The ECF Classification: A Phylogenetic Reflection of the Regulatory Diversity in the Extracytoplasmic Function σ Factor Protein Family
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Contributors
Abstract
Specific and tight control of gene expression is an essential prerequisite for a cell to survive in changing habitats. In bacteria, alternative σ factors are an important regulatory principle to control the expression of a defined set of genes in response to environmental cues or in the course of cellular differentiation programs. The extracytoplasmic function (ECF) σ factors represent the most diverse and abundant group of alternative σ factors that typically play a role in the bacterial stress response. The diversity of ECF σ factors is reflected in the mechanisms by which their activity is regulated, their protein architecture, and their target promoter sequence. Five years ago, we proposed a classification of this protein family, based on sequence similarity and domain architecture of both the ECF σ factor and its cognate anti-σ factor, genomic context conservation, and putative target promoter motifs. This classification not only reflects the phylogeny of ECF σ factors but also allows proposing detailed hypotheses on potential novel ECF-dependent regulatory mechanisms that can be tested experimentally. Initially, we identified 66 groups; since then, follow-up studies have identified 28 additional groups. In this chapter, we provide a comprehensive and up-to-date compilation of the currently available information on these 94 defined ECF groups. It was written with the intention of serving as a concise desk reference for those interested in the regulatory diversity of this third pillar of bacterial signal transduction.
Details
Original language | English |
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Title of host publication | Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria |
Publisher | Blackwell |
Pages | 64-96 |
Number of pages | 33 |
Volume | 1 |
ISBN (electronic) | 9781119004813 |
ISBN (print) | 9781119004882 |
Publication status | Published - 12 Aug 2016 |
Peer-reviewed | Yes |
Keywords
ASJC Scopus subject areas
Keywords
- Gene regulation, RNA polymerase, Signal transduction, Stress response, Transcription initiation