biostudies-literatureLi XNSFNHLBI NIH HHSNational Institutes of HealthNational Science Foundation254-266https://www.ebi.ac.uk/biostudies/studies/S-EPMC9822797biostudies-literatureUnknown122(1)Under certain cellular conditions, transcription and mRNA translation in prokaryotes appear to be "coupled," in which the formation of mRNA transcript and production of its associated protein are temporally correlated. Such transcription-translation coupling (TTC) has been evoked as a mechanism that speeds up the overall process, provides protection against premature termination, and/or regulates the timing of transcript and protein formation. What molecular mechanisms underlie ribosome-RNAP coupling and how they can perform these functions have not been explicitly modeled. We develop and analyze a continuous-time stochastic model that incorporates ribosome and RNAP elongation rates, initiation and termination rates, RNAP pausing, and direct ribosome and RNAP interactions (exclusion and biBiophysical journalStochastic dynamics and ribosome-RNAP interactions in transcription-translation coupling.PMC9822797DMS-1814364R01 HL146552R01HL146552Li XChou TfalseStochastic dynamics and ribosome-RNAP interactions in transcription-translation coupling.Under certain cellular conditions, transcription and mRNA translation in prokaryotes appear to be "coupled," in which the formation of mRNA transcript and production of its associated protein are temporally correlated. Such transcription-translation coupling (TTC) has been evoked as a mechanism that speeds up the overall process, provides protection against premature termination, and/or regulates the timing of transcript and protein formation. What molecular mechanisms underlie ribosome-RNAP coupling and how they can perform these functions have not been explicitly modeled. We develop and analyze a continuous-time stochastic model that incorporates ribosome and RNAP elongation rates, initiation and termination rates, RNAP pausing, and direct ribosome and RNAP interactions (exclusion and bi2023-01-01T00:00:00Z2023 Jan2025-04-26T07:53:30.49Z2025-04-06T12:27:35.976ZS-EPMC98227973619925010.1016/j.bpj.2022.09.041