Structural basis of transcriptional regulation by a nascent RNA element, HK022 putRNA
Seungha Hwang, Paul Dominic B. Olinares, Jimin Lee, Jinwoo Kim, Brian T. Chait, Rodney A. King, Jin Young Kang
Abstract
Abstract Transcription, in which RNA polymerases (RNAPs) produce RNA from DNA, is the first step of gene expression. As such, it is highly regulated either by trans -elements like protein factors and/or by cis -elements like specific sequences on the DNA. Lambdoid phage HK022 contains a cis -element, put , which suppresses pausing and termination during transcription of the early phage genes. The put RNA transcript solely performs the anti-pausing/termination activities by interacting directly with the E.coli RNAP elongation complex (EC) by an unknown structural mechanism. In this study, we reconstituted put RNA-associated ECs and determined the structures using cryo-electron microscopy. The determined structures of put RNA-associated EC, put RNA-absent EC, and σ 70 -bound EC suggest that the put RNA interaction with the EC counteracts swiveling, a conformational change previously identified to promote pausing and σ 70 might modulate put RNA folding via σ 70 -dependent pausing during elongation.