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Microarray analysis of RpoS-mediated gene expression in Escherichia coli K-12

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Abstract

The alternative sigma factor RpoS controls the expression of many stationary-phase genes in Escherichia coli and other bacteria. Though the RpoS regulon is a large, conserved system that is critical for adaptation to nutrient deprivation and other stresses, it remains incompletely characterized. In this study, we have used oligonucleotide arrays to delineate the transcriptome that is controlled by RpoS during entry into stationary phase of cultures growing in rich medium. The expression of known RpoS-dependent genes was confirmed to be regulated by RpoS, thus validating the use of microarrays for expression analysis. The total number of positively regulated stationary-phase genes was found to be greater than 100. More than 45 new genes were identified as positively controlled by RpoS. Surprisingly, a similar number of genes were found to be negatively regulated by RpoS, and these included almost all genes required for flagellum biosynthesis, genes encoding enzymes of the TCA cycle, and a physically contiguous group of genes located in the Rac prophage region. Negative regulation by RpoS is thus much more extensive than has previously been recognized, and is likely to be an important contributing factor to the competitive growth advantage of rpoS mutants reported in previous studies.

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Acknowledgements

We thank Matt Trudeau, Sabine Maxwell and Daniel Li for valuable technical assistance. This work was funded by grants from the National Research Council of Canada (NSERC) and Canadian Institutes of Health Research (CIHR) to HES

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  1. M. G. Kirchhof

    Present address: Robarts Research Institute, University of Western Ontario, London, Ontario, N6A 5K8, Canada

Authors and Affiliations

  1. Department of Biology, McMaster University, Hamilton, Ontario, L8S 4K1, Canada

    C. L. Patten, M. G. Kirchhof, M. R. Schertzberg, R. A. Morton & H. E. Schellhorn

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  1. C. L. Patten
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Correspondence to H. E. Schellhorn.

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Communicated by A. M. Hirsch

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Patten, C.L., Kirchhof, M.G., Schertzberg, M.R. et al. Microarray analysis of RpoS-mediated gene expression in Escherichia coli K-12. Mol Genet Genomics 272, 580–591 (2004). https://doi.org/10.1007/s00438-004-1089-2

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