Comprehensive mapping of transcription terminator Rho utilization (Rut) sites across the Bacillus subtilis genome
Mildred Delaleau, Vladimir Bidnenko, Eric Eveno, Gergana Kostova, Johnathan C Black, Stephen McGovern, Olivier Pellegrini, Sandra Dérozier, Matthieu Jules, Ciaran Condon, Sylvain Durand, Elena Bidnenko, Marc Boudvillain
TL;DR
This study maps Rho utilization sites in Bacillus subtilis to understand how Rho-dependent transcription termination regulates gene expression.
Contribution
The study provides a comprehensive genome-wide map of Rho utilization (Rut) sites in B. subtilis using Helicase-SELEX.
Findings
Helicase-SELEX identified 600 Rut sites using BsRho and 4189 using EcRho.
BsRho prefers short unstructured motifs, while EcRho acts on more structured RNAs.
Rho-dependent regulation and PNPase-mediated processing were confirmed in vivo.
Abstract
Recent evidence indicates that the bacterial Rho helicase regulates Bacillus subtilis gene expression in a growth-dependent manner. This regulation, along with extensive in vivo trimming of Rho-dependent transcript 3′-ends, complicates the identification of Rho-dependent transcription terminators using standard transcriptomic approaches. To overcome this challenge, we applied Helicase-SELEX to precisely map Rho utilization (Rut) sites genome-wide. Using B. subtilis Rho (BsRho), we identified 600 putative Rut sites, while the more permissive Escherichia coli Rho (EcRho) revealed 4189 sites, including specimens known to regulate B. subtilis genes. Comparative analysis showed that both enzymes recognize similar pyrimidine-rich sequences, though BsRho favors short unstructured Rut motifs whereas EcRho can act on presumably more structured RNAs without requiring accessory factors. In vivo…
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Taxonomy
TopicsBacterial Genetics and Biotechnology · Genomics and Phylogenetic Studies · Bacteriophages and microbial interactions