σ38-dependent promoter-proximal pausing by bacterial RNA polymerase

Area of Science:

• Molecular Biology
• Bacterial Transcription
• Gene Regulation

Background:

• Bacterial transcription initiation relies on RNA polymerase (RNAP) and sigma (σ) subunits for promoter recognition.
• Housekeeping genes utilize a principal σ subunit that can induce RNAP pausing post-initiation.
• The role of the stationary phase and stress response σ38 subunit in RNAP pausing was not fully understood.

Purpose of the Study:

• To investigate the ability of the σ38 subunit to induce pausing in bacterial transcription.
• To elucidate the mechanism by which σ38 induces pausing and identify factors involved.
• To assess the prevalence of σ38-dependent pausing in bacterial gene expression.

Main Methods:

• Utilized DNA templates with promoter-like motifs in transcribed regions.
• Studied pausing of Escherichia coli RNAP dependent on σ38.
• Investigated the role of σ38-DNA and σ38-RNAP core enzyme interactions.
• Examined reactivation of paused complexes by Gre factors.

Main Results:

• The σ38 subunit induces pausing of Escherichia coli RNAP on specific DNA templates.
• Pausing depends on σ38 contacts with DNA and the RNAP core enzyme.
• σ38-induced pausing results in backtracked transcription elongation complexes.
• Gre factors can reactivate these backtracked complexes via RNA cleavage.
• Analysis suggests σ38 acts in cis during initiation, recognizing pause signals.

Conclusions:

• The σ38 subunit plays a role in regulating bacterial transcription by inducing RNAP pausing.
• σ38-dependent pausing may be a common regulatory mechanism in bacteria.
• Understanding σ38-mediated pausing provides insights into bacterial gene expression control.