RNA polymerase and the ribosome: the close relationship

Abstract

In bacteria transcription and translation are linked in time and space. When coupled to RNA polymerase (RNAP), the translating ribosome ensures transcriptional processivity by preventing RNAP backtracking. Recent advances in the field have characterized important linker proteins that bridge the gap between transcription and translation: In particular, the NusE(S10):NusG complex and the NusG homolog, RfaH. The direct link between the moving ribosome and RNAP provides a basis for maintaining genomic integrity while enabling efficient transcription and timely translation of various genes within the bacterial cell.

Figure 1. Ribosome coupling and Rho mediated polarity

Schematics show the ribosome coupled with RNAP to prevent transcription termination by Rho. Translation that begins prior to Rho loading onto RNA is not subject to transcription polarity (A). Rho binds RNAP throughout the transcription cycle and is readily available to terminate transcription in the absence of a ribosome (B)(7). Strong RBS can engage multiple ribosomes to the same nascent transcript, but only the leading one controls the rate of transcription elongation by preventing RNAP backtracking (C)(10).

Figure 2. Ribosome coupling and genomic integrity

Schematics demonstrate the outcomes for co-directional collisions between the replisome and RNAP. Such collisions with non-backtracked RNAP are mostly benign with respect to genomic integrity (A). However, encounters between the replisome and backtracked RNAP can introduce breaks in the DNA leading strand that could eventually lead to DSBs during the next round of replication (B). In this way the ribosome helps to maintain genomic stability by preventing RNAP backtracking (22). Additional factors that deal with backtracked elongation complexes and contribute to genomic stability are termination factors (Rho and Mfd) and transcript cleavage factors (GreA and GreB) (6, 14, 22).

Figure 3. Bridging the ribosome to RNA polymerase

Schematics demonstrate the known mechanisms for ribosome recruitment to RNAP through the ribosomal subunit NusE (S10). NusG binds to RNAP and complexes with NusE to link the ribosome to RNAP (A)(12). Alternatively, the CTD of NusG can bind Rho-factor, facilitating Rho-mediated termination and precluding binding to NusE (B). The NTD of RfaH binds to RNAP and an ops regulatory site while the CTD of RfaH links RNAP to the ribosome through interactions with NusE (C)(37). Based on the recently identified RfaH fold switching mechanism, it is possible that additional structurally similar factors can recognize specific regulatory elements to draw the ribosome to RNAP and ensure expression of those genes (D).