Extensive functional overlap between sigma factors in Escherichia coli

Area of Science:

• Bacterial molecular biology
• Gene regulation
• Transcription initiation

Background:

• Bacterial RNA polymerase (RNAP) requires sigma factors for promoter recognition.
• Escherichia coli possesses seven sigma factors, each thought to regulate distinct promoter sets.
• The precise in vivo targets and regulatory scope of sigma factors are not fully elucidated.

Purpose of the Study:

• To identify the in vivo targets of the sigma32 (heat-shock) sigma factor in E. coli.
• To investigate the extent of promoter overlap between different sigma factors, specifically sigma32 and sigma70 (housekeeping).
• To explore potential novel regulatory functions of sigma32.

Main Methods:

• Genome-wide microarray analysis to identify in vivo sigma32 promoter targets.
• In vitro transcription assays to assess promoter utilization efficiency and initiation sites.
• Bioinformatic analysis of DNA sequence motifs for promoter regions.

Main Results:

• Identified 87 in vivo targets for sigma32, estimating 120-150 total sigma32 promoters.
• Discovered that 25% of sigma32 targets reside within coding regions, indicating potential non-canonical roles.
• Observed significant overlap between sigma32 and sigma70 promoter targets, with interdigitated DNA motifs.
• Found similar transcription initiation efficiency and site selection by RNAP-sigma70 and RNAP-sigma32 in vitro.
• Noted extensive overlap between sigmaE and sigma70 regulated promoters.

Conclusions:

• Sigma factors in E. coli exhibit substantial functional overlap in promoter recognition.
• Sigma32 plays regulatory roles beyond canonical heat-shock response, including within coding regions.
• The extensive overlap suggests a complex regulatory network where multiple sigma factors can access and utilize similar promoter elements.