Functionally uncoupled transcription-translation in Bacillus subtilis

Tight coupling of transcription and translation is considered a defining feature of bacterial gene expression^1,2. The pioneering ribosome can both physically associate and kinetically coordinate with RNA polymerase (RNAP)^3-11, forming a signal-integration hub for co-transcriptional regulation that includes translation-based attenuation^12,13 and RNA quality control². However, it remains unclear whether transcription-translation coupling—together with its broad functional consequences—is indeed a fundamental characteristic of bacteria other than Escherichia coli. Here we show that RNAPs outpace pioneering ribosomes in the Gram-positive model bacterium Bacillus subtilis, and that this `runaway transcription' creates alternative rules for both global RNA surveillance and translational control of nascent RNA. In particular, uncoupled RNAPs in B. subtilis explain the diminished role of Rho-dependent transcription termination, as well as the prevalence of mRNA leaders that use riboswitches and RNA-binding proteins. More broadly, we identified widespread genomic signatures of runaway transcription in distinct phyla across the bacterial domain. Our results show that coupled RNAP-ribosome movement is not a general hallmark of bacteria. Instead, translation-coupled transcription and runaway transcription constitute two principal modes of gene expression that determine genome-specific regulatory mechanisms in prokaryotes.