Promoter-proximal transcription-translation coupling controls early transcription in Escherichia coli

We report a new but determining pathway of mRNA quality control by transcription-translation coupling (TTC), which inhibits the generation of untranslatable mRNAs from the promoter-proximal region when transcription is decoupled from translation. Single-molecule mRNA FISH shows that the 5’ end-proximal regions of mRNA, of which amount reflects transcription initiation, are not generated without translation. The decoupling between transcription and translation results in the occupancy of RNAPs only within 250 base pairs from the transcription start site. It is further supported by the observation that RNAP decoupled with translation elongates mRNA only 80-90 bp on average in vivo. We show that the length of RNAP elongation before coupling with the ribosome (i.e., 5’-UTR length) determines the mRNA expression level. Our results demonstrate that the ribosome-coupling near the promoter-proximal region, within 100 bp from the transcription start site, functions as an mRNA-quality control, critical for the efficient synthesis of translatable mRNAs by RNAPs. The limited processivity of RNAP before coupling with ribosome provides a potential explanation of the natural distribution of 5’-UTR lengths in E. coli, where longer than 100 bp 5’-UTRs are rare. We performed chromatin immunoprecipitation with exonuclease sequencing (ChIP-exo) on E. coli strains harboring either wild-type or dRBSdATG (ribosome binding site- and start codon-removed) genes. The target proteins for ChIP-exo were the RNA polymerase beta subunit and a synthetic 8-myc-tagged NusG.