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Similar and divergent effects of ppGpp and DksA deficiencies on transcription in Escherichia coli
Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
Departament de Microbiologia, Universitat de Barcelona, Avgda. Diagonal 645, 08028 Barcelona, Spain.
Departament de Microbiologia, Universitat de Barcelona, Avgda. Diagonal 645, 08028 Barcelona, Spain.
Departament d'Estadística, Universitat de Barcelona, Avgda. Diagonal 645, 08028 Barcelona, Spain.
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2009 (English)In: Journal of Bacteriology, ISSN 0021-9193, E-ISSN 1098-5530, Vol. 191, no 10, 3226-3236 p.Article in journal (Refereed) Published
Abstract [en]

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 (ppGpp(0)) and/or DksA (DeltadksA). Approximately 6 and 7% of all genes were significantly affected by more than twofold in ppGpp- and DksA-deficient strains, respectively, increasing to 13% of all genes in the ppGpp(0) DeltadksA 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.

Place, publisher, year, edition, pages
American Society for Microbiology , 2009. Vol. 191, no 10, 3226-3236 p.
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Microbiology in the medical area
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URN: urn:nbn:se:umu:diva-36180DOI: 10.1128/JB.01410-08PubMedID: 19251846OAI: oai:DiVA.org:umu-36180DiVA: diva2:352585
Available from: 2010-09-21 Created: 2010-09-21 Last updated: 2017-12-12Bibliographically approved

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Åberg, Anna

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