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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<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>
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<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>
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<creators><creator xml:id="pmic7460-cr-0001" creatorRole="author" affiliationRef="#pmic7460-aff-0001 #pmic7460-aff-0002"><personName><givenNames>Jana</givenNames>
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<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>
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<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>
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<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>
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<affiliation xml:id="pmic7460-aff-0005" countryCode="ES"><orgDiv>CEIT and TECNUN</orgDiv>
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<affiliation xml:id="pmic7460-aff-0006" countryCode="ES"><orgName>CSIC, Institute of Catalysis</orgName>
<address><city>Madrid</city>
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<fundingInfo><fundingAgency>European Community Project MAGICPAH</fundingAgency>
<fundingNumber>FP7‐KBBE‐2009‐245226</fundingNumber>
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<fundingNumber>SPP1319</fundingNumber>
<fundingNumber>FOR 1530</fundingNumber>
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<fundingInfo><fundingAgency>Spanish Ministry of Economy and Competitiveness (formerly MICINN)</fundingAgency>
<fundingNumber>CSD2007‐00005</fundingNumber>
<fundingNumber>BIO2011‐25012</fundingNumber>
<fundingNumber>BFU2008‐04501‐E</fundingNumber>
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<fundingInfo><fundingAgency>European Community projects MAMBA</fundingAgency>
<fundingNumber>FP7‐KBBE‐2008‐226977</fundingNumber>
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<fundingInfo><fundingAgency>MAGICPAH</fundingAgency>
<fundingNumber>FP7‐KBBE‐2009‐245226</fundingNumber>
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<fundingInfo><fundingAgency>ULIXES</fundingAgency>
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<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>
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<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>
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<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>
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<part><date>2013</date>
<detail type="title"><title>Environmental Microbial Proteomics</title>
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<detail type="volume"><caption>vol.</caption>
<number>13</number>
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<detail type="issue"><caption>no.</caption>
<number>18-19</number>
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