DksA Guards Elongating RNA Polymerase against Ribosome-Stalling-Induced Arrest

In bacteria, translation-transcription coupling inhibits RNA polymerase (RNAP) stalling. We present evidence suggesting that, upon amino acid starvation, inactive ribosomes promote rather than inhibit RNAP stalling. We developed an algorithm to evaluate genome-wide polymerase progression independently of local noise and used it to reveal that the transcription factor DksA inhibits promoter-proximal pausing and increases RNAP elongation when uncoupled from translation by depletion of charged tRNAs. DksA has minimal effect on RNAP elongation in vitro and on untranslated RNAs in vivo. In these cases, transcripts can form RNA structures that prevent backtracking. Thus, the effect of DksA on transcript elongation may occur primarily upon ribosome slowing/stalling or at promoter-proximal locations that limit the potential for RNA structure. We propose that inactive ribosomes prevent formation of backtrack-blocking mRNA structures and that, in this circumstance, DksA acts as a transcription elongation factor in vivo. [Display omitted] •Stalled ribosomes promote genome-wide transcription stalling•DksA prevents transcription arrest upon ribosome stalling•RPP is a sensitive and robust measurement for polymerase elongation in vivo•DksA modulates both transcription initiation and elongation in bacteria Translation and transcription are spatially coupled in bacteria. Zhang et al. develop a measurement for polymerase elongation to reveal that stalled translation promotes transcription stalling beyond promoter-proximal regions. The secondary-channel-interacting protein DksA modulates both transcription initiation and elongation and prevents transcription arrest upon ribosome stalling in amino acid-starved cells.