Comprehensive transcription terminator atlas for Bacillus subtilis

Area of Science:

• Bacteriology
• Molecular Biology
• Genetics

Background:

• The roles of Rho-dependent and intrinsic transcription termination in bacterial transcriptomes are not fully understood.
• Investigating these mechanisms is crucial for comprehending gene regulation and bacterial physiology.

Purpose of the Study:

• To create a comprehensive atlas of transcription terminators in Bacillus subtilis.
• To elucidate the contributions of NusA, NusG, and Rho proteins to both intrinsic and Rho-dependent termination.
• To identify novel termination mechanisms and regulatory interactions.

Main Methods:

• Transcriptome-wide sequencing of released transcripts from wild-type and mutant Bacillus subtilis strains (deficient in NusA, NusG, and/or Rho).
• Computational analyses using RNAstructure, MEME suite, and DiffLogo.
• In vitro transcription experiments to validate findings.

Main Results:

• NusA and NusG proteins stimulate 77% and 19% of intrinsic terminators, respectively.
• Rho stimulates termination at 10% of intrinsic terminators in vivo, requiring the NusG KOW domain for one instance.
• Rho remodels RNA upstream of weak intrinsic terminators, preventing competing structures and enabling termination.
• Identified 56 putative 'hybrid Rho-dependent termination' events.

Conclusions:

• NusA and NusG are major facilitators of intrinsic transcription termination in Bacillus subtilis.
• Rho actively participates in intrinsic termination, particularly at terminators with suboptimal structures.
• A novel hybrid termination mechanism, combining Rho-stimulated intrinsic termination with Rho-dependent termination, has been discovered.