The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) sigma factor protein family

Mol Microbiol. 2009 Nov;74(3):557-81. doi: 10.1111/j.1365-2958.2009.06870.x. Epub 2009 Sep 8.


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) sigma factors - the largest group of alternative sigma 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-sigma factors, they represent a highly modular design that primarily facilitates transmembrane signal transduction. A comprehensive analysis of the ECF sigma factor protein family identified more than 40 distinct major groups of ECF sigma factors. The functional relevance of this classification is supported by the sequence similarity and domain architecture of cognate anti-sigma 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 sigma factor-dependent gene regulation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs / genetics
  • Amino Acid Sequence
  • Bacteria / genetics
  • Bacteria / metabolism*
  • Bacterial Proteins / classification
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Gene Expression Profiling
  • Gene Expression Regulation, Bacterial
  • Genes, Bacterial
  • Genome, Bacterial
  • Genomics
  • Mycobacterium tuberculosis / genetics
  • Mycobacterium tuberculosis / metabolism
  • Protein Kinases / genetics
  • Protein Kinases / metabolism
  • Protein Structure, Tertiary / genetics
  • RNA, Bacterial / analysis
  • RNA, Bacterial / genetics
  • Reverse Transcriptase Polymerase Chain Reaction
  • Sequence Alignment
  • Sigma Factor / classification
  • Sigma Factor / genetics
  • Sigma Factor / metabolism*
  • Signal Transduction* / genetics
  • Virulence Factors / genetics


  • Bacterial Proteins
  • RNA, Bacterial
  • Sigma Factor
  • Virulence Factors
  • Protein Kinases