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

BMC Genomics

Research Article

Yanick Hagemeijer¹  Vincent Sluijter¹  Roland J Siezen²  Christof Francke²  Tom Groot Kormelink³  Roy Moezelaar⁴  Lex Overmars⁵ 

[1] Center for Molecular and Biomolecular Informatics (260), NCMLS, Radboud University Nijmegen Medical Center, P.O.Box 9101, 6500HB, Nijmegen, The Netherlands;TI Food and Nutrition, P.O.Box 557, 6700AN, Wageningen, The Netherlands;Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC, Delft, The Netherlands;Netherlands Bioinformatics Centre, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands;Center for Molecular and Biomolecular Informatics (260), NCMLS, Radboud University Nijmegen Medical Center, P.O.Box 9101, 6500HB, Nijmegen, The Netherlands;TI Food and Nutrition, P.O.Box 557, 6700AN, Wageningen, The Netherlands;Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC, Delft, The Netherlands;Wageningen University and Research Center, Laboratory of Microbiology, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands;Center for Molecular and Biomolecular Informatics (260), NCMLS, Radboud University Nijmegen Medical Center, P.O.Box 9101, 6500HB, Nijmegen, The Netherlands;TI Food and Nutrition, P.O.Box 557, 6700AN, Wageningen, The Netherlands;Wageningen University and Research Center, Food and Biobased Research, PO Box 17, 6700 AA, The Netherlands;TI Food and Nutrition, P.O.Box 557, 6700AN, Wageningen, The Netherlands;Wageningen University and Research Center, Laboratory of Microbiology, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands;Center for Molecular and Biomolecular Informatics (260), NCMLS, Radboud University Nijmegen Medical Center, P.O.Box 9101, 6500HB, Nijmegen, The Netherlands;

关键词: biofilm;    enhancer binding protein;    exopolysaccharide;    lipopolysaccharide;    nitrogen assimilation;    motility;    peptidoglycan;   

DOI  :  10.1186/1471-2164-12-385

 received in 2011-02-09, accepted in 2011-08-01,  发布年份 2011

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© Francke et al; licensee BioMed Central Ltd. 2011