Blocked transcription-translation complexes are rescued by transcript release followed by trans-translation.

UNLABELLED: Bacterial ribosomes initiate translation while the nascent transcript is still engaged with RNA polymerase, creating a risk that translating ribosomes will become trapped if RNA polymerase is blocked before transcription of the stop codon. Here we show that DNA-binding proteins block RNA polymerase and translating ribosomes in vitro and in vivo. Translating ribosomes are rescued after they trigger the release of the nascent transcript from RNA polymerase. Following the release of the transcript, ribosomes translate to the 3' end of the mRNA and are rescued by trans-translation. This mechanism allows the rescue of all components of blocked transcription-translation reactions. IMPORTANCE: Co-transcriptional translation in bacteria provides an efficient means to produce proteins but creates a risk that translating ribosomes could become trapped if RNA polymerase is blocked during transcription. We show that when RNA polymerase is blocked, a translating ribosome triggers the release of the nascent mRNA from the polymerase, and the ribosome is rescued by trans-translation. This mechanism for resolving blocked transcription-translation complexes explains how bacteria avoid detrimental accumulation of stalled ribosomes.