Identification of promoter sequence elements involved in specific recognition by the ?S subunit of bacterial RNA polymerase.

ABSTRACT: Promoter recognition by bacterial RNA polymerase is mediated by ? subunits, which assemble transiently to RNA polymerase core enzyme (E) during transcription initiation. ? subunits drive transcription of specific sets of genes by allowing RNA polymerase to interact with different promoter sequences. However, ?70, the housekeeping ? subunit, and ?S, an alternative ? subunit mainly active during slow growth and in response to cellular stresses, appear to recognize almost identical promoter sequences, raising the question of how promoter selectivity is achieved in the bacterial cell. To identify?sequence determinants for selective promoter recognition, we performed a run-off/microarray experiment (ROMA): in vitro transcription experiments were carried out with RNA polymerase saturated either with ?70 (E?70) or with ?S (E?S) using the whole Escherichia coli genome as DNA template, and transcript levels were determined by microarray analysis. We found that several genes associated with bacterial growth (e.g., ribosomal operons) were transcribed more efficiently by E?70. In contrast, E?S transcribed preferentially genes involved in stress responses, secondary metabolism, as well as regulatory RNAs and intergenic regions with yet unknown function. Genes preferentially recognized in vitro by E?S showed reduced expression in a??S-deficient mutant strain of E. coli. Sequence comparison of E?70- versus E?S –dependent promoters confirms that the presence of a -35 sequence and the relative location of UP elements affect promoter interaction with either form of RNA polymerase, and suggests that a G/C bias in the -2/+1 nucleotides would favour efficient promoter recognition by E?70. We have performed in vitro transcription experiments with either E?70 or E?S, using the whole E. coli genome as template, to identify promoter regions selectively recognized by two forms of RNA polymerase by using E.coli genome 2.0 GeneChips.

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

SUBMITTER: Clelia Peano 

PROVIDER: E-GEOD-22207 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress