Community Proteomics of a Natural Microbial Biofilm
Using genomic and mass spectrometry-based proteomic methods, we evaluated gene expression, identified key activities, and examined partitioning of metabolic functions in a natural acid mine drainage (AMD) microbial biofilm community. We detected 2033 proteins from the five most abundant species in t...
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| Veröffentlicht in: | Science (American Association for the Advancement of Science) 2005-06, Vol.308 (5730), p.1915-1920 |
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| container_title | Science (American Association for the Advancement of Science) |
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| creator | Ram, Rachna J VerBerkmoes, Nathan C Thelen, Michael P Tyson, Gene W Baker, Brett J Blake, Robert C Shah, Manesh Hettich, Robert L Banfield, Jillian F |
| description | Using genomic and mass spectrometry-based proteomic methods, we evaluated gene expression, identified key activities, and examined partitioning of metabolic functions in a natural acid mine drainage (AMD) microbial biofilm community. We detected 2033 proteins from the five most abundant species in the biofilm, including 48% of the predicted proteins from the dominant biofilm organism, Leptospirillum group II. Proteins involved in protein refolding and response to oxidative stress appeared to be highly expressed, which suggests that damage to biomolecules is a key challenge for survival. We validated and estimated the relative abundance and cellular localization of 357 unique and 215 conserved novel proteins and determined that one abundant novel protein is a cytochrome central to iron oxidation and AMD formation. |
| doi_str_mv | 10.1126/science.1109070 |
| format | Article |
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We validated and estimated the relative abundance and cellular localization of 357 unique and 215 conserved novel proteins and determined that one abundant novel protein is a cytochrome central to iron oxidation and AMD formation.</description><identifier>ISSN: 0036-8075</identifier><identifier>ISSN: 0193-4511</identifier><identifier>EISSN: 1095-9203</identifier><identifier>DOI: 10.1126/science.1109070</identifier><identifier>PMID: 15879173</identifier><identifier>CODEN: SCIEAS</identifier><language>eng</language><publisher>Washington, DC: American Association for the Advancement of Science</publisher><subject>ABUNDANCE ; ACID MINE DRAINAGE ; Algorithms ; Amino acids ; Amino Acids - metabolism ; Analysis ; Animal, plant and microbial ecology ; Archaeal Proteins - analysis ; Archaeal Proteins - chemistry ; Bacteria - chemistry ; Bacteria - genetics ; Bacteria - metabolism ; Bacterial Proteins - analysis ; Bacterial Proteins - chemistry ; Bacterial Proteins - genetics ; Bacterial Proteins - physiology ; BASIC BIOLOGICAL SCIENCES ; Biofilms ; Biofilms - growth & development ; Biological and medical sciences ; Community Relations ; CYTOCHROMES ; Cytochromes - analysis ; Cytochromes - chemistry ; Ecosystem ; Environment ; ENVIRONMENTAL SCIENCES ; Fractions ; Freshwater ; Fundamental and applied biological sciences. Psychology ; Gene Expression ; GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE ; GENES ; Genes, Archaeal ; Genes, Bacterial ; Genetic aspects ; Genome, Archaeal ; Genome, Bacterial ; Genomes ; Genomics ; Hydrogen-Ion Concentration ; IRON ; Iron - metabolism ; Isoelectric Point ; Mass Spectrometry ; Microbial ecology ; Microbial mats ; Mining ; Molecular Sequence Data ; Operons ; OXIDATION ; Oxidation-Reduction ; Protein Biosynthesis ; Protein Folding ; Protein metabolism ; PROTEINS ; Proteome ; Proteomes ; Proteomics ; Structure ; Thermoplasmales - chemistry ; Thermoplasmales - genetics ; Thermoplasmales - metabolism ; Various environments (extraatmospheric space, air, water)</subject><ispartof>Science (American Association for the Advancement of Science), 2005-06, Vol.308 (5730), p.1915-1920</ispartof><rights>Copyright 2005 American Association for the Advancement of Science</rights><rights>2005 INIST-CNRS</rights><rights>COPYRIGHT 2005 American Association for the Advancement of Science</rights><rights>Copyright American Association for the Advancement of Science Jun 24, 2005</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c830t-bab83857b682337e53e3dbe8bc046c11abd9e41422d464ffd97b3c9be7a5f6663</citedby><cites>FETCH-LOGICAL-c830t-bab83857b682337e53e3dbe8bc046c11abd9e41422d464ffd97b3c9be7a5f6663</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/3841454$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/3841454$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>314,776,780,799,881,2871,2872,27901,27902,57992,58225</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=16898839$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/15879173$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/biblio/978041$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Ram, Rachna J</creatorcontrib><creatorcontrib>VerBerkmoes, Nathan C</creatorcontrib><creatorcontrib>Thelen, Michael P</creatorcontrib><creatorcontrib>Tyson, Gene W</creatorcontrib><creatorcontrib>Baker, Brett J</creatorcontrib><creatorcontrib>Blake, Robert C</creatorcontrib><creatorcontrib>Shah, Manesh</creatorcontrib><creatorcontrib>Hettich, Robert L</creatorcontrib><creatorcontrib>Banfield, Jillian F</creatorcontrib><creatorcontrib>Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)</creatorcontrib><title>Community Proteomics of a Natural Microbial Biofilm</title><title>Science (American Association for the Advancement of Science)</title><addtitle>Science</addtitle><description>Using genomic and mass spectrometry-based proteomic methods, we evaluated gene expression, identified key activities, and examined partitioning of metabolic functions in a natural acid mine drainage (AMD) microbial biofilm community. We detected 2033 proteins from the five most abundant species in the biofilm, including 48% of the predicted proteins from the dominant biofilm organism, Leptospirillum group II. Proteins involved in protein refolding and response to oxidative stress appeared to be highly expressed, which suggests that damage to biomolecules is a key challenge for survival. We validated and estimated the relative abundance and cellular localization of 357 unique and 215 conserved novel proteins and determined that one abundant novel protein is a cytochrome central to iron oxidation and AMD formation.</description><subject>ABUNDANCE</subject><subject>ACID MINE DRAINAGE</subject><subject>Algorithms</subject><subject>Amino acids</subject><subject>Amino Acids - metabolism</subject><subject>Analysis</subject><subject>Animal, plant and microbial ecology</subject><subject>Archaeal Proteins - analysis</subject><subject>Archaeal Proteins - chemistry</subject><subject>Bacteria - chemistry</subject><subject>Bacteria - genetics</subject><subject>Bacteria - metabolism</subject><subject>Bacterial Proteins - analysis</subject><subject>Bacterial Proteins - chemistry</subject><subject>Bacterial Proteins - genetics</subject><subject>Bacterial Proteins - physiology</subject><subject>BASIC BIOLOGICAL SCIENCES</subject><subject>Biofilms</subject><subject>Biofilms - growth & development</subject><subject>Biological and medical sciences</subject><subject>Community Relations</subject><subject>CYTOCHROMES</subject><subject>Cytochromes - analysis</subject><subject>Cytochromes - chemistry</subject><subject>Ecosystem</subject><subject>Environment</subject><subject>ENVIRONMENTAL SCIENCES</subject><subject>Fractions</subject><subject>Freshwater</subject><subject>Fundamental and applied biological sciences. 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chemistry</subject><subject>Thermoplasmales - genetics</subject><subject>Thermoplasmales - metabolism</subject><subject>Various environments (extraatmospheric space, air, water)</subject><issn>0036-8075</issn><issn>0193-4511</issn><issn>1095-9203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>BEC</sourceid><sourceid>BENPR</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNqN081v0zAUAPAIgVgZnLkgKCCQOGSz48Qfx62CMqmsSGNcLcd5Ka6SeLMdif33c5eIqqiCKofY8u89yc_vJclLjE4wzuip1wY6DXGDBGLoUTKJiyIVGSKPkwlChKYcseIoeeb9GqF4JsjT5AgXnAnMyCQhM9u2fWfC3fS7swFsa7Sf2nqqppcq9E41029GO1uauDo3tjZN-zx5UqvGw4vxf5xcf_n8Y_Y1XSznF7OzRao5QSEtVckJL1hJeUYIg4IAqUrgpUY51RirshKQ4zzLqpzmdV0JVhItSmCqqCml5Dh5O-S1PhgZrxpA_9K260AHKRhHOY7m42BunL3twQfZGq-haVQHtveSMkELVuT_hZhRzDMuInz3F1zb3nXxojLDhGJWIBbR-wGtVAPSdLUNTulNRnmGCeE0RzSLKt2jVtBBrKvtIBYTdv3JHh-_CuKz7A34tBMQTYDfYaV67-XF1eXhdvnzcHs-P9jy-eJfBRmttk0DK5Cxe2bLXY8GHzvQewe1vHGmVe5OYiQ3AyDHAZBynIAYcnpgyDbi9fjgfdlCtfXjkETwYQTKa9XUTnXa-K2jXHBONp3zanBrH6z7c054bPKHDnwzHNfKSrVyMcX1VYYwQRghimKKe7AOKDI</recordid><startdate>20050624</startdate><enddate>20050624</enddate><creator>Ram, Rachna J</creator><creator>VerBerkmoes, Nathan C</creator><creator>Thelen, Michael P</creator><creator>Tyson, Gene W</creator><creator>Baker, Brett J</creator><creator>Blake, Robert C</creator><creator>Shah, Manesh</creator><creator>Hettich, Robert L</creator><creator>Banfield, Jillian F</creator><general>American Association for the Advancement of Science</general><general>The American Association for the Advancement of Science</general><scope>FBQ</scope><scope>IQODW</scope><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>8GL</scope><scope>IBG</scope><scope>IOV</scope><scope>ISN</scope><scope>0-V</scope><scope>3V.</scope><scope>7QF</scope><scope>7QG</scope><scope>7QL</scope><scope>7QP</scope><scope>7QQ</scope><scope>7QR</scope><scope>7SC</scope><scope>7SE</scope><scope>7SN</scope><scope>7SP</scope><scope>7SR</scope><scope>7SS</scope><scope>7T7</scope><scope>7TA</scope><scope>7TB</scope><scope>7TK</scope><scope>7TM</scope><scope>7U5</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88B</scope><scope>88E</scope><scope>88I</scope><scope>8AF</scope><scope>8BQ</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ALSLI</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BEC</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>BKSAR</scope><scope>C1K</scope><scope>CCPQU</scope><scope>CJNVE</scope><scope>D1I</scope><scope>DWQXO</scope><scope>F28</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>H8D</scope><scope>H8G</scope><scope>H94</scope><scope>HCIFZ</scope><scope>JG9</scope><scope>JQ2</scope><scope>K9-</scope><scope>K9.</scope><scope>KB.</scope><scope>KR7</scope><scope>L6V</scope><scope>L7M</scope><scope>LK8</scope><scope>L~C</scope><scope>L~D</scope><scope>M0K</scope><scope>M0P</scope><scope>M0R</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>M2P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>MBDVC</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PCBAR</scope><scope>PDBOC</scope><scope>PQEDU</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>Q9U</scope><scope>R05</scope><scope>RC3</scope><scope>F1W</scope><scope>H95</scope><scope>H97</scope><scope>L.G</scope><scope>7X8</scope><scope>OTOTI</scope></search><sort><creationdate>20050624</creationdate><title>Community Proteomics of a Natural Microbial Biofilm</title><author>Ram, Rachna J ; VerBerkmoes, Nathan C ; Thelen, Michael P ; Tyson, Gene W ; Baker, Brett J ; Blake, Robert C ; Shah, Manesh ; Hettich, Robert L ; Banfield, Jillian F</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c830t-bab83857b682337e53e3dbe8bc046c11abd9e41422d464ffd97b3c9be7a5f6663</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2005</creationdate><topic>ABUNDANCE</topic><topic>ACID MINE DRAINAGE</topic><topic>Algorithms</topic><topic>Amino acids</topic><topic>Amino Acids - 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(ORNL), Oak Ridge, TN (United States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Community Proteomics of a Natural Microbial Biofilm</atitle><jtitle>Science (American Association for the Advancement of Science)</jtitle><addtitle>Science</addtitle><date>2005-06-24</date><risdate>2005</risdate><volume>308</volume><issue>5730</issue><spage>1915</spage><epage>1920</epage><pages>1915-1920</pages><issn>0036-8075</issn><issn>0193-4511</issn><eissn>1095-9203</eissn><coden>SCIEAS</coden><abstract>Using genomic and mass spectrometry-based proteomic methods, we evaluated gene expression, identified key activities, and examined partitioning of metabolic functions in a natural acid mine drainage (AMD) microbial biofilm community. We detected 2033 proteins from the five most abundant species in the biofilm, including 48% of the predicted proteins from the dominant biofilm organism, Leptospirillum group II. Proteins involved in protein refolding and response to oxidative stress appeared to be highly expressed, which suggests that damage to biomolecules is a key challenge for survival. We validated and estimated the relative abundance and cellular localization of 357 unique and 215 conserved novel proteins and determined that one abundant novel protein is a cytochrome central to iron oxidation and AMD formation.</abstract><cop>Washington, DC</cop><pub>American Association for the Advancement of Science</pub><pmid>15879173</pmid><doi>10.1126/science.1109070</doi><tpages>6</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0036-8075 |
| ispartof | Science (American Association for the Advancement of Science), 2005-06, Vol.308 (5730), p.1915-1920 |
| issn | 0036-8075 0193-4511 1095-9203 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_67965754 |
| source | Jstor Complete Legacy; MEDLINE; Science Magazine |
| subjects | ABUNDANCE ACID MINE DRAINAGE Algorithms Amino acids Amino Acids - metabolism Analysis Animal, plant and microbial ecology Archaeal Proteins - analysis Archaeal Proteins - chemistry Bacteria - chemistry Bacteria - genetics Bacteria - metabolism Bacterial Proteins - analysis Bacterial Proteins - chemistry Bacterial Proteins - genetics Bacterial Proteins - physiology BASIC BIOLOGICAL SCIENCES Biofilms Biofilms - growth & development Biological and medical sciences Community Relations CYTOCHROMES Cytochromes - analysis Cytochromes - chemistry Ecosystem Environment ENVIRONMENTAL SCIENCES Fractions Freshwater Fundamental and applied biological sciences. Psychology Gene Expression GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE GENES Genes, Archaeal Genes, Bacterial Genetic aspects Genome, Archaeal Genome, Bacterial Genomes Genomics Hydrogen-Ion Concentration IRON Iron - metabolism Isoelectric Point Mass Spectrometry Microbial ecology Microbial mats Mining Molecular Sequence Data Operons OXIDATION Oxidation-Reduction Protein Biosynthesis Protein Folding Protein metabolism PROTEINS Proteome Proteomes Proteomics Structure Thermoplasmales - chemistry Thermoplasmales - genetics Thermoplasmales - metabolism Various environments (extraatmospheric space, air, water) |
| title | Community Proteomics of a Natural Microbial Biofilm |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-02T17%3A33%3A57IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_osti_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Community%20Proteomics%20of%20a%20Natural%20Microbial%20Biofilm&rft.jtitle=Science%20(American%20Association%20for%20the%20Advancement%20of%20Science)&rft.au=Ram,%20Rachna%20J&rft.aucorp=Oak%20Ridge%20National%20Lab.%20(ORNL),%20Oak%20Ridge,%20TN%20(United%20States)&rft.date=2005-06-24&rft.volume=308&rft.issue=5730&rft.spage=1915&rft.epage=1920&rft.pages=1915-1920&rft.issn=0036-8075&rft.eissn=1095-9203&rft.coden=SCIEAS&rft_id=info:doi/10.1126/science.1109070&rft_dat=%3Cgale_osti_%3EA133864062%3C/gale_osti_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=213617507&rft_id=info:pmid/15879173&rft_galeid=A133864062&rft_jstor_id=3841454&rfr_iscdi=true |