Robo-Therm, a pipeline to RNA thermometer discovery and validation.

Area of Science:

• Molecular Biology
• Bioinformatics
• Genomics

Background:

• RNA thermometers are structured noncoding RNAs in 5'-UTRs controlling gene expression via temperature-induced conformational changes.
• Discovering RNA thermometers using bioinformatics is challenging due to limited sequence conservation.
• The prevalence of these thermosensitive regulatory elements is not well understood.

Purpose of the Study:

• To develop an advanced pipeline for discovering and validating RNA thermometers.
• To identify novel RNA thermometers in bacterial and bacteriophage genomes.

Main Methods:

• Developed Robo-Therm, a pipeline integrating in silico motif searching with a reporter system.
• Applied Robo-Therm to search for RNA thermometers in various genomes.

Main Results:

• Discovered two novel RNA thermometers using the Robo-Therm pipeline.
• Identified one thermometer in the 5'-UTR of a sigma RNA polymerase subunit gene in *Mediterraneibacter gnavus* and *Bacteroides pectinophilus*, and in Caudoviricetes bacteriophage.
• Found another thermometer in the 5'-UTR of a tetracycline resistance gene (*tetR*) in *Escherichia coli* and *Shigella flexneri*.

Conclusions:

• The Robo-Therm pipeline is effective for discovering RNA thermometers across diverse genomes.
• This study expands the known repertoire of RNA thermometers in the human gut microbiome.
• Robo-Therm facilitates the identification of thermosensitive regulatory elements, crucial for understanding gene expression.