Comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exteriorReportar como inadecuado

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BMC Genomics

, 12:385

Comparative and evolutionary genomics


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.

Keywordsbiofilm enhancer binding protein exopolysaccharide lipopolysaccharide nitrogen assimilation motility peptidoglycan List of abbreviationsCOGCluster of Orthologous Genes

CWCell Wall


EBPEnhancer Binding Protein

ECEnzyme Code

ECF sigma factorExtraCytoplasmic Function sigma factor


GOGene Ontology

HMMHidden Markov Model

HTHHelix Turn Helix




NJNeighbor Joining

OMOuter Membrane


PTSPhosphoTransferase System

SMSSimilar Motif Search

TCATriCarboxylic Acid

TCSTwo Component System.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-12-385 contains supplementary material, which is available to authorized users.

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Autor: Christof Francke - Tom Groot Kormelink - Yanick Hagemeijer - Lex Overmars - Vincent Sluijter - Roy Moezelaar - Roland J Si


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