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In vitro transcription profiling of the sigmaS subunit of bacterial RNA polymerase: re-definition of the sigmaS regulon and identifitcation fo sigmaS-specific promoter sequence elements

Type of publication Peer-reviewed
Publikationsform Original article (peer-reviewed)
Author Maciag Anna, Peano Clelia, Peitrelli Alessandro, Egli Thomas, De Bellis Gianluca, Landini Paolo,
Project Role of the sigma factor RpoS in the adaptation of E. coli to different growth and stress conditions
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Original article (peer-reviewed)

Journal Nucleic Acids Research
Volume (Issue) 39(13)
Page(s) 5338 - 5355
Title of proceedings Nucleic Acids Research
DOI 10.1093/nar/gkr129

Open Access

Type of Open Access Publisher (Gold Open Access)


Specific promoter recognition by bacterial RNA polymerase is mediated by p subunits, which assemble with RNA polymerase core enzyme (E) during transcription initiation. However, p70 (the housekeeping p subunit) and pS (an alternative p subunit mostly active during slow growth) recognize almost identical promoter sequences, thus raising the question of how promoter selectivity is achieved in the bacterial cell. To identify novel sequence determinants for selective promoter recognition, we performed run-off/microarray (ROMA) experiments with RNA polymerase saturated either with p70 (Ep70) or with pS (EpS) using the whole Escherichia coli genome as DNA template. We found that Ep70, in the absence of any additional transcription factor, preferentially transcribes genes associated with fast growth (e.g. ribosomal operons). In contrast, EpS efficiently transcribes genes involved in stress responses, secondary metabolism as well as RNAs from intergenic regions with yet-unknown function. Promoter sequence comparison suggests that, in addition to different conservation of the 35 sequence and of the UP element, selective promoter recognition by either form of RNA polymerase can be affected by the A/ T content in the 10/+1 region. Indeed, site-directed mutagenesis experiments confirmed that an A/T bias in the 10/+1 region could improve promoter recognition by EpS.