Dynamic insights on transcription initiation and RNA processing during bacterial adaptation

Area of Science:

• Molecular Biology
• Microbiology
• Genetics

Background:

• Gene expression regulation is crucial for bacterial adaptation.
• Transcription initiation and RNA processing are key processes that reshape the RNA landscape.
• Simultaneously observing these processes provides insights into bacterial responses.

Purpose of the Study:

• To simultaneously observe transcription initiation and RNA processing during bacterial adaptation to an environmental signal.
• To investigate the kinetics and patterns of these fundamental processes.
• To understand the interplay between transcription and RNA processing in gene expression control.

Main Methods:

• Utilized a controlled sigma-E (σ^E) system in *E. coli*.
• Employed a previously described tagRNA-seq method to obtain process kinetics.
• Tracked changes in transcription initiation frequencies (TIF) and RNA processing frequencies (PF) using 5' RNA tags.

Main Results:

• Observed a binary pattern of increased/decreased TIF, leading to transcriptional oscillation.
• Identified three categories of RNA processing frequencies: constant, RNA-level dependent, and TIF-correlated.
• Revealed a dynamic interplay between transcription initiation and RNA cleavage site activity.

Conclusions:

• This study offers a comprehensive view of transcriptomic reshaping during bacterial adaptation.
• The findings highlight a novel interplay between transcription initiation and RNA processing.
• The methodology serves as a blueprint for studying bacterial gene expression control via RNA metabolism.