Themes and variations in gene regulation by extracytoplasmic function (ECF) sigma factors

Abstract

The ECF sigma family was identified 23 years ago as a distinct group of σ70-like factors. ECF sigma factors have since emerged as a major form of bacterial signal transduction that can be grouped into over 50 phylogenetically distinct subfamilies. Advances in our understanding of these sigma factors and the signaling pathways governing their activity have elucidated conserved features as well as aspects that have evolved over time. All ECF sigma factors are predicted to share a common streamlined domain structure and mode of promoter interaction. The activity of most ECF sigma factors is controlled by an anti-sigma factor. The nature of the anti-sigma factor and the activating signaling pathways appear to be conserved within ECF families, while considerable diversity exists between different families.

What bacteria want

“…In B. subtilis , one of its three DACs monitors the integrity of chromosomal DNA and serves as a checkpoint for the cells entering the sporulation process. c‐di‐AMP‐specific phosphodiesterases (CDAs, containing either GGDEF‐DHHA‐DHHA1 or HD‐type domains) hydrolyse c‐di‐AMP. Most, albeit not all of them do not contain any sensor domains and apparently simply reverse the effects of DACs. ECF sigma factors comprise a vast signal transduction machinery that regulates transcription primarily in response to intracellular cues but can also respond to environmental factors, such as envelope stress (Helmann, ; Asai, ), blue light (Gaidenko et al ., ) or extracellular polysaccharides (Kahel‐Raifer et al ., ; Yaniv et al ., ; see Mascher, ; Paget, ; Sineva et al ., for reviews). Signal transduction from Ser/Thr/Tyr protein kinases (STYKs) involves direct or indirect phosphorylation of various (mostly unknown) targets. The few experimentally characterized targets of Ser/Thr/Tyr protein phosphorylation include metabolic (e.g.…”

Structural Basis of ECF-σ-Factor-Dependent Transcription Initiation

“…The close structural similarity of group-2 and group-3 σ factors to group-1 σ factors, together with crystal structures of transcription initiation complexes containing group-2 σ factors (Liu et al, 2016), facilitates an understanding of the mechanism of group-2-and group-3-σ-factor-dependent transcription initiation.Group-4 alternative σ factors--also referred to as "extracytoplasmic σ factors" (ECF σ factors), based on functional roles in response to cell-surface and other extracytoplasmic stresses--are only distantly related to group-1 σ factors and are substantially smaller than group-1 σ factors, lacking four of the six functional modules present in group-1 σ factors ( Fig. 1A; reviewed in Lonetto et alCampagne et al, 2015;Sineva and Ades, 2017). ECF σ factors comprise only a module related to σR2 (the module that recognizes promoter -10 elements in group-1 σ factors), a module related to σR4 (the module that recognizes promoter -35 elements in group-1 σ factors)., and a short σR2/4 linker that has no detectable sequence similarity to the σR3/4 linker of group-1 σ factors.…”

Co-evolutionary analysis reveals a conserved dual binding interface between extracytoplasmic function (ECF) σ factors and class I anti-σ factors

“…We used this extended model to search for ASDIs in the genetic neighborhood of all classified ECFs identified in (3), using only the 33,843 ECFs from representative and reference organisms as labelled by the National Center for Biotechnology Information (NCBI). This yielded 11,939 proteins, from which we removed the ones with ASDI shorter than 50 amino acids, since these could be divergent class II anti-σ factors (19). The final number of ASDIs retrieved by this pipeline was 10,930, of which 10,806 have a non-redundant anti-σ domain.…”