Stabilizing Obligatory Non-native Intermediates Along Co-transcriptional Folding Trajectories of SRP RNA Affects Cell Viability

Abstract

SummarySignal recognition particle (SRP) inEscherichia colicomprises protein Ffh and SRP RNA. Its essential functionality—co-translational protein-targeting/delivery to cellular membranes— hinges on the RNA attaining a native long-hairpin fold that facilitates protein conformational rearrangements within the SRP complex. Since RNA folds co-transcriptionally on RNA polymerase, we use high-resolution optical tweezers to first characterize the mechanical unfolding/refolding of incrementally lengthened RNAs from stalled transcription complexes until reaching the full-length transcript. This analysis allows identification of folding intermediates adopted during the real-time co-transcriptional folding of SRP RNA. The co-transcriptional folding trajectories are surprisingly invariant to transcription rates, and involve formation of an obligatory non-native hairpin intermediate that eventually resolves into the native fold. SRP RNA variants designed to stabilize this non-native intermediate—likely sequestering the SRP ribonucleoprotein complex in an inactive form—greatly reduce cell viability, indicating that the same co-transcriptional folding mechanism operatesin vivoand possible alternative antibiotic strategies.HighlightsFolding pathway of an essential functional RNA has been resolved co-transcriptionally.The co-transcriptional folding pathway of SRP RNA is invariant to transcription rates.Nascent SRP RNA obligatorily forms a non-native intermediate before adopting the native fold.Modulating transitions from the non-native to native SRP RNA hairpin fold alters cell viability.