Transcriptome changes associated with anaerobic growth in Yersinia intermedia (ATCC29909)
The yersiniae (Enterobacteriaceae) occupy a variety of niches, including some in human and flea hosts. Metabolic adaptations of the yersiniae, which contribute to their success in these specialized environments, remain largely unknown. We report results of an investigation of the transcriptome under...
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| description | The yersiniae (Enterobacteriaceae) occupy a variety of niches, including some in human and flea hosts. Metabolic adaptations of the yersiniae, which contribute to their success in these specialized environments, remain largely unknown. We report results of an investigation of the transcriptome under aerobic and anaerobic conditions for Y. intermedia, a non-pathogenic member of the genus that has been used as a research surrogate for Y. pestis. Y. intermedia shares characteristics of pathogenic yersiniae, but is not known to cause disease in humans. Oxygen restriction is an important environmental stimulus experienced by many bacteria during their life-cycles and greatly influences their survival in specific environments. How oxygen availability affects physiology in the yersiniae is of importance in their life cycles but has not been extensively characterized.
Tiled oligonucleotide arrays based on a draft genome sequence of Y. intermedia were used in transcript profiling experiments to identify genes that change expression in response to oxygen availability during growth in minimal media with glucose. The expression of more than 400 genes, constituting about 10% of the genome, was significantly altered due to oxygen-limitation in early log phase under these conditions. Broad functional categorization indicated that, in addition to genes involved in central metabolism, genes involved in adaptation to stress and genes likely involved with host interactions were affected by oxygen-availability. Notable among these, were genes encoding functions for motility, chemotaxis and biosynthesis of cobalamin, which were up-regulated and those for iron/heme utilization, methionine metabolism and urease, which were down-regulated.
This is the first transcriptome analysis of a non-pathogenic Yersinia spp. and one of few elucidating the global response to oxygen limitation for any of the yersiniae. Thus this study lays the foundation for further experimental characterization of oxygen-responsive genes and pathways in this ecologically diverse genus. |
| doi_str_mv | 10.1371/journal.pone.0076567 |
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Tiled oligonucleotide arrays based on a draft genome sequence of Y. intermedia were used in transcript profiling experiments to identify genes that change expression in response to oxygen availability during growth in minimal media with glucose. The expression of more than 400 genes, constituting about 10% of the genome, was significantly altered due to oxygen-limitation in early log phase under these conditions. Broad functional categorization indicated that, in addition to genes involved in central metabolism, genes involved in adaptation to stress and genes likely involved with host interactions were affected by oxygen-availability. Notable among these, were genes encoding functions for motility, chemotaxis and biosynthesis of cobalamin, which were up-regulated and those for iron/heme utilization, methionine metabolism and urease, which were down-regulated.
This is the first transcriptome analysis of a non-pathogenic Yersinia spp. and one of few elucidating the global response to oxygen limitation for any of the yersiniae. Thus this study lays the foundation for further experimental characterization of oxygen-responsive genes and pathways in this ecologically diverse genus.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0076567</identifier><identifier>PMID: 24116118</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Adaptations ; Anaerobic conditions ; Anaerobiosis ; Analysis ; Animals ; Availability ; Biosynthesis ; Biotechnology ; Chemotaxis ; Deoxyribonucleic acid ; DNA ; DNA microarrays ; E coli ; Escherichia coli ; Fleas ; Gene expression ; Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Developmental ; Genes ; Genes, Bacterial - genetics ; Genetics ; Genomes ; Genomics ; Growth ; Heme ; Humans ; Iron ; Life cycles ; Metabolism ; Methionine ; Niches ; Nucleotide sequence ; Oligonucleotide Array Sequence Analysis ; Oligonucleotides ; Oxygen ; Oxygen - metabolism ; Oxygen - pharmacology ; Pathogens ; Transcription ; Transcriptome ; Urease ; Urine ; Vitamin B12 ; Yersinia ; Yersinia - drug effects ; Yersinia - genetics ; Yersinia - growth & development ; Yersinia Infections - microbiology ; Yersinia intermedia ; Yersinia pseudotuberculosis</subject><ispartof>PloS one, 2013-10, Vol.8 (10), p.e76567</ispartof><rights>COPYRIGHT 2013 Public Library of Science</rights><rights>2013 Babujee 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. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2013 Babujee et al 2013 Babujee et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-a47f068557da09020b8441376b17055dedb31911ecab4253ffa7fd6c900339f3</citedby><cites>FETCH-LOGICAL-c692t-a47f068557da09020b8441376b17055dedb31911ecab4253ffa7fd6c900339f3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3792023/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3792023/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24116118$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Pereira, Inês A. Cardoso</contributor><creatorcontrib>Babujee, Lavanya</creatorcontrib><creatorcontrib>Balakrishnan, Venkatesh</creatorcontrib><creatorcontrib>Kiley, Patricia J</creatorcontrib><creatorcontrib>Glasner, Jeremy D</creatorcontrib><creatorcontrib>Perna, Nicole T</creatorcontrib><title>Transcriptome changes associated with anaerobic growth in Yersinia intermedia (ATCC29909)</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The yersiniae (Enterobacteriaceae) occupy a variety of niches, including some in human and flea hosts. Metabolic adaptations of the yersiniae, which contribute to their success in these specialized environments, remain largely unknown. We report results of an investigation of the transcriptome under aerobic and anaerobic conditions for Y. intermedia, a non-pathogenic member of the genus that has been used as a research surrogate for Y. pestis. Y. intermedia shares characteristics of pathogenic yersiniae, but is not known to cause disease in humans. Oxygen restriction is an important environmental stimulus experienced by many bacteria during their life-cycles and greatly influences their survival in specific environments. How oxygen availability affects physiology in the yersiniae is of importance in their life cycles but has not been extensively characterized.
Tiled oligonucleotide arrays based on a draft genome sequence of Y. intermedia were used in transcript profiling experiments to identify genes that change expression in response to oxygen availability during growth in minimal media with glucose. The expression of more than 400 genes, constituting about 10% of the genome, was significantly altered due to oxygen-limitation in early log phase under these conditions. Broad functional categorization indicated that, in addition to genes involved in central metabolism, genes involved in adaptation to stress and genes likely involved with host interactions were affected by oxygen-availability. Notable among these, were genes encoding functions for motility, chemotaxis and biosynthesis of cobalamin, which were up-regulated and those for iron/heme utilization, methionine metabolism and urease, which were down-regulated.
This is the first transcriptome analysis of a non-pathogenic Yersinia spp. and one of few elucidating the global response to oxygen limitation for any of the yersiniae. Thus this study lays the foundation for further experimental characterization of oxygen-responsive genes and pathways in this ecologically diverse genus.</description><subject>Adaptations</subject><subject>Anaerobic conditions</subject><subject>Anaerobiosis</subject><subject>Analysis</subject><subject>Animals</subject><subject>Availability</subject><subject>Biosynthesis</subject><subject>Biotechnology</subject><subject>Chemotaxis</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA microarrays</subject><subject>E coli</subject><subject>Escherichia coli</subject><subject>Fleas</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Bacterial</subject><subject>Gene Expression Regulation, Developmental</subject><subject>Genes</subject><subject>Genes, Bacterial - genetics</subject><subject>Genetics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Growth</subject><subject>Heme</subject><subject>Humans</subject><subject>Iron</subject><subject>Life cycles</subject><subject>Metabolism</subject><subject>Methionine</subject><subject>Niches</subject><subject>Nucleotide sequence</subject><subject>Oligonucleotide Array Sequence Analysis</subject><subject>Oligonucleotides</subject><subject>Oxygen</subject><subject>Oxygen - metabolism</subject><subject>Oxygen - pharmacology</subject><subject>Pathogens</subject><subject>Transcription</subject><subject>Transcriptome</subject><subject>Urease</subject><subject>Urine</subject><subject>Vitamin B12</subject><subject>Yersinia</subject><subject>Yersinia - drug effects</subject><subject>Yersinia - genetics</subject><subject>Yersinia - growth & development</subject><subject>Yersinia Infections - microbiology</subject><subject>Yersinia intermedia</subject><subject>Yersinia pseudotuberculosis</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNkl9rFDEUxQdRbK1-A9EBQezDrskkk0xehGXxz0KhoIvQp3Ank8ymzCbbJGv125u607IDCpKHXG5-9yQ5nKJ4idEcE47fX_t9cDDMd97pOUKc1Yw_Kk6xINWMVYg8PqpPimcxXiNUk4axp8VJRTFmGDenxdU6gIsq2F3yW12qDbhexxJi9MpC0l15a9OmBAc6-Naqsg_-NjesK690iNZZyHXSYau7XL5brJfLSggkzp8XTwwMUb8Y97Ni_enjevlldnH5ebVcXMwUE1WaAeUGsaaueQdIoAq1DaX5g6zFHNV1p7uWYIGxVtDSqibGADcdUwIhQoQhZ8Xrg-xu8FGOpkSJKc2eUFajTKwOROfhWu6C3UL4JT1Y-afhQy8hJKsGLRm0XcO5BoEaioQCYyrGOSEYUdW2PGt9GG_bt_nHSrsUYJiITk-c3cje_5CEiwpVJAu8GQWCv9nrmP7x5JHqIb_KOuOzmNraqOSC8oY0GcOZmv-FyqvTW6tyLIzN_cnA-WQgM0n_TD3sY5Srb1__n738PmXfHrEbDUPaRD_sk_UuTkF6AFXwMQZtHpzDSN6l-t4NeZdqOaY6j706dv1h6D7G5DfR1PCv</recordid><startdate>20131007</startdate><enddate>20131007</enddate><creator>Babujee, Lavanya</creator><creator>Balakrishnan, Venkatesh</creator><creator>Kiley, Patricia J</creator><creator>Glasner, Jeremy D</creator><creator>Perna, Nicole T</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</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>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20131007</creationdate><title>Transcriptome changes associated with anaerobic growth in Yersinia intermedia (ATCC29909)</title><author>Babujee, Lavanya ; Balakrishnan, Venkatesh ; Kiley, Patricia J ; Glasner, Jeremy D ; Perna, Nicole T</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-a47f068557da09020b8441376b17055dedb31911ecab4253ffa7fd6c900339f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Adaptations</topic><topic>Anaerobic conditions</topic><topic>Anaerobiosis</topic><topic>Analysis</topic><topic>Animals</topic><topic>Availability</topic><topic>Biosynthesis</topic><topic>Biotechnology</topic><topic>Chemotaxis</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA microarrays</topic><topic>E coli</topic><topic>Escherichia coli</topic><topic>Fleas</topic><topic>Gene expression</topic><topic>Gene Expression Regulation, Bacterial</topic><topic>Gene Expression Regulation, Developmental</topic><topic>Genes</topic><topic>Genes, Bacterial - genetics</topic><topic>Genetics</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Growth</topic><topic>Heme</topic><topic>Humans</topic><topic>Iron</topic><topic>Life cycles</topic><topic>Metabolism</topic><topic>Methionine</topic><topic>Niches</topic><topic>Nucleotide sequence</topic><topic>Oligonucleotide Array Sequence Analysis</topic><topic>Oligonucleotides</topic><topic>Oxygen</topic><topic>Oxygen - metabolism</topic><topic>Oxygen - pharmacology</topic><topic>Pathogens</topic><topic>Transcription</topic><topic>Transcriptome</topic><topic>Urease</topic><topic>Urine</topic><topic>Vitamin B12</topic><topic>Yersinia</topic><topic>Yersinia - drug effects</topic><topic>Yersinia - genetics</topic><topic>Yersinia - growth & development</topic><topic>Yersinia Infections - microbiology</topic><topic>Yersinia intermedia</topic><topic>Yersinia pseudotuberculosis</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Babujee, Lavanya</creatorcontrib><creatorcontrib>Balakrishnan, Venkatesh</creatorcontrib><creatorcontrib>Kiley, Patricia J</creatorcontrib><creatorcontrib>Glasner, Jeremy D</creatorcontrib><creatorcontrib>Perna, Nicole T</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - 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Cardoso</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Transcriptome changes associated with anaerobic growth in Yersinia intermedia (ATCC29909)</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2013-10-07</date><risdate>2013</risdate><volume>8</volume><issue>10</issue><spage>e76567</spage><pages>e76567-</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The yersiniae (Enterobacteriaceae) occupy a variety of niches, including some in human and flea hosts. Metabolic adaptations of the yersiniae, which contribute to their success in these specialized environments, remain largely unknown. We report results of an investigation of the transcriptome under aerobic and anaerobic conditions for Y. intermedia, a non-pathogenic member of the genus that has been used as a research surrogate for Y. pestis. Y. intermedia shares characteristics of pathogenic yersiniae, but is not known to cause disease in humans. Oxygen restriction is an important environmental stimulus experienced by many bacteria during their life-cycles and greatly influences their survival in specific environments. How oxygen availability affects physiology in the yersiniae is of importance in their life cycles but has not been extensively characterized.
Tiled oligonucleotide arrays based on a draft genome sequence of Y. intermedia were used in transcript profiling experiments to identify genes that change expression in response to oxygen availability during growth in minimal media with glucose. The expression of more than 400 genes, constituting about 10% of the genome, was significantly altered due to oxygen-limitation in early log phase under these conditions. Broad functional categorization indicated that, in addition to genes involved in central metabolism, genes involved in adaptation to stress and genes likely involved with host interactions were affected by oxygen-availability. Notable among these, were genes encoding functions for motility, chemotaxis and biosynthesis of cobalamin, which were up-regulated and those for iron/heme utilization, methionine metabolism and urease, which were down-regulated.
This is the first transcriptome analysis of a non-pathogenic Yersinia spp. and one of few elucidating the global response to oxygen limitation for any of the yersiniae. Thus this study lays the foundation for further experimental characterization of oxygen-responsive genes and pathways in this ecologically diverse genus.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>24116118</pmid><doi>10.1371/journal.pone.0076567</doi><tpages>e76567</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | PloS one, 2013-10, Vol.8 (10), p.e76567 |
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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 | Adaptations Anaerobic conditions Anaerobiosis Analysis Animals Availability Biosynthesis Biotechnology Chemotaxis Deoxyribonucleic acid DNA DNA microarrays E coli Escherichia coli Fleas Gene expression Gene Expression Regulation, Bacterial Gene Expression Regulation, Developmental Genes Genes, Bacterial - genetics Genetics Genomes Genomics Growth Heme Humans Iron Life cycles Metabolism Methionine Niches Nucleotide sequence Oligonucleotide Array Sequence Analysis Oligonucleotides Oxygen Oxygen - metabolism Oxygen - pharmacology Pathogens Transcription Transcriptome Urease Urine Vitamin B12 Yersinia Yersinia - drug effects Yersinia - genetics Yersinia - growth & development Yersinia Infections - microbiology Yersinia intermedia Yersinia pseudotuberculosis |
| title | Transcriptome changes associated with anaerobic growth in Yersinia intermedia (ATCC29909) |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-22T09%3A54%3A32IST&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=Transcriptome%20changes%20associated%20with%20anaerobic%20growth%20in%20Yersinia%20intermedia%20(ATCC29909)&rft.jtitle=PloS%20one&rft.au=Babujee,%20Lavanya&rft.date=2013-10-07&rft.volume=8&rft.issue=10&rft.spage=e76567&rft.pages=e76567-&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0076567&rft_dat=%3Cgale_plos_%3EA478387461%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=1440074650&rft_id=info:pmid/24116118&rft_galeid=A478387461&rft_doaj_id=oai_doaj_org_article_6abd877ea908409caff267733104cbb7&rfr_iscdi=true |