Functionally uncoupled transcription-translation in Bacillus subtilis

Coupled 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 the RNA polymerase (RNAP)(3-11), forming a signal-integration hub for co-transcriptional regulation that includes translation-based attenuation(12,13) and RNA quality control(2). However, whether transcription-translation coupling – together with its broad functional consequences – is indeed a fundamental characteristic outside the well-studied Escherichia coli remains unresolved. 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 a diminished role of Rho-dependent transcription termination, as well as the prevalence of mRNA leaders that utilize riboswitches and RNA-binding proteins. More broadly, we identified widespread genomic signatures of runaway transcription in distinct phyla across the bacterial domain of life. Our results demonstrate 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.