Rhodopseudomonas palustris CGA010 Proteome Implicates Extracytoplasmic Function Sigma Factor in Stress Response
Rhodopseudomonas palustris encodes 16 extracytoplasmic function (ECF) σ factors. To begin to investigate the regulatory network of one of these ECF σ factors, the whole proteome of R. palustris CGA010 was quantitatively analyzed by tandem mass spectrometry from cultures episomally expressing the ECF...
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| Veröffentlicht in: | Journal of proteome research 2015-05, Vol.14 (5), p.2158-2168 |
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| creator | Allen, Michael S Hurst, Gregory B Lu, Tse-Yuan S Perry, Leslie M Pan, Chongle Lankford, Patricia K Pelletier, Dale A |
| description | Rhodopseudomonas palustris encodes 16 extracytoplasmic function (ECF) σ factors. To begin to investigate the regulatory network of one of these ECF σ factors, the whole proteome of R. palustris CGA010 was quantitatively analyzed by tandem mass spectrometry from cultures episomally expressing the ECF σRPA4225 (ecfT) versus a WT control. Among the proteins with the greatest increase in abundance were catalase KatE, trehalose synthase, a DPS-like protein, and several regulatory proteins. Alignment of the cognate promoter regions driving expression of several upregulated proteins suggested a conserved binding motif in the −35 and −10 regions with the consensus sequence GGAAC-18N-TT. Additionally, the putative anti-σ factor RPA4224, whose gene is contained in the same predicted operon as RPA4225, was identified as interacting directly with the predicted response regulator RPA4223 by mass spectrometry of affinity-isolated protein complexes. Furthermore, another gene (RPA4226) coding for a protein that contains a cytoplasmic histidine kinase domain is located immediately upstream of RPA4225. The genomic organization of orthologs for these four genes is conserved in several other strains of R. palustris as well as in closely related α-Proteobacteria. Taken together, these data suggest that ECF σRPA4225 and the three additional genes make up a sigma factor mimicry system in R. palustris. |
| doi_str_mv | 10.1021/pr5012558 |
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To begin to investigate the regulatory network of one of these ECF σ factors, the whole proteome of R. palustris CGA010 was quantitatively analyzed by tandem mass spectrometry from cultures episomally expressing the ECF σRPA4225 (ecfT) versus a WT control. Among the proteins with the greatest increase in abundance were catalase KatE, trehalose synthase, a DPS-like protein, and several regulatory proteins. Alignment of the cognate promoter regions driving expression of several upregulated proteins suggested a conserved binding motif in the −35 and −10 regions with the consensus sequence GGAAC-18N-TT. Additionally, the putative anti-σ factor RPA4224, whose gene is contained in the same predicted operon as RPA4225, was identified as interacting directly with the predicted response regulator RPA4223 by mass spectrometry of affinity-isolated protein complexes. Furthermore, another gene (RPA4226) coding for a protein that contains a cytoplasmic histidine kinase domain is located immediately upstream of RPA4225. The genomic organization of orthologs for these four genes is conserved in several other strains of R. palustris as well as in closely related α-Proteobacteria. Taken together, these data suggest that ECF σRPA4225 and the three additional genes make up a sigma factor mimicry system in R. palustris.</description><identifier>ISSN: 1535-3893</identifier><identifier>EISSN: 1535-3907</identifier><identifier>DOI: 10.1021/pr5012558</identifier><identifier>PMID: 25853567</identifier><language>eng</language><publisher>United States: American Chemical Society</publisher><subject>Bacterial Proteins - genetics ; Bacterial Proteins - isolation & purification ; Bacterial Proteins - metabolism ; BASIC BIOLOGICAL SCIENCES ; Binding Sites ; Catalase - genetics ; Catalase - metabolism ; Chromatography, Liquid ; Conserved Sequence ; DNA, Bacterial - genetics ; DNA, Bacterial - metabolism ; ECF σ factor ; Gene Expression Regulation, Bacterial ; gene regulation ; Glucosyltransferases - genetics ; Glucosyltransferases - metabolism ; Molecular Sequence Data ; Nucleotide Motifs ; Operon ; Promoter Regions, Genetic ; Protein Binding ; Protein Isoforms - genetics ; Protein Isoforms - metabolism ; Proteome - genetics ; Proteome - isolation & purification ; Proteome - metabolism ; proteomics ; Rhodopseudomonas - genetics ; Rhodopseudomonas - metabolism ; Rhodopseudomonas palustris ; Sequence Alignment ; Sigma Factor - genetics ; Sigma Factor - isolation & purification ; Sigma Factor - metabolism ; stress ; Stress, Physiological - genetics ; Tandem Mass Spectrometry ; Transcription, Genetic</subject><ispartof>Journal of proteome research, 2015-05, Vol.14 (5), p.2158-2168</ispartof><rights>Copyright © American Chemical Society</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a377t-95d239c506eb479b7e97243fd50e9e25e1b7b3183e8a37c8cb2160768961c4793</citedby><cites>FETCH-LOGICAL-a377t-95d239c506eb479b7e97243fd50e9e25e1b7b3183e8a37c8cb2160768961c4793</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://pubs.acs.org/doi/pdf/10.1021/pr5012558$$EPDF$$P50$$Gacs$$H</linktopdf><linktohtml>$$Uhttps://pubs.acs.org/doi/10.1021/pr5012558$$EHTML$$P50$$Gacs$$H</linktohtml><link.rule.ids>230,314,776,780,881,2752,27053,27901,27902,56713,56763</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25853567$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/servlets/purl/1286681$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Allen, Michael S</creatorcontrib><creatorcontrib>Hurst, Gregory B</creatorcontrib><creatorcontrib>Lu, Tse-Yuan S</creatorcontrib><creatorcontrib>Perry, Leslie M</creatorcontrib><creatorcontrib>Pan, Chongle</creatorcontrib><creatorcontrib>Lankford, Patricia K</creatorcontrib><creatorcontrib>Pelletier, Dale A</creatorcontrib><creatorcontrib>Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)</creatorcontrib><title>Rhodopseudomonas palustris CGA010 Proteome Implicates Extracytoplasmic Function Sigma Factor in Stress Response</title><title>Journal of proteome research</title><addtitle>J. Proteome Res</addtitle><description>Rhodopseudomonas palustris encodes 16 extracytoplasmic function (ECF) σ factors. To begin to investigate the regulatory network of one of these ECF σ factors, the whole proteome of R. palustris CGA010 was quantitatively analyzed by tandem mass spectrometry from cultures episomally expressing the ECF σRPA4225 (ecfT) versus a WT control. Among the proteins with the greatest increase in abundance were catalase KatE, trehalose synthase, a DPS-like protein, and several regulatory proteins. Alignment of the cognate promoter regions driving expression of several upregulated proteins suggested a conserved binding motif in the −35 and −10 regions with the consensus sequence GGAAC-18N-TT. Additionally, the putative anti-σ factor RPA4224, whose gene is contained in the same predicted operon as RPA4225, was identified as interacting directly with the predicted response regulator RPA4223 by mass spectrometry of affinity-isolated protein complexes. Furthermore, another gene (RPA4226) coding for a protein that contains a cytoplasmic histidine kinase domain is located immediately upstream of RPA4225. The genomic organization of orthologs for these four genes is conserved in several other strains of R. palustris as well as in closely related α-Proteobacteria. Taken together, these data suggest that ECF σRPA4225 and the three additional genes make up a sigma factor mimicry system in R. palustris.</description><subject>Bacterial Proteins - genetics</subject><subject>Bacterial Proteins - isolation & purification</subject><subject>Bacterial Proteins - metabolism</subject><subject>BASIC BIOLOGICAL SCIENCES</subject><subject>Binding Sites</subject><subject>Catalase - genetics</subject><subject>Catalase - metabolism</subject><subject>Chromatography, Liquid</subject><subject>Conserved Sequence</subject><subject>DNA, Bacterial - genetics</subject><subject>DNA, Bacterial - metabolism</subject><subject>ECF σ factor</subject><subject>Gene Expression Regulation, Bacterial</subject><subject>gene regulation</subject><subject>Glucosyltransferases - genetics</subject><subject>Glucosyltransferases - metabolism</subject><subject>Molecular Sequence Data</subject><subject>Nucleotide Motifs</subject><subject>Operon</subject><subject>Promoter Regions, Genetic</subject><subject>Protein Binding</subject><subject>Protein Isoforms - genetics</subject><subject>Protein Isoforms - metabolism</subject><subject>Proteome - genetics</subject><subject>Proteome - isolation & purification</subject><subject>Proteome - metabolism</subject><subject>proteomics</subject><subject>Rhodopseudomonas - genetics</subject><subject>Rhodopseudomonas - metabolism</subject><subject>Rhodopseudomonas palustris</subject><subject>Sequence Alignment</subject><subject>Sigma Factor - genetics</subject><subject>Sigma Factor - isolation & purification</subject><subject>Sigma Factor - metabolism</subject><subject>stress</subject><subject>Stress, Physiological - genetics</subject><subject>Tandem Mass Spectrometry</subject><subject>Transcription, Genetic</subject><issn>1535-3893</issn><issn>1535-3907</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNptkU9P3DAQxa2KqlDaA1-gspCQ2sMW_8GxfUQrliIhtYL2bDnOLBglmdTjSPDtm3aBU08zo_m9d3iPsSMpvkqh5OlUjJDKGPeGHUijzUp7Yfdeduf1PntP9CCENFbod2xfGbe8GnvA8OYeO5wI5g4HHCPxKfYz1ZKJry_PhRT8R8EKOAC_GqY-p1iB-MVjLTE9VZz6SENOfDOPqWYc-W2-GyLfxFSx8LzctQARvwGacCT4wN5uY0_w8Xkesl-bi5_rb6vr75dX6_PrVdTW1pU3ndI-GdFAe2Z9a8Fbdaa3nRHgQRmQrW21dBrcIkgutUo2wjbONzItAn3Ijne-SDUHSrlCuk84jpBqkMo1jZML9HkHTQV_z0A1DJkS9H0cAWcKsrHWeWX--X3ZoakgUYFtmEoeYnkKUoS_JYTXEhb207Pt3A7QvZIvqS_AyQ6IicIDzmVcoviP0R_n0I06</recordid><startdate>20150501</startdate><enddate>20150501</enddate><creator>Allen, Michael S</creator><creator>Hurst, Gregory B</creator><creator>Lu, Tse-Yuan S</creator><creator>Perry, Leslie M</creator><creator>Pan, Chongle</creator><creator>Lankford, Patricia K</creator><creator>Pelletier, Dale A</creator><general>American Chemical Society</general><general>American Chemical Society (ACS)</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>7X8</scope><scope>OIOZB</scope><scope>OTOTI</scope></search><sort><creationdate>20150501</creationdate><title>Rhodopseudomonas palustris CGA010 Proteome Implicates Extracytoplasmic Function Sigma Factor in Stress Response</title><author>Allen, Michael S ; Hurst, Gregory B ; Lu, Tse-Yuan S ; Perry, Leslie M ; Pan, Chongle ; Lankford, Patricia K ; Pelletier, Dale A</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a377t-95d239c506eb479b7e97243fd50e9e25e1b7b3183e8a37c8cb2160768961c4793</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Bacterial Proteins - genetics</topic><topic>Bacterial Proteins - isolation & purification</topic><topic>Bacterial Proteins - metabolism</topic><topic>BASIC BIOLOGICAL SCIENCES</topic><topic>Binding Sites</topic><topic>Catalase - genetics</topic><topic>Catalase - metabolism</topic><topic>Chromatography, Liquid</topic><topic>Conserved Sequence</topic><topic>DNA, Bacterial - genetics</topic><topic>DNA, Bacterial - metabolism</topic><topic>ECF σ factor</topic><topic>Gene Expression Regulation, Bacterial</topic><topic>gene regulation</topic><topic>Glucosyltransferases - genetics</topic><topic>Glucosyltransferases - metabolism</topic><topic>Molecular Sequence Data</topic><topic>Nucleotide Motifs</topic><topic>Operon</topic><topic>Promoter Regions, Genetic</topic><topic>Protein Binding</topic><topic>Protein Isoforms - genetics</topic><topic>Protein Isoforms - metabolism</topic><topic>Proteome - genetics</topic><topic>Proteome - isolation & purification</topic><topic>Proteome - metabolism</topic><topic>proteomics</topic><topic>Rhodopseudomonas - genetics</topic><topic>Rhodopseudomonas - metabolism</topic><topic>Rhodopseudomonas palustris</topic><topic>Sequence Alignment</topic><topic>Sigma Factor - genetics</topic><topic>Sigma Factor - isolation & purification</topic><topic>Sigma Factor - metabolism</topic><topic>stress</topic><topic>Stress, Physiological - genetics</topic><topic>Tandem Mass Spectrometry</topic><topic>Transcription, Genetic</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Allen, Michael S</creatorcontrib><creatorcontrib>Hurst, Gregory B</creatorcontrib><creatorcontrib>Lu, Tse-Yuan S</creatorcontrib><creatorcontrib>Perry, Leslie M</creatorcontrib><creatorcontrib>Pan, Chongle</creatorcontrib><creatorcontrib>Lankford, Patricia K</creatorcontrib><creatorcontrib>Pelletier, Dale A</creatorcontrib><creatorcontrib>Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>OSTI.GOV - Hybrid</collection><collection>OSTI.GOV</collection><jtitle>Journal of proteome research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Allen, Michael S</au><au>Hurst, Gregory B</au><au>Lu, Tse-Yuan S</au><au>Perry, Leslie M</au><au>Pan, Chongle</au><au>Lankford, Patricia K</au><au>Pelletier, Dale A</au><aucorp>Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Rhodopseudomonas palustris CGA010 Proteome Implicates Extracytoplasmic Function Sigma Factor in Stress Response</atitle><jtitle>Journal of proteome research</jtitle><addtitle>J. Proteome Res</addtitle><date>2015-05-01</date><risdate>2015</risdate><volume>14</volume><issue>5</issue><spage>2158</spage><epage>2168</epage><pages>2158-2168</pages><issn>1535-3893</issn><eissn>1535-3907</eissn><abstract>Rhodopseudomonas palustris encodes 16 extracytoplasmic function (ECF) σ factors. To begin to investigate the regulatory network of one of these ECF σ factors, the whole proteome of R. palustris CGA010 was quantitatively analyzed by tandem mass spectrometry from cultures episomally expressing the ECF σRPA4225 (ecfT) versus a WT control. Among the proteins with the greatest increase in abundance were catalase KatE, trehalose synthase, a DPS-like protein, and several regulatory proteins. Alignment of the cognate promoter regions driving expression of several upregulated proteins suggested a conserved binding motif in the −35 and −10 regions with the consensus sequence GGAAC-18N-TT. Additionally, the putative anti-σ factor RPA4224, whose gene is contained in the same predicted operon as RPA4225, was identified as interacting directly with the predicted response regulator RPA4223 by mass spectrometry of affinity-isolated protein complexes. Furthermore, another gene (RPA4226) coding for a protein that contains a cytoplasmic histidine kinase domain is located immediately upstream of RPA4225. The genomic organization of orthologs for these four genes is conserved in several other strains of R. palustris as well as in closely related α-Proteobacteria. Taken together, these data suggest that ECF σRPA4225 and the three additional genes make up a sigma factor mimicry system in R. palustris.</abstract><cop>United States</cop><pub>American Chemical Society</pub><pmid>25853567</pmid><doi>10.1021/pr5012558</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Bacterial Proteins - genetics Bacterial Proteins - isolation & purification Bacterial Proteins - metabolism BASIC BIOLOGICAL SCIENCES Binding Sites Catalase - genetics Catalase - metabolism Chromatography, Liquid Conserved Sequence DNA, Bacterial - genetics DNA, Bacterial - metabolism ECF σ factor Gene Expression Regulation, Bacterial gene regulation Glucosyltransferases - genetics Glucosyltransferases - metabolism Molecular Sequence Data Nucleotide Motifs Operon Promoter Regions, Genetic Protein Binding Protein Isoforms - genetics Protein Isoforms - metabolism Proteome - genetics Proteome - isolation & purification Proteome - metabolism proteomics Rhodopseudomonas - genetics Rhodopseudomonas - metabolism Rhodopseudomonas palustris Sequence Alignment Sigma Factor - genetics Sigma Factor - isolation & purification Sigma Factor - metabolism stress Stress, Physiological - genetics Tandem Mass Spectrometry Transcription, Genetic |
| title | Rhodopseudomonas palustris CGA010 Proteome Implicates Extracytoplasmic Function Sigma Factor in Stress Response |
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