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Escherichia coli str. K-12 substr. MG1655

ABSTRACT: Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.

PROVIDER: PRJNA128873 | ENA |

REPOSITORIES: ENA

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Project description:Promoter recognition by bacterial RNA polymerase is mediated by σ subunits, which assemble transiently to RNA polymerase core enzyme (E) during transcription initiation. σ subunits drive transcription of specific sets of genes by allowing RNA polymerase to interact with different promoter sequences. However, σ70, the housekeeping σ subunit, and σS, an alternative σ 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 σ70 (Eσ70) or with σS (EσS) 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 Eσ70. In contrast, EσS 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 EσS showed reduced expression in EσS -deficient mutant strain of E. coli. Sequence comparison of Eσ70- versus EσS –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 Eσ70.

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