High intrinsic hydrolytic activity of cyanobacterial RNA polymerase compensates for the absence of transcription proofreading factors

• Published in: Nucleic acids research Vol. 48; no. 3; pp. 1341 - 1352
• Main Authors: Riaz-Bradley, Amber, James, Katherine, Yuzenkova, Yulia
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 20.02.2020
• Subjects: Cyanobacteria - genetics; Database Issue; DNA-Directed RNA Polymerases - genetics; Escherichia coli - genetics; Hydrolysis; RNA, Bacterial - genetics; Transcription Elongation, Genetic; Transcription, Genetic; Transcriptional Elongation Factors - genetics
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkz1130

Abstract The vast majority of organisms possess transcription elongation factors, the functionally similar bacterial Gre and eukaryotic/archaeal TFIIS/TFS. Their main cellular functions are to proofread errors of transcription and to restart elongation via stimulation of RNA hydrolysis by the active centre of RNA polymerase (RNAP). However, a number of taxons lack these factors, including one of the largest and most ubiquitous groups of bacteria, cyanobacteria. Using cyanobacterial RNAP as a model, we investigated alternative mechanisms for maintaining a high fidelity of transcription and for RNAP arrest prevention. We found that this RNAP has very high intrinsic proofreading activity, resulting in nearly as low a level of in vivo mistakes in RNA as Escherichia coli. Features of the cyanobacterial RNAP hydrolysis are reminiscent of the Gre-assisted reaction—the energetic barrier is similarly low, and the reaction involves water activation by a general base. This RNAP is resistant to ubiquitous and most regulatory pausing signals, decreasing the probability to go off-pathway and thus fall into arrest. We suggest that cyanobacterial RNAP has a specific Trigger Loop domain conformation, and isomerises easier into a hydrolytically proficient state, possibly aided by the RNA 3′-end. Cyanobacteria likely passed these features of transcription to their evolutionary descendants, chloroplasts.