  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 during the transcription,
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 binding). Our model predicts how distributions
of delay times depend on these molecular features of transcription and
translation. We also propose additional measures for TTC: a direct
ribosome-RNAP binding probability and the fraction of time the
translation-transcription process is "protected" from attack by
transcription-terminating proteins. These metrics quantify different aspects of
TTC and differentially depend on parameters of known molecular processes. We
use our metrics to reveal how and when our model can exhibit either
acceleration or deceleration of transcription, as well as protection from
termination. Our detailed mechanistic model provides a basis for designing new
experimental assays that can better elucidate the mechanisms of TTC.
