Alternative transcription cycle for bacterial RNA polymerase

Timothy T Harden,Jane Kondev,Mathew Chamberlain,Jeff Gelles,Karina S Herlambang,Christopher D Wells,Ann Hochschild,Gene-Wei Li,Jean-Benoît Lalanne,Robert Landick

doi:10.1038/s41467-019-14208-9

Abstract

RNA polymerases (RNAPs) transcribe genes through a cycle of recruitment to promoter DNA, initiation, elongation, and termination. After termination, RNAP is thought to initiate the next round of transcription by detaching from DNA and rebinding a new promoter. Here we use single-molecule fluorescence microscopy to observe individual RNAP molecules after transcript release at a terminator. Following termination, RNAP almost always remains bound to DNA and sometimes exhibits one-dimensional sliding over thousands of basepairs. Unexpectedly, the DNA-bound RNAP often restarts transcription, usually in reverse direction, thus producing an antisense transcript. Furthermore, we report evidence of this secondary initiation in live cells, using genome-wide RNA sequencing. These findings reveal an alternative transcription cycle that allows RNAP to reinitiate without dissociating from DNA, which is likely to have important implications for gene regulation.

Highlights

RNA polymerases (RNAPs) transcribe genes through a cycle of recruitment to promoter DNA, initiation, elongation, and termination
Our results suggest an expanded version of the bacterial transcription pathway (Fig. 6), in which core RNAP retention on DNA after intrinsic termination can lead to synthesis of antisense transcripts
In the canonical transcription cycle (Fig. 6, gray arrows) holoenzyme formed by association of a sigma protein with core RNAP initiates at a sense transcription promoter and elongates a transcript

Summary

Introduction

RNA polymerases (RNAPs) transcribe genes through a cycle of recruitment to promoter DNA, initiation, elongation, and termination. We report evidence of this secondary initiation in live cells, using genome-wide RNA sequencing These findings reveal an alternative transcription cycle that allows RNAP to reinitiate without dissociating from DNA, which is likely to have important implications for gene regulation. In the canonical bacterial transcription cycle, transcript synthesis concludes when release of the nascent RNA molecule from the polymerase is triggered by specific DNA sequences (intrinsic terminators) or by termination factors (e.g., the E. coli Rho protein)[4]. We show evidence from endenhanced genome-wide RNA sequencing suggesting that the alternative cycle is a widespread mechanism for synthesis of antisense transcripts in bacteria

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Results

Conclusion