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E-GEOD-22207 - Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase

Status
Released on 31 May 2011, last updated on 27 March 2012
Organism
Escherichia coli str. K-12 substr. MG1655
Samples (4)
Array (1)
Protocols (6)
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 aσS-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. We have performed in vitro transcription experiments with either Eσ70 or EσS, 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.
Experiment type
transcription profiling by array 
Contacts
Clelia Peano <clelia.peano@itb.cnr.it>, Alessandro Pietrelli, Anna Maciąg, Gianluca De Bellis, Paolo Landini, Thomas Egli
Citation
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-22207.idf.txt
Sample and data relationshipE-GEOD-22207.sdrf.txt
Raw data (1)E-GEOD-22207.raw.1.zip
Processed data (1)E-GEOD-22207.processed.1.zip
Array designA-AFFY-56.adf.txt
R ExpressionSetE-GEOD-22207.eSet.r
Links