</topic><topic>Biomass</topic><topic>Carbon sources</topic><topic>Carotenoids</topic><topic>Carotenoids - biosynthesis</topic><topic>Carotenoids - genetics</topic><topic>Cellular biology</topic><topic>Clonal deletion</topic><topic>Computational and Systems Biology</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Experiments</topic><topic>Fatty acids</topic><topic>functional genomics</topic><topic>Fungi</topic><topic>Gene deletion</topic><topic>Gene expression</topic><topic>Gene Expression Regulation, Fungal - genetics</topic><topic>Genes</topic><topic>Genomics</topic><topic>Insertion</topic><topic>Laboratories</topic><topic>lipid droplet</topic><topic>Lipid metabolism</topic><topic>Lipid Metabolism - genetics</topic><topic>Lipids</topic><topic>Lipids - biosynthesis</topic><topic>Metabolic Engineering</topic><topic>Metabolism</topic><topic>Microbiology and Infectious Disease</topic><topic>Microscopy</topic><topic>Mutagenesis</topic><topic>Mutagenesis, Insertional</topic><topic>Nitrogen</topic><topic>Nucleotide sequence</topic><topic>oleaginous yeast</topic><topic>Phagocytosis</topic><topic>Phenotype</topic><topic>Protein transport</topic><topic>Proteins</topic><topic>Rhodosporidium toruloides</topic><topic>Rhodotorula - genetics</topic><topic>Rhodotorula - metabolism</topic><topic>Rhodotorula toruloides</topic><topic>Saccharomyces cerevisiae</topic><topic>Saccharomyces cerevisiae - genetics</topic><topic>T-DNA</topic><topic>TnSeq</topic><topic>Transformation, Genetic</topic><topic>tRNA</topic><topic>tRNA Ala</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Coradetti, Samuel T</creatorcontrib><creatorcontrib>Pinel, Dominic</creatorcontrib><creatorcontrib>Geiselman, Gina M</creatorcontrib><creatorcontrib>Ito, Masakazu</creatorcontrib><creatorcontrib>Mondo, Stephen J</creatorcontrib><creatorcontrib>Reilly, Morgann C</creatorcontrib><creatorcontrib>Cheng, Ya-Fang</creatorcontrib><creatorcontrib>Bauer, Stefan</creatorcontrib><creatorcontrib>Grigoriev, Igor V</creatorcontrib><creatorcontrib>Gladden, John M</creatorcontrib><creatorcontrib>Simmons, Blake A</creatorcontrib><creatorcontrib>Brem, Rachel B</creatorcontrib><creatorcontrib>Arkin, Adam P</creatorcontrib><creatorcontrib>Skerker, Jeffrey M</creatorcontrib><creatorcontrib>Lawrence Berkeley National Lab. 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(also known as
) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcoded
T-DNA insertions. We identified 1,337 putative essential genes with low T-DNA insertion rates. We functionally profiled genes required for fatty acid catabolism and lipid accumulation, validating results with 35 targeted deletion strains. We identified a high-confidence set of 150 genes affecting lipid accumulation, including genes with predicted function in signaling cascades, gene expression, protein modification and vesicular trafficking, autophagy, amino acid synthesis and tRNA modification, and genes of unknown function. These results greatly advance our understanding of lipid metabolism in this oleaginous species and demonstrate a general approach for barcoded mutagenesis that should enable functional genomics in diverse fungi.</abstract><cop>England</cop><pub>eLife Sciences Publications Ltd</pub><pmid>29521624</pmid><doi>10.7554/eLife.32110</doi><orcidid>https://orcid.org/0000-0003-0173-0403</orcidid><orcidid>https://orcid.org/0000-0003-2653-1566</orcidid><orcidid>https://orcid.org/0000-0002-4999-2931</orcidid><orcidid>https://orcid.org/0000-0001-5797-0647</orcidid><orcidid>https://orcid.org/0000-0002-6985-2485</orcidid><orcidid>https://orcid.org/0000000157970647</orcidid><orcidid>https://orcid.org/0000000326531566</orcidid><orcidid>https://orcid.org/0000000301730403</orcidid><orcidid>https://orcid.org/0000000269852485</orcidid><orcidid>https://orcid.org/0000000249992931</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 2050-084X |
| ispartof | eLife, 2018-03, Vol.7 |
| issn | 2050-084X 2050-084X |
| language | eng |
| recordid | cdi_doaj_primary_oai_doaj_org_article_5de9445ccc6b43e490ac2b4d4b1c8ce7 |
| source | Publicly Available Content Database; PubMed Central |
| subjects | Agrobacterium tumefaciens Amino acids Autophagy BASIC BIOLOGICAL SCIENCES Bioengineering Biomass Carbon sources Carotenoids Carotenoids - biosynthesis Carotenoids - genetics Cellular biology Clonal deletion Computational and Systems Biology Deoxyribonucleic acid DNA Experiments Fatty acids functional genomics Fungi Gene deletion Gene expression Gene Expression Regulation, Fungal - genetics Genes Genomics Insertion Laboratories lipid droplet Lipid metabolism Lipid Metabolism - genetics Lipids Lipids - biosynthesis Metabolic Engineering Metabolism Microbiology and Infectious Disease Microscopy Mutagenesis Mutagenesis, Insertional Nitrogen Nucleotide sequence oleaginous yeast Phagocytosis Phenotype Protein transport Proteins Rhodosporidium toruloides Rhodotorula - genetics Rhodotorula - metabolism Rhodotorula toruloides Saccharomyces cerevisiae Saccharomyces cerevisiae - genetics T-DNA TnSeq Transformation, Genetic tRNA tRNA Ala |
| title | Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides |
| url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-18T17%3A08%3A31IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_doaj_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Functional%20genomics%20of%20lipid%20metabolism%20in%20the%20oleaginous%20yeast%20Rhodosporidium%20toruloides&rft.jtitle=eLife&rft.au=Coradetti,%20Samuel%20T&rft.aucorp=Lawrence%20Berkeley%20National%20Lab.%20(LBNL),%20Berkeley,%20CA%20(United%20States)&rft.date=2018-03-09&rft.volume=7&rft.issn=2050-084X&rft.eissn=2050-084X&rft_id=info:doi/10.7554/eLife.32110&rft_dat=%3Cproquest_doaj_%3E2032699554%3C/proquest_doaj_%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c568t-824c139eec137bf2359a41912305d3b1ba6c5c58d62448dab8c121681ad5c7a63%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=2032699554&rft_id=info:pmid/29521624&rfr_iscdi=true |