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

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 an...

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Autores principales: Francke, Christof, Groot Kormelink, Tom, Hagemeijer, Yanick, Overmars, Lex, Sluijter, Vincent, Moezelaar, Roy, Siezen, Roland J
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3162934/
https://www.ncbi.nlm.nih.gov/pubmed/21806785
http://dx.doi.org/10.1186/1471-2164-12-385
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author Francke, Christof
Groot Kormelink, Tom
Hagemeijer, Yanick
Overmars, Lex
Sluijter, Vincent
Moezelaar, Roy
Siezen, Roland J
author_facet Francke, Christof
Groot Kormelink, Tom
Hagemeijer, Yanick
Overmars, Lex
Sluijter, Vincent
Moezelaar, Roy
Siezen, Roland J
author_sort Francke, Christof
collection PubMed
description 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. CONCLUSION: 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.
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spelling pubmed-31629342011-08-28 Comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior Francke, Christof Groot Kormelink, Tom Hagemeijer, Yanick Overmars, Lex Sluijter, Vincent Moezelaar, Roy Siezen, Roland J BMC Genomics Research Article 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. CONCLUSION: 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. BioMed Central 2011-08-01 /pmc/articles/PMC3162934/ /pubmed/21806785 http://dx.doi.org/10.1186/1471-2164-12-385 Text en Copyright ©2011 Francke et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Francke, Christof
Groot Kormelink, Tom
Hagemeijer, Yanick
Overmars, Lex
Sluijter, Vincent
Moezelaar, Roy
Siezen, Roland J
Comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior
title Comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior
title_full Comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior
title_fullStr Comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior
title_full_unstemmed Comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior
title_short Comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior
title_sort comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3162934/
https://www.ncbi.nlm.nih.gov/pubmed/21806785
http://dx.doi.org/10.1186/1471-2164-12-385
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