Abstract
Long 5′ UTRs in bacteria often contain regulatory elements that modulate expression of the downstream gene in response to environmental stimuli. In most examples of such regulation, the mechanism involves switching between alternative 5′ UTR RNA structures that impact transcription, stability, or translation of the mRNA. Here, we show that transcription of the Escherichia coli topAI gene is prematurely terminated by the termination factor Rho under standard laboratory growth conditions, and that this occurs as a result of translational repression. Regulation of topAI translation is controlled by a sensory ORF, toiL, located within the topAI 5′ UTR. We show that ribosomes translating toiL stall in a sequence-specific manner in the presence of specific ribosome-targeting antibiotics. Ribosome stalling at toiL induces conformational changes in the RNA structure of the topAI 5′ UTR, unmasking the topAI ribosome-binding site, thereby relieving translational repression and preventing premature transcription termination. Thus, toiL acts as a sensor of translation stress, leading to regulation of topAI at both the translational and transcriptional levels.