Comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior

Abstract

BackgroundSigma-54 is a central regulator in many pathogenic bacteria and has been linked to a multitude of cellular processes like nitrogen assimilation and important functional traits such as motility, virulence, and biofilm formation. Until now it has remained obscure whether these phenomena and the control by Sigma-54 share an underlying theme.ResultsWe have uncovered the commonality by performing a range of comparative genome analyses. A) The presence of Sigma-54 and its associated activators was determined for all sequenced prokaryotes. We observed a phylum-dependent distribution that is suggestive of an evolutionary relationship between Sigma-54 and lipopolysaccharide and flagellar biosynthesis. B) All Sigma-54 activators were identified and annotated. The relation with phosphotransfer-mediated signaling (TCS and PTS) and the transport and assimilation of carboxylates and nitrogen containing metabolites was substantiated. C) The function annotations, that were represented within the genomic context of all genes encoding Sigma-54, its activators and its promoters, were analyzed for intra-phylum representation and inter-phylum conservation. Promoters were localized using a straightforward scoring strategy that was formulated to identify similar motifs. We found clear highly-represented and conserved genetic associations with genes that concern the transport and biosynthesis of the metabolic intermediates of exopolysaccharides, flagella, lipids, lipopolysaccharides, lipoproteins and peptidoglycan.ConclusionOur analyses directly implicate Sigma-54 as a central player in the control over the processes that involve the physical interaction of an organism with its environment like in the colonization of a host (virulence) or the formation of biofilm.

Bacillus cereus growth and biofilm formation: the impact of substratum, iron sources, and transcriptional regulator Sigma 54

“…The presence of a Sigma 54-encoding gene and the number of its EBPs generally correlates with the genome size of the microorganism (Francke et al 2011). Interestingly, Sigma 54 is present in all diderm (Gr-) bacteria which have an outer membrane consisting of lipopolysaccharides (LPS).…”

“…It is absent in most of endosymbionts or facultative intracellular species which also have a small genome and less versatile habitats. In monoderm (gram positive) bacteria it is present in Firmicutes, mostly in Clostridia and sporulating species of the class Bacilli (Francke et al 2011). …”

“…Francke et al (2011) made such an attempt 1 based on in silico analysis of Sigma 54 binding sites, EBPs and their genomic context in all sequenced prokaryotes. Phylum-dependent distribution of the rpoN suggested a possible evolutionary relationship between Sigma 54 and lipopolysaccharide and flagellar biosynthesis (Francke et al 2011). The enigmatic Sigma 54 was implicated as a central controller of the bacterial exterior (Francke et al 2011).…”

“…Phylum-dependent distribution of the rpoN suggested a possible evolutionary relationship between Sigma 54 and lipopolysaccharide and flagellar biosynthesis (Francke et al 2011). The enigmatic Sigma 54 was implicated as a central controller of the bacterial exterior (Francke et al 2011). This means that it is involved in cellular functions related to the physical interaction of the organism with its environment, including host colonisation and biofilm formation.…”

“…The transcriptional regulator Sigma 54 (RpoN) is another regulatory protein which is not a part of the so far described biofilm regulatory pathways, however it is reported to affect biofilm formation in a range of bacterial species (Thompson et al 2003, Wolfe et al 2004, Iyer and Hancock 2012, Hao et al 2013, Francke et al 2011, although its impact on B. cereus growth and biofilm formation has not been addressed. Therefore, the impact of Sigma 54 on cellular processes in B. cereus was studied in this thesis.…”