Similar and Divergent Effects of ppGpp and DksA Deficiencies on Transcription in Escherichia coli.

The concerted action of ppGpp and DksA in transcription has been widely documented. In disparity with this model, phenotypic studies showed that ppGpp and DksA might also have independent and opposing roles in gene expression in Escherichia coli. In this study we used a transcriptomic approach to co...

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Autores: Aberg, Anna, Fernández Vázquez, Jorge, Cabrer Panes, Juan David, Sànchez, Àlex (Sànchez Pla), Balsalobre Parra, Carlos
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2009
País:España
Institución:Universidad de Barcelona
Repositorio:Dipòsit Digital de la UB
OAI Identifier:oai:diposit.ub.edu:2445/34458
Acceso en línea:https://hdl.handle.net/2445/34458
Access Level:acceso abierto
Palabra clave:Escheríchia coli
Genètica bacteriana
Expressió gènica
Escherichia coli
Bacterial genetics
Gene expression
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spelling Similar and Divergent Effects of ppGpp and DksA Deficiencies on Transcription in Escherichia coli.Aberg, AnnaFernández Vázquez, JorgeCabrer Panes, Juan DavidSànchez, Àlex (Sànchez Pla)Balsalobre Parra, CarlosEscheríchia coliGenètica bacterianaExpressió gènicaEscherichia coliBacterial geneticsGene expressionThe concerted action of ppGpp and DksA in transcription has been widely documented. In disparity with this model, phenotypic studies showed that ppGpp and DksA might also have independent and opposing roles in gene expression in Escherichia coli. In this study we used a transcriptomic approach to compare the global transcriptional patterns of gene expression in strains deficient in ppGpp (ppGpp0) and/or DksA ( dksA). Approximately 6 and 7% of all genes were significantly affected by more than twofold in ppGpp- and DksAdeficient strains, respectively, increasing to 13% of all genes in the ppGpp0 dksA strain. Although the data indicate that most of the affected genes were copositively or conegatively regulated by ppGpp and DksA, some genes that were independently and/or differentially regulated by the two factors were found. The large functional group of chemotaxis and flagellum synthesis genes were notably differentially affected, with all genes being upregulated in the DksA-deficient strain but 60% of them being downregulated in the ppGpp-deficient strain. Revealingly, mutations in the antipausing Gre factors suppress the upregulation observed in the DksA-deficient strain, emphasizing the importance of the secondary channel of the RNA polymerase for regulation and fine-tuning of gene expression in E. coli.American Society for Microbiology2009info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfhttps://hdl.handle.net/2445/34458Articles publicats en revistes (Genètica, Microbiologia i Estadística)reponame:Dipòsit Digital de la UBinstname:Universidad de BarcelonaInglésReproducció del document publicat a: http://dx.doi.org/10.1128/JB.01410-08Journal of Bacteriology, 2009, vol. 191, num. 10, p. 3226-3236http://dx.doi.org/10.1128/JB.01410-08(c) American Society for Microbiology, 2009info:eu-repo/semantics/openAccessoai:diposit.ub.edu:2445/344582026-05-27T06:46:51Z
dc.title.none.fl_str_mv Similar and Divergent Effects of ppGpp and DksA Deficiencies on Transcription in Escherichia coli.
title Similar and Divergent Effects of ppGpp and DksA Deficiencies on Transcription in Escherichia coli.
spellingShingle Similar and Divergent Effects of ppGpp and DksA Deficiencies on Transcription in Escherichia coli.
Aberg, Anna
Escheríchia coli
Genètica bacteriana
Expressió gènica
Escherichia coli
Bacterial genetics
Gene expression
title_short Similar and Divergent Effects of ppGpp and DksA Deficiencies on Transcription in Escherichia coli.
title_full Similar and Divergent Effects of ppGpp and DksA Deficiencies on Transcription in Escherichia coli.
title_fullStr Similar and Divergent Effects of ppGpp and DksA Deficiencies on Transcription in Escherichia coli.
title_full_unstemmed Similar and Divergent Effects of ppGpp and DksA Deficiencies on Transcription in Escherichia coli.
title_sort Similar and Divergent Effects of ppGpp and DksA Deficiencies on Transcription in Escherichia coli.
dc.creator.none.fl_str_mv Aberg, Anna
Fernández Vázquez, Jorge
Cabrer Panes, Juan David
Sànchez, Àlex (Sànchez Pla)
Balsalobre Parra, Carlos
author Aberg, Anna
author_facet Aberg, Anna
Fernández Vázquez, Jorge
Cabrer Panes, Juan David
Sànchez, Àlex (Sànchez Pla)
Balsalobre Parra, Carlos
author_role author
author2 Fernández Vázquez, Jorge
Cabrer Panes, Juan David
Sànchez, Àlex (Sànchez Pla)
Balsalobre Parra, Carlos
author2_role author
author
author
author
dc.subject.none.fl_str_mv Escheríchia coli
Genètica bacteriana
Expressió gènica
Escherichia coli
Bacterial genetics
Gene expression
topic Escheríchia coli
Genètica bacteriana
Expressió gènica
Escherichia coli
Bacterial genetics
Gene expression
description The concerted action of ppGpp and DksA in transcription has been widely documented. In disparity with this model, phenotypic studies showed that ppGpp and DksA might also have independent and opposing roles in gene expression in Escherichia coli. In this study we used a transcriptomic approach to compare the global transcriptional patterns of gene expression in strains deficient in ppGpp (ppGpp0) and/or DksA ( dksA). Approximately 6 and 7% of all genes were significantly affected by more than twofold in ppGpp- and DksAdeficient strains, respectively, increasing to 13% of all genes in the ppGpp0 dksA strain. Although the data indicate that most of the affected genes were copositively or conegatively regulated by ppGpp and DksA, some genes that were independently and/or differentially regulated by the two factors were found. The large functional group of chemotaxis and flagellum synthesis genes were notably differentially affected, with all genes being upregulated in the DksA-deficient strain but 60% of them being downregulated in the ppGpp-deficient strain. Revealingly, mutations in the antipausing Gre factors suppress the upregulation observed in the DksA-deficient strain, emphasizing the importance of the secondary channel of the RNA polymerase for regulation and fine-tuning of gene expression in E. coli.
publishDate 2009
dc.date.none.fl_str_mv 2009
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/34458
url https://hdl.handle.net/2445/34458
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Reproducció del document publicat a: http://dx.doi.org/10.1128/JB.01410-08
Journal of Bacteriology, 2009, vol. 191, num. 10, p. 3226-3236
http://dx.doi.org/10.1128/JB.01410-08
dc.rights.none.fl_str_mv (c) American Society for Microbiology, 2009
info:eu-repo/semantics/openAccess
rights_invalid_str_mv (c) American Society for Microbiology, 2009
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv American Society for Microbiology
publisher.none.fl_str_mv American Society for Microbiology
dc.source.none.fl_str_mv Articles publicats en revistes (Genètica, Microbiologia i Estadística)
reponame:Dipòsit Digital de la UB
instname:Universidad de Barcelona
instname_str Universidad de Barcelona
reponame_str Dipòsit Digital de la UB
collection Dipòsit Digital de la UB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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