title: Comparative analyses imply that the enigmatic Sigma factor 54 is a central controller of the bacterial exterior.
abstract: BACKGROUND
  Sigma-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.
  
  
  RESULTS
  We 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.
  
  
  CONCLUSIONS
  Our 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.
authors.affiliation: TI Food and Nutrition, P,O,Box 557, 6700AN Wageningen, The Netherlands. c.francke@cmbi.ru.nl
authors.forename: Christof
authors.initials: C
authors.lastname: Francke
authors.forename: Tom
authors.initials: T
authors.lastname: Groot Kormelink
authors.forename: Yanick
authors.initials: Y
authors.lastname: Hagemeijer
authors.forename: Lex
authors.initials: L
authors.lastname: Overmars
authors.forename: Vincent
authors.initials: V
authors.lastname: Sluijter
authors.forename: Roy
authors.initials: R
authors.lastname: Moezelaar
authors.forename: Roland J
authors.initials: RJ
authors.lastname: Siezen
mesh_terms: D000595:Amino Acid Sequence; D001419:Bacteria / Q000166:cytology / Q000201:enzymology* / Q000235:genetics* / Q000378:metabolism; D002473:Cell Wall / Q000378:metabolism; D002874:Chromosome Mapping; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D004742:Enhancer Elements, Genetic / Q000235:genetics; D005110:Extracellular Space / Q000378:metabolism; D005407:Flagella / Q000378:metabolism; D023281:Genomics; D008070:Lipopolysaccharides / Q000378:metabolism; D008074:Lipoproteins / Q000378:metabolism; D008969:Molecular Sequence Data; D010457:Peptidoglycan / Q000378:metabolism; D011401:Promoter Regions, Genetic / Q000235:genetics; D051877:RNA Polymerase Sigma 54 / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; D008070:Lipopolysaccharides; D008074:Lipoproteins; D010457:Peptidoglycan; D051877:RNA Polymerase Sigma 54