Extracytoplasmic function σ factors of the widely distributed group ECF41 contain a fused regulatory domain

Abstract

Bacteria need signal transducing systems to respond to environmental changes. Next to one- and two-component systems, alternative σ factors of the extra-cytoplasmic function (ECF) protein family represent the third fundamental mechanism of bacterial signal transduction. A comprehensive classification of these proteins identified more than 40 phylogenetically distinct groups, most of which are not experimentally investigated. Here, we present the characterization of such a group with unique features, termed ECF41. Among analyzed bacterial genomes, ECF41 σ factors are widely distributed with about 400 proteins from 10 different phyla. They lack obvious anti-σ factors that typically control activity of other ECF σ factors, but their structural genes are often predicted to be cotranscribed with carboxymuconolactone decarboxylases, oxidoreductases, or epimerases based on genomic context conservation. We demonstrate for Bacillus licheniformis and Rhodobacter sphaeroides that the corresponding genes are preceded by a highly conserved promoter motif and are the only detectable targets of ECF41-dependent gene regulation. In contrast to other ECF σ factors, proteins of group ECF41 contain a large C-terminal extension, which is crucial for σ factor activity. Our data demonstrate that ECF41 σ factors are regulated by a novel mechanism based on the presence of a fused regulatory domain.

Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti1021

“…This motif was used in global string searches to identify additional putative σ E1 motifs upstream of TSS (Methods). For RpoE9, we also performed string searching, but with the promoter motif recently predicted in [69], TGTCACA-N16-CGTC, which is located 9 nt upstream of the TSS we identified for the SMb20029- rpoE9 operon.…”

“…In contrast, only two additional promoter motifs were predicted for σ E9 (Additional file 3: Table S13). This was not unexpected, as the RpoE9-type σ factors of Rhodobacter sphaeroides and Bacillus licheniformis were proposed to activate only their own operons [69]. …”

The LIKE system, a novel protein expression toolbox for Bacillus subtilis based on the liaI promoter

“…This protein is a putative carboxymuconolactone decarboxylase. We could recently demonstrate that its gene represents the only target of the extracytoplasmic function σ factor ECF41 Bli [35]. It consists of 148 amino acids and an estimated molecular weight of 16,6 kDa.…”

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

“…Once such family is the ECF41 group of sigma factors whose members have been identified in bacterial genomes from 10 different phyla [13]. These ECF sigma factors appear to be regulated by a C-terminal domain, partial truncation of which leads to increased sigma factor activity in vivo , but lower RNAP binding in vitro compared to the full-length protein [39]. Surprisingly, complete truncation of the C-terminal extension eliminated sigma factor activity in vivo and RNAP binding, even though the σ2 and σ4 domains were intact [39].…”

“…These ECF sigma factors appear to be regulated by a C-terminal domain, partial truncation of which leads to increased sigma factor activity in vivo , but lower RNAP binding in vitro compared to the full-length protein [39]. Surprisingly, complete truncation of the C-terminal extension eliminated sigma factor activity in vivo and RNAP binding, even though the σ2 and σ4 domains were intact [39]. The details about how the regulatory domain senses signals and controls RNAP interaction remain to be elucidated.…”