The aim of this investigation was to discover the promoters that drive expression of the sig genes encoding sigma factors of RNA polymerase in Rhodococcus erythropolis CCM2595 and classify these promoters according to the sigma factors which control their activity. To analyze the regulation of major sigma factors, which control large regulons that also contain genes expressed under exponential growth and non-stressed conditions, we used the R. erythropolis CCM2595 culture, which grew rapidly in minimal medium. The transcriptional start sites (TSSs) of the genes sigA, sigB, sigD, sigE, sigG, sigH, sigJ, and sigK were detected by primary 5'-end-specific RNA sequencing. The promoters localized upstream of the detected TSSs were defined by their -35 and -10 elements, which were identical or closely similar to these sequences in the related species Corynebacterium glutamicum and Mycobacterium tuberculosis. Regulation of the promoter activities by different sigma factors was demonstrated by two independent techniques (in vivo and in vitro). All analyzed sig genes encoding the sigma factors with extracytoplasmic function (ECF) were found to be also driven from additional housekeeping promoters. Based on the classification of the sig gene promoters, a model of the basic sigma transcriptional regulatory network in R. erythropolis was designed.

Center for Biotechnology Bielefeld University Universitätsstrasse 27 D 33615 Bielefeld Germany

Faculty of Food and Biochemical Technology University of Chemistry and Technology Technická 5 CZ 166 28 Prague 6 Czech Republic

Genetics and Microbiology Faculty of Science Charles University Viničná 5 CZ 128 44 Praha 2 Czech Republic

Institute of Microbiology of the CAS v v i Videňská 1083 CZ 14220 Prague 4 Czech Republic

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Overlapping SigH and SigE sigma factor regulons in Corynebacterium glutamicum