third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) σ factor protein family
The ability of a bacterial cell to monitor and adaptively respond to its environment is crucial for survival. After one- and two-component systems, extracytoplasmic function (ECF) σ factors - the largest group of alternative σ factors - represent the third fundamental mechanism of bacterial signal t...
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| Veröffentlicht in: | Molecular microbiology 2009-11, Vol.74 (3), p.557-581 |
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| creator | Staroń, Anna Sofia, Heidi J Dietrich, Sascha Ulrich, Luke E Liesegang, Heiko Mascher, Thorsten |
| description | The ability of a bacterial cell to monitor and adaptively respond to its environment is crucial for survival. After one- and two-component systems, extracytoplasmic function (ECF) σ factors - the largest group of alternative σ factors - represent the third fundamental mechanism of bacterial signal transduction, with about six such regulators on average per bacterial genome. Together with their cognate anti-σ factors, they represent a highly modular design that primarily facilitates transmembrane signal transduction. A comprehensive analysis of the ECF σ factor protein family identified more than 40 distinct major groups of ECF σ factors. The functional relevance of this classification is supported by the sequence similarity and domain architecture of cognate anti-σ factors, genomic context conservation, and potential target promoter motifs. Moreover, this phylogenetic analysis revealed unique features indicating novel mechanisms of ECF-mediated signal transduction. This classification, together with the web tool ECFfinder and the information stored in the Microbial Signal Transduction (MiST) database, provides a comprehensive resource for the analysis of ECF σ factor-dependent gene regulation. |
| doi_str_mv | 10.1111/j.1365-2958.2009.06870.x |
| format | Article |
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After one- and two-component systems, extracytoplasmic function (ECF) σ factors - the largest group of alternative σ factors - represent the third fundamental mechanism of bacterial signal transduction, with about six such regulators on average per bacterial genome. Together with their cognate anti-σ factors, they represent a highly modular design that primarily facilitates transmembrane signal transduction. A comprehensive analysis of the ECF σ factor protein family identified more than 40 distinct major groups of ECF σ factors. The functional relevance of this classification is supported by the sequence similarity and domain architecture of cognate anti-σ factors, genomic context conservation, and potential target promoter motifs. Moreover, this phylogenetic analysis revealed unique features indicating novel mechanisms of ECF-mediated signal transduction. This classification, together with the web tool ECFfinder and the information stored in the Microbial Signal Transduction (MiST) database, provides a comprehensive resource for the analysis of ECF σ factor-dependent gene regulation.</description><subject>Amino Acid Motifs - genetics</subject><subject>Amino Acid Sequence</subject><subject>Bacteria - genetics</subject><subject>Bacteria - metabolism</subject><subject>Bacterial Proteins - classification</subject><subject>Bacterial Proteins - genetics</subject><subject>Bacterial Proteins - metabolism</subject><subject>Biological and medical sciences</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Bacterial</subject><subject>Genes, Bacterial</subject><subject>Genome, Bacterial</subject><subject>Genomics</subject><subject>Microbiology</subject><subject>Mycobacterium tuberculosis - genetics</subject><subject>Mycobacterium tuberculosis - metabolism</subject><subject>Protein Kinases - genetics</subject><subject>Protein Kinases - metabolism</subject><subject>Protein Structure, Tertiary - genetics</subject><subject>Reverse Transcriptase Polymerase Chain Reaction</subject><subject>RNA, Bacterial - analysis</subject><subject>RNA, Bacterial - genetics</subject><subject>Sequence Alignment</subject><subject>Sigma Factor - classification</subject><subject>Sigma Factor - genetics</subject><subject>Sigma Factor - metabolism</subject><subject>Signal Transduction - genetics</subject><subject>Virulence Factors - genetics</subject><issn>0950-382X</issn><issn>1365-2958</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkctuFDEQRS0EIkPgF8AbRLLoxo_2o5FYRKMEIiXKAiKxsypuO_GoHxO7W8wsWPGB_FLcmVHYxptyqc6tKl8jhCkpaT6fVyXlUhSsFrpkhNQlkVqRcvMCLZ4KL9GC1IIUXLNfB-hNSitCKCeSv0YHtFZccSEX6M94F2KD16FtIeLB4xuwo4sBWpzCbZ_DGKFPzWTHMPRfsG0hpeCDhTmfBeOdw26TKbsdh3Uud8FiP_WPAnx0ujw7xv_-Yp_7DhGv4zC60Oe0C-32LXrloU3u3T4eouuz05_L78XF1bfz5clFYSvFSAFcgQDWKOmYl1JRDZ5bwRUVruJVVRHldEM8A-UFNMI3um5kI2sBlZIV54fo065vHn8_uTSaLiTr8pt7N0zJKM5VTQhRmdQ70sYhpei8WcfQQdwaSszsvVmZ2WIzW2xm782j92aTpe_3Q6abzjX_hXuzM_BxD0Cy0PpsrA3piWOMaCV0lbmvO-53aN322QuYy8vz-Zb1H3Z6D4OB25hnXP9g8-dTWXOtNX8AOWiq3w</recordid><startdate>200911</startdate><enddate>200911</enddate><creator>Staroń, Anna</creator><creator>Sofia, Heidi J</creator><creator>Dietrich, Sascha</creator><creator>Ulrich, Luke E</creator><creator>Liesegang, Heiko</creator><creator>Mascher, Thorsten</creator><general>Oxford, UK : Blackwell Publishing Ltd</general><general>Blackwell Publishing Ltd</general><general>Blackwell</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>7X8</scope></search><sort><creationdate>200911</creationdate><title>third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) σ factor protein family</title><author>Staroń, Anna ; Sofia, Heidi J ; Dietrich, Sascha ; Ulrich, Luke E ; Liesegang, Heiko ; Mascher, Thorsten</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4720-a37a5a2d76e2f66718af3c53715e4344407e8d0f2a7f5ad5fd89d6d695a476433</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>Amino Acid Motifs - genetics</topic><topic>Amino Acid Sequence</topic><topic>Bacteria - genetics</topic><topic>Bacteria - metabolism</topic><topic>Bacterial Proteins - classification</topic><topic>Bacterial Proteins - genetics</topic><topic>Bacterial Proteins - metabolism</topic><topic>Biological and medical sciences</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene Expression Profiling</topic><topic>Gene Expression Regulation, Bacterial</topic><topic>Genes, Bacterial</topic><topic>Genome, Bacterial</topic><topic>Genomics</topic><topic>Microbiology</topic><topic>Mycobacterium tuberculosis - genetics</topic><topic>Mycobacterium tuberculosis - metabolism</topic><topic>Protein Kinases - genetics</topic><topic>Protein Kinases - metabolism</topic><topic>Protein Structure, Tertiary - genetics</topic><topic>Reverse Transcriptase Polymerase Chain Reaction</topic><topic>RNA, Bacterial - analysis</topic><topic>RNA, Bacterial - genetics</topic><topic>Sequence Alignment</topic><topic>Sigma Factor - classification</topic><topic>Sigma Factor - genetics</topic><topic>Sigma Factor - metabolism</topic><topic>Signal Transduction - genetics</topic><topic>Virulence Factors - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Staroń, Anna</creatorcontrib><creatorcontrib>Sofia, Heidi J</creatorcontrib><creatorcontrib>Dietrich, Sascha</creatorcontrib><creatorcontrib>Ulrich, Luke E</creatorcontrib><creatorcontrib>Liesegang, Heiko</creatorcontrib><creatorcontrib>Mascher, Thorsten</creatorcontrib><collection>AGRIS</collection><collection>Pascal-Francis</collection><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><jtitle>Molecular microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Staroń, Anna</au><au>Sofia, Heidi J</au><au>Dietrich, Sascha</au><au>Ulrich, Luke E</au><au>Liesegang, Heiko</au><au>Mascher, Thorsten</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) σ factor protein family</atitle><jtitle>Molecular microbiology</jtitle><addtitle>Mol Microbiol</addtitle><date>2009-11</date><risdate>2009</risdate><volume>74</volume><issue>3</issue><spage>557</spage><epage>581</epage><pages>557-581</pages><issn>0950-382X</issn><eissn>1365-2958</eissn><abstract>The ability of a bacterial cell to monitor and adaptively respond to its environment is crucial for survival. After one- and two-component systems, extracytoplasmic function (ECF) σ factors - the largest group of alternative σ factors - represent the third fundamental mechanism of bacterial signal transduction, with about six such regulators on average per bacterial genome. Together with their cognate anti-σ factors, they represent a highly modular design that primarily facilitates transmembrane signal transduction. A comprehensive analysis of the ECF σ factor protein family identified more than 40 distinct major groups of ECF σ factors. The functional relevance of this classification is supported by the sequence similarity and domain architecture of cognate anti-σ factors, genomic context conservation, and potential target promoter motifs. Moreover, this phylogenetic analysis revealed unique features indicating novel mechanisms of ECF-mediated signal transduction. 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| subjects | Amino Acid Motifs - genetics Amino Acid Sequence Bacteria - genetics Bacteria - metabolism Bacterial Proteins - classification Bacterial Proteins - genetics Bacterial Proteins - metabolism Biological and medical sciences Fundamental and applied biological sciences. Psychology Gene Expression Profiling Gene Expression Regulation, Bacterial Genes, Bacterial Genome, Bacterial Genomics Microbiology Mycobacterium tuberculosis - genetics Mycobacterium tuberculosis - metabolism Protein Kinases - genetics Protein Kinases - metabolism Protein Structure, Tertiary - genetics Reverse Transcriptase Polymerase Chain Reaction RNA, Bacterial - analysis RNA, Bacterial - genetics Sequence Alignment Sigma Factor - classification Sigma Factor - genetics Sigma Factor - metabolism Signal Transduction - genetics Virulence Factors - genetics |
| title | third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) σ factor protein family |
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