Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities
Identifieur interne : 000597 ( Istex/Corpus ); précédent : 000596; suivant : 000598Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities
Auteurs : Jana Seifert ; Florian-Alexander Herbst ; Per Halkj R Nielsen ; Francisco J. Planes ; Nico Jehmlich ; Manuel Ferrer ; Martin Von BergenSource :
- PROTEOMICS [ 1615-9853 ] ; 2013-10.
Abstract
Metaproteomics of microbial communities promises to add functional information to the blueprint of genes derived from metagenomics. Right from its beginning, the achievements and developments in metaproteomics were closely interlinked with metagenomics. In addition, the evaluation, visualization, and interpretation of metaproteome data demanded for the developments in bioinformatics. This review will give an overview about recent strategies to use genomic data either from public databases or organismal specific genomes/metagenomes to increase the number of identified proteins obtained by mass spectrometric measurements. We will review different published metaproteogenomic approaches in respect to the used MS pipeline and to the used protein identification workflow. Furthermore, different approaches of data visualization and strategies for phylogenetic interpretation of metaproteome data are discussed as well as approaches for functional mapping of the results to the investigated biological systems. This information will in the end allow a comprehensive analysis of interactions and interdependencies within microbial communities.
Url:
DOI: 10.1002/pmic.201200566
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ISTEX:A501858AB58F8ED7DD2BDEBF5EC6F9DD7F97014DLe document en format XML
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KGaA, Weinheim</p></availability><date>2013-05-07</date></publicationStmt><notesStmt><note>European Community Project MAGICPAH - No. FP7‐KBBE‐2009‐245226;</note><note>Deutsche Forschungsgemeinschaft - No. SPP1319; No. FOR 1530;</note><note>Spanish Ministry of Economy and Competitiveness (formerly MICINN) - No. CSD2007‐00005; No. BIO2011‐25012; No. BFU2008‐04501‐E;</note><note>European Community projects MAMBA - No. FP7‐KBBE‐2008‐226977;</note><note>MAGICPAH - No. FP7‐KBBE‐2009‐245226;</note><note>ULIXES - No. FP7‐KBBE‐2010‐266473;</note><note>KILL SPILL - No. FP7‐KBBE‐CALL 6‐312139;</note></notesStmt><sourceDesc><biblStruct type="inbook"><analytic><title level="a" type="main" xml:lang="en">Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities</title><author xml:id="author-1"><persName><forename type="first">Jana</forename><surname>Seifert</surname></persName><affiliation>Department of Proteomics, UFZ—Helmholtz Centre for Environmental Research, Leipzig, Germany</affiliation><affiliation>Institute of Animal Nutrition, University of Hohenheim, Stuttgart, Germany</affiliation></author><author xml:id="author-2"><persName><forename type="first">Florian‐Alexander</forename><surname>Herbst</surname></persName><affiliation>Department of Proteomics, UFZ—Helmholtz Centre for Environmental Research, Leipzig, Germany</affiliation><affiliation>Faculty of Biology, University of Freiburg, Freiburg, Germany</affiliation></author><author xml:id="author-3"><persName><forename type="first">Per</forename><surname>Halkjær Nielsen</surname></persName><affiliation>Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark</affiliation></author><author xml:id="author-4"><persName><forename type="first">Francisco J.</forename><surname>Planes</surname></persName><affiliation>CEIT and TECNUN, University of Navarra, San Sebastian, Spain</affiliation></author><author xml:id="author-5"><persName><forename type="first">Nico</forename><surname>Jehmlich</surname></persName><affiliation>Department of Proteomics, UFZ—Helmholtz Centre for Environmental Research, Leipzig, Germany</affiliation></author><author xml:id="author-6"><persName><forename type="first">Manuel</forename><surname>Ferrer</surname></persName><affiliation>CSIC, Institute of Catalysis, Madrid, Spain</affiliation></author><author xml:id="author-7"><persName><forename type="first">Martin</forename><surname>von Bergen</surname></persName><email>martin.vonbergen@ufz.de</email><affiliation>Department of Proteomics, UFZ—Helmholtz Centre for Environmental Research, Leipzig, Germany</affiliation><affiliation>Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark</affiliation><affiliation>Department of Metabolomics, UFZ—Helmholtz Centre for Environmental Research, Leipzig, Germany</affiliation><affiliation>Dr. Martin von Bergen, Department of Proteomics, UFZ—Helmholtz Centre for Environmental Research, Permoserstrasse 15, D‐04318 Leipzig, Germany +49‐235‐454485</affiliation></author></analytic><monogr><title level="j">PROTEOMICS</title><title level="j" type="abbrev">Proteomics</title><idno type="pISSN">1615-9853</idno><idno type="eISSN">1615-9861</idno><idno type="DOI">10.1002/(ISSN)1615-9861</idno><editor><persName><forename type="first">Ralf</forename><surname>Rabus</surname></persName></editor><imprint><publisher>Blackwell Publishing Ltd</publisher><date type="published" when="2013-10"></date><biblScope unit="volume">13</biblScope><biblScope unit="issue">18-19</biblScope><biblScope unit="page" from="2786">2786</biblScope><biblScope unit="page" to="2804">2804</biblScope></imprint></monogr><idno type="istex">A501858AB58F8ED7DD2BDEBF5EC6F9DD7F97014D</idno><idno type="DOI">10.1002/pmic.201200566</idno><idno type="ArticleID">PMIC7460</idno></biblStruct></sourceDesc></fileDesc><profileDesc><creation><date>2013-05-07</date></creation><langUsage><language ident="en">en</language></langUsage><abstract><p>Metaproteomics of microbial communities promises to add functional information to the blueprint of genes derived from metagenomics. 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KGaA, Weinheim</copyright><eventGroup><event type="manuscriptReceived" date="2012-12-17"></event><event type="manuscriptRevised" date="2013-03-07"></event><event type="manuscriptAccepted" date="2013-03-28"></event><event type="xmlCreated" agent="Aptara" date="2013-05-07"></event><event type="publishedOnlineAccepted" date="2013-04-27"></event><event type="publishedOnlineEarlyUnpaginated" date="2013-08-07"></event><event type="firstOnline" date="2013-08-07"></event><event type="publishedOnlineFinalForm" date="2013-10-01"></event><event type="xmlConverted" agent="Converter:WILEY_ML3G_TO_WILEY_ML3GV2 version:4.0.1" date="2014-03-20"></event><event type="xmlConverted" agent="Converter:WML3G_To_WML3G version:4.6.4 mode:FullText" date="2015-10-02"></event></eventGroup><numberingGroup><numbering type="pageFirst">2786</numbering><numbering type="pageLast">2804</numbering></numberingGroup><correspondenceTo><lineatedText><line><b>Correspondence:</b> Dr. Martin von Bergen, Department of Proteomics, UFZ—Helmholtz Centre for Environmental Research, Permoserstrasse 15, D‐04318 Leipzig, Germany</line><line><b>E‐mail:</b> <email>martin.vonbergen@ufz.de</email></line><line><b>Fax:</b> +49‐235‐454485</line></lineatedText></correspondenceTo><linkGroup><link type="toTypesetVersion" href="file:PMIC.PMIC7460.pdf"></link></linkGroup></publicationMeta><contentMeta><titleGroup><title type="main">Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities</title><title type="shortAuthors">J. Seifert et al.</title></titleGroup><creators><creator xml:id="pmic7460-cr-0001" creatorRole="author" affiliationRef="#pmic7460-aff-0001 #pmic7460-aff-0002"><personName><givenNames>Jana</givenNames><familyName>Seifert</familyName></personName></creator><creator xml:id="pmic7460-cr-0002" creatorRole="author" affiliationRef="#pmic7460-aff-0001 #pmic7460-aff-0003"><personName><givenNames>Florian‐Alexander</givenNames><familyName>Herbst</familyName></personName></creator><creator xml:id="pmic7460-cr-0003" creatorRole="author" affiliationRef="#pmic7460-aff-0004"><personName><givenNames>Per</givenNames><familyName>Halkjær Nielsen</familyName></personName></creator><creator xml:id="pmic7460-cr-0004" creatorRole="author" affiliationRef="#pmic7460-aff-0005"><personName><givenNames>Francisco J.</givenNames><familyName>Planes</familyName></personName></creator><creator xml:id="pmic7460-cr-0005" creatorRole="author" affiliationRef="#pmic7460-aff-0001"><personName><givenNames>Nico</givenNames><familyName>Jehmlich</familyName></personName></creator><creator xml:id="pmic7460-cr-0006" creatorRole="author" affiliationRef="#pmic7460-aff-0006"><personName><givenNames>Manuel</givenNames><familyName>Ferrer</familyName></personName></creator><creator xml:id="pmic7460-cr-0007" creatorRole="author" affiliationRef="#pmic7460-aff-0001 #pmic7460-aff-0004 #pmic7460-aff-0007" corresponding="yes"><personName><givenNames>Martin</givenNames><familyNamePrefix>von</familyNamePrefix><familyName>Bergen</familyName></personName></creator></creators><affiliationGroup><affiliation xml:id="pmic7460-aff-0001" countryCode="DE"><orgDiv>Department of Proteomics</orgDiv><orgName>UFZ—Helmholtz Centre for Environmental Research</orgName><address><city>Leipzig</city><country>Germany</country></address></affiliation><affiliation xml:id="pmic7460-aff-0002" countryCode="DE"><orgDiv>Institute of Animal Nutrition</orgDiv><orgName>University of Hohenheim</orgName><address><city>Stuttgart</city><country>Germany</country></address></affiliation><affiliation xml:id="pmic7460-aff-0003" countryCode="DE"><orgDiv>Faculty of Biology</orgDiv><orgName>University of Freiburg</orgName><address><city>Freiburg</city><country>Germany</country></address></affiliation><affiliation xml:id="pmic7460-aff-0004" countryCode="DK"><orgDiv>Department of Biotechnology</orgDiv><orgDiv>Chemistry and Environmental Engineering</orgDiv><orgName>Aalborg University</orgName><address><city>Aalborg</city><country>Denmark</country></address></affiliation><affiliation xml:id="pmic7460-aff-0005" countryCode="ES"><orgDiv>CEIT and TECNUN</orgDiv><orgName>University of Navarra</orgName><address><city>San Sebastian</city><country>Spain</country></address></affiliation><affiliation xml:id="pmic7460-aff-0006" countryCode="ES"><orgName>CSIC, Institute of Catalysis</orgName><address><city>Madrid</city><country>Spain</country></address></affiliation><affiliation xml:id="pmic7460-aff-0007" countryCode="DE"><orgDiv>Department of Metabolomics</orgDiv><orgName>UFZ—Helmholtz Centre for Environmental Research</orgName><address><city>Leipzig</city><country>Germany</country></address></affiliation></affiliationGroup><keywordGroup type="author"><keyword xml:id="pmic7460-kwd-0001">Bioinformatics</keyword><keyword xml:id="pmic7460-kwd-0002">Data mining</keyword><keyword xml:id="pmic7460-kwd-0003">High‐throughput proteomics</keyword><keyword xml:id="pmic7460-kwd-0004">Microbiology</keyword></keywordGroup><fundingInfo><fundingAgency>European Community Project MAGICPAH</fundingAgency><fundingNumber>FP7‐KBBE‐2009‐245226</fundingNumber></fundingInfo><fundingInfo><fundingAgency>Deutsche Forschungsgemeinschaft</fundingAgency><fundingNumber>SPP1319</fundingNumber><fundingNumber>FOR 1530</fundingNumber></fundingInfo><fundingInfo><fundingAgency>Spanish Ministry of Economy and Competitiveness (formerly MICINN)</fundingAgency><fundingNumber>CSD2007‐00005</fundingNumber><fundingNumber>BIO2011‐25012</fundingNumber><fundingNumber>BFU2008‐04501‐E</fundingNumber></fundingInfo><fundingInfo><fundingAgency>European Community projects MAMBA</fundingAgency><fundingNumber>FP7‐KBBE‐2008‐226977</fundingNumber></fundingInfo><fundingInfo><fundingAgency>MAGICPAH</fundingAgency><fundingNumber>FP7‐KBBE‐2009‐245226</fundingNumber></fundingInfo><fundingInfo><fundingAgency>ULIXES</fundingAgency><fundingNumber>FP7‐KBBE‐2010‐266473</fundingNumber></fundingInfo><fundingInfo><fundingAgency>KILL SPILL</fundingAgency><fundingNumber>FP7‐KBBE‐CALL 6‐312139</fundingNumber></fundingInfo><abstractGroup><abstract type="main"><p>Metaproteomics of microbial communities promises to add functional information to the blueprint of genes derived from metagenomics. Right from its beginning, the achievements and developments in metaproteomics were closely interlinked with metagenomics. In addition, the evaluation, visualization, and interpretation of metaproteome data demanded for the developments in bioinformatics. This review will give an overview about recent strategies to use genomic data either from public databases or organismal specific genomes/metagenomes to increase the number of identified proteins obtained by mass spectrometric measurements. We will review different published metaproteogenomic approaches in respect to the used <fc>MS</fc> pipeline and to the used protein identification workflow. Furthermore, different approaches of data visualization and strategies for phylogenetic interpretation of metaproteome data are discussed as well as approaches for functional mapping of the results to the investigated biological systems. This information will in the end allow a comprehensive analysis of interactions and interdependencies within microbial communities.</p></abstract></abstractGroup></contentMeta><noteGroup><note xml:id="pmic7460-note-0001" numbered="no"><p><b>Colour Online:</b> See the article online to view Figs. 1, 2, 4 and 6 in colour.</p></note></noteGroup></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities</title></titleInfo><name type="personal"><namePart type="given">Jana</namePart><namePart type="family">Seifert</namePart><affiliation>Department of Proteomics, UFZ—Helmholtz Centre for Environmental Research, Leipzig, Germany</affiliation><affiliation>Institute of Animal Nutrition, University of Hohenheim, Stuttgart, Germany</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Florian‐Alexander</namePart><namePart type="family">Herbst</namePart><affiliation>Department of Proteomics, UFZ—Helmholtz Centre for Environmental Research, Leipzig, Germany</affiliation><affiliation>Faculty of Biology, University of Freiburg, Freiburg, Germany</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Per</namePart><namePart type="family">Halkjær Nielsen</namePart><affiliation>Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Francisco J.</namePart><namePart type="family">Planes</namePart><affiliation>CEIT and TECNUN, University of Navarra, San Sebastian, Spain</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Nico</namePart><namePart type="family">Jehmlich</namePart><affiliation>Department of Proteomics, UFZ—Helmholtz Centre for Environmental Research, Leipzig, Germany</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Manuel</namePart><namePart type="family">Ferrer</namePart><affiliation>CSIC, Institute of Catalysis, Madrid, Spain</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Martin</namePart><namePart type="family">von Bergen</namePart><affiliation>Department of Proteomics, UFZ—Helmholtz Centre for Environmental Research, Leipzig, Germany</affiliation><affiliation>Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark</affiliation><affiliation>Department of Metabolomics, UFZ—Helmholtz Centre for Environmental Research, Leipzig, Germany</affiliation><affiliation>Dr. Martin von Bergen, Department of Proteomics, UFZ—Helmholtz Centre for Environmental Research, Permoserstrasse 15, D‐04318 Leipzig, Germany +49‐235‐454485</affiliation><affiliation>E-mail: martin.vonbergen@ufz.de</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="review-article" displayLabel="reviewArticle"></genre><originInfo><publisher>Blackwell Publishing Ltd</publisher><dateIssued encoding="w3cdtf">2013-10</dateIssued><dateCreated encoding="w3cdtf">2013-05-07</dateCreated><dateCaptured encoding="w3cdtf">2012-12-17</dateCaptured><dateValid encoding="w3cdtf">2013-03-28</dateValid><copyrightDate encoding="w3cdtf">2013</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><physicalDescription><internetMediaType>text/html</internetMediaType></physicalDescription><abstract>Metaproteomics of microbial communities promises to add functional information to the blueprint of genes derived from metagenomics. Right from its beginning, the achievements and developments in metaproteomics were closely interlinked with metagenomics. In addition, the evaluation, visualization, and interpretation of metaproteome data demanded for the developments in bioinformatics. This review will give an overview about recent strategies to use genomic data either from public databases or organismal specific genomes/metagenomes to increase the number of identified proteins obtained by mass spectrometric measurements. We will review different published metaproteogenomic approaches in respect to the used MS pipeline and to the used protein identification workflow. Furthermore, different approaches of data visualization and strategies for phylogenetic interpretation of metaproteome data are discussed as well as approaches for functional mapping of the results to the investigated biological systems. This information will in the end allow a comprehensive analysis of interactions and interdependencies within microbial communities.</abstract><note type="funding">European Community Project MAGICPAH - No. FP7‐KBBE‐2009‐245226; </note><note type="funding">Deutsche Forschungsgemeinschaft - No. SPP1319; No. FOR 1530; </note><note type="funding">Spanish Ministry of Economy and Competitiveness (formerly MICINN) - No. CSD2007‐00005; No. BIO2011‐25012; No. BFU2008‐04501‐E; </note><note type="funding">European Community projects MAMBA - No. FP7‐KBBE‐2008‐226977; </note><note type="funding">MAGICPAH - No. FP7‐KBBE‐2009‐245226; </note><note type="funding">ULIXES - No. FP7‐KBBE‐2010‐266473; </note><note type="funding">KILL SPILL - No. FP7‐KBBE‐CALL 6‐312139; </note><subject><genre>keywords</genre><topic>Bioinformatics</topic><topic>Data mining</topic><topic>High‐throughput proteomics</topic><topic>Microbiology</topic></subject><relatedItem type="host"><titleInfo><title>PROTEOMICS</title></titleInfo><titleInfo type="abbreviated"><title>Proteomics</title></titleInfo><name type="personal"><namePart type="given">Ralf</namePart><namePart type="family">Rabus</namePart><role><roleTerm type="text">editor</roleTerm></role></name><genre type="journal">journal</genre><subject><genre>article-category</genre><topic>Review</topic></subject><identifier type="ISSN">1615-9853</identifier><identifier type="eISSN">1615-9861</identifier><identifier type="DOI">10.1002/(ISSN)1615-9861</identifier><identifier type="PublisherID">PMIC</identifier><part><date>2013</date><detail type="title"><title>Environmental Microbial Proteomics</title></detail><detail type="volume"><caption>vol.</caption><number>13</number></detail><detail type="issue"><caption>no.</caption><number>18-19</number></detail><extent unit="pages"><start>2786</start><end>2804</end><total>19</total></extent></part></relatedItem><identifier type="istex">A501858AB58F8ED7DD2BDEBF5EC6F9DD7F97014D</identifier><identifier type="DOI">10.1002/pmic.201200566</identifier><identifier type="ArticleID">PMIC7460</identifier><accessCondition type="use and reproduction" contentType="copyright">© 2013 WILEY‐VCH Verlag GmbH & Co. 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