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Journal of Bacteriology, May 2009, p. 3226-3236, Vol. 191, No. 10
0021-9193/09/$08.00+0     doi:10.1128/JB.01410-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

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

Anna Åberg,¹ Jorge Fernández-Vázquez,² Juan David Cabrer-Panes,² Alex Sánchez,³ and Carlos Balsalobre^2*

Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden,¹ Departament de Microbiologia, Universitat de Barcelona, Avgda. Diagonal 645, 08028 Barcelona, Spain,² Departament d'Estadística, Universitat de Barcelona, Avgda. Diagonal 645, 08028 Barcelona, Spain³

Received 8 October 2008/ Accepted 18 February 2009

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 DksA-deficient 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.

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* Corresponding author. Mailing address: Departament de Microbiologia, Universitat de Barcelona, Avgda. Diagonal 645, 08028 Barcelona, Spain. Phone: 34 93 4021492. Fax: 34 93 4034629. E-mail: cbalsalobre{at}ub.edu

Published ahead of print on 27 February 2009.

Supplemental material for this article is available at http://jb.asm.org/.

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Journal of Bacteriology, May 2009, p. 3226-3236, Vol. 191, No. 10
0021-9193/09/$08.00+0     doi:10.1128/JB.01410-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

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