Improved RNA stability estimation through Bayesian modeling reveals most Salmonella transcripts have subminute...

Area of Science:

• Microbiology
• Molecular Biology
• Genetics

Background:

• RNA decay is vital for gene expression regulation, particularly under environmental stress.
• Bacterial RNA-binding proteins (RBPs) influence posttranscriptional regulation, but their global effect on RNA stability is not fully understood.

Purpose of the Study:

• To investigate the role of major RBPs, ProQ and CspC/E, in maintaining RNA stability in *Salmonella enterica*.
• To identify transcripts with altered decay rates in the presence and absence of these RBPs.

Main Methods:

• Utilized rifampicin-induced RNA sequencing (RIF-seq) over a time course.
• Developed a hierarchical Bayesian model to analyze differential RNA decay.
• Integrated RIF-seq data with cross-linking and immunoprecipitation followed by RNA sequencing (CLIP-seq).

Main Results:

• The median RNA half-life in *Salmonella* was found to be less than 1 minute, significantly shorter than previously estimated.
• Over 50% of the longest-lived transcripts are bound by at least one major RBP.
• Absence of ProQ or CspC/E led to differential decay in 30-40% of their respective target transcripts, with ProQ implicated in oxidative stress response.

Conclusions:

• RBPs play a significant role in shaping the bacterial transcriptome by regulating RNA stability.
• ProQ and CspC/E are key regulators of RNA decay, influencing gene expression and stress responses in bacteria.