Old dogmas revisited (and reshaped): bacterial coupled transcription-translation through the eyes of ribosome profiling

Coupled transcription-translation (CTT) is a hallmark of prokaryotic gene expression. CTT occurs when ribosomes bind to and initiate translation of mRNAs whose transcription has not yet terminated, therefore forming RNAP·mRNA·ribosome complexes. Despite illustrating textbooks for decades, the universality and the transcriptome-level predominance of CTT have recently been challenged.

To assess the actual occurrence of CTT in vivo, we have developed a novel ribosome profiling approach that captures the global CTT landscape with single-codon resolution. Preliminary results show that CTT performed by ribosomes translating in physical association with RNAPs is mechanistically different from that performed by ribosomes engaged in remote CTT. Relative comparisons with the overall translation landscape showed that the degree of CTT varies greatly both within and between genes. In particular, genes involved in DNA-related functions show high degrees of CTT, which could ensure the association of the protein product with the nucleoid and prevent its dilution in the cellular volume. Very importantly, CTT appears to be rare for genes encoding proteins forming complexes, such as ribosomes. This implies that the expression of many genes can be initiated by translation-independent transcription and followed by co-localization of untranslated mRNAs, which undergo translation and complex assembly locally.

Our results show that CTT is not as universal as currently assumed. The emerging compartmentalization of gene expression could open so far ignored spatiotemporal windows for gene regulation. Furthermore, this work revolutionizes our view of the subcellular organization of bacterial cells.