In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements.

Nucleic Acids Res 2011 Jul 11;39(13):5338-55. Epub 2011 Mar 11.

Department of Biomolecular Sciences and Biotechnology, Università degli Studi di Milano, Milan, Italy.

Specific promoter recognition by bacterial RNA polymerase is mediated by σ subunits, which assemble with RNA polymerase core enzyme (E) during transcription initiation. However, σ(70) (the housekeeping σ subunit) and σ(S) (an alternative σ 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 σ(70) (Eσ(70)) or with σ(S) (Eσ(S)) using the whole Escherichia coli genome as DNA template. We found that Eσ(70), in the absence of any additional transcription factor, preferentially transcribes genes associated with fast growth (e.g. ribosomal operons). In contrast, Eσ(S) 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 Eσ(S).

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkr129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248PMC
July 2011
6 Reads

Publication Analysis

Top Keywords

rna polymerase
20
promoter recognition
16
selective promoter
8
bacterial rna
8
transcribes genes
8
promoter
8
promoter sequence
8
-10/+1 region
8
polymerase
5
rna
5
secondary metabolism
4
sequence determinants
4
intergenic regions
4
run-off/microarray roma
4
rnas intergenic
4
determinants selective
4
well rnas
4
recognition performed
4
metabolism well
4
performed run-off/microarray
4

References

(Supplied by CrossRef)

Similar Publications