The ECF Classification: A Phylogenetic Reflection of the Regulatory Diversity in the Extracytoplasmic Function σ Factor Protein Family

Research output: Contribution to book/conference proceedings/anthology/reportChapter in book/anthology/reportContributedpeer-review

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 languageEnglish
Title of host publicationStress and Environmental Regulation of Gene Expression and Adaptation in Bacteria
PublisherBlackwell
Pages64-96
Number of pages33
Volume1
ISBN (electronic)9781119004813
ISBN (print)9781119004882
Publication statusPublished - 12 Aug 2016
Peer-reviewedYes

Keywords

ASJC Scopus subject areas

Keywords

  • Gene regulation, RNA polymerase, Signal transduction, Stress response, Transcription initiation