Rho-dependent transcription termination is the dominant mechanism in Mycobacterium tuberculosis

• Published in: Biochimica et biophysica acta. Gene regulatory mechanisms 2023-06, Vol.1866 (2), p.194923-194923, Article 194923
• Main Authors: Ahmad, Ezaz, Mitra, Anirban, Ahmed, Wareed, Mahapatra, Varsha, Hegde, Shubhada R., Sala, Claudia, Cole, Stewart T., Nagaraja, Valakunja
• Format: Article
• Language: English
• Subjects: Escherichia coli - genetics; Factor-dependent termination; Gene expression; Genome-Wide Association Study; Mycobacteria; Mycobacterium tuberculosis - genetics; Rho; RNA - metabolism; Transcription; Transcription, Genetic
• ISSN: 1874-9399; 1876-4320
• DOI: 10.1016/j.bbagrm.2023.194923

Intrinsic and Rho-dependent transcription termination mechanisms regulate gene expression and recycle RNA polymerase in bacteria. Both the modes are well studied in Escherichia coli, and a few other organisms. The understanding of Rho function is limited in most other bacteria including mycobacteria. Here, we highlight the dominance of Rho-dependent termination in mycobacteria and validate Rho as a key regulatory factor. The lower abundance of intrinsic terminators, high cellular levels of Rho, and its genome-wide association with a majority of transcriptionally active genes indicate the pronounced role of Rho-mediated termination in Mycobacterium tuberculosis (Mtb). Rho modulates the termination of RNA synthesis for both protein-coding and stable RNA genes in Mtb. Concordantly, the depletion of Rho in mycobacteria impact its growth and enhances the transcription read-through at 3′ ends of the transcription units. We demonstrate that MtbRho is catalytically active in the presence of RNA with varied secondary structures. These properties suggest an evolutionary adaptation of Rho as the efficient and preponderant mode of transcription termination in mycobacteria. [Display omitted] •Under-representation of intrinsic terminators in mycobacteria.•Rho is abundant in Mycobacterium tuberculosis (Mtb) and Mycobacterium smegmatis.•Genome-wide Rho distribution follows RNA polymerase occupancy profile in mycobacteria.•Mtb Rho binds and interacts with tRNA and other secondary structure containing RNA.•Mycobacteria predominantly rely on Rho for terminating transcription.