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| Status |
Public on May 31, 2011 |
| Title |
Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase. |
| Platform organism |
Escherichia coli |
| Sample organism |
Escherichia coli str. K-12 substr. MG1655 |
| Experiment type |
Expression profiling by array
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| Summary |
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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| Overall design |
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.
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| Contributor(s) |
Maciąg A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P |
| Citation(s) |
21398637 |
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| Submission date |
Jun 08, 2010 |
| Last update date |
Mar 08, 2019 |
| Contact name |
Clelia Peano |
| E-mail(s) |
clelia.peano@itb.cnr.it
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| Phone |
0039-0226422705
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| Fax |
0039-0226422770
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| Organization name |
National Research Council
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| Department |
Institute of Biomedical Technologies
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| Street address |
Via Fratelli Cervi 93
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| City |
Segrate, Milano |
| ZIP/Postal code |
20090 |
| Country |
Italy |
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| Platforms (1) |
| GPL3154 |
[E_coli_2] Affymetrix E. coli Genome 2.0 Array |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA128873 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE22207_RAW.tar |
4.9 Mb |
(http)(custom) |
TAR (of CEL, CHP) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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