RT Journal Article
SR Electronic
T1 Pausing controls branching between productive and non-productive pathways during initial transcription
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 199307
DO 10.1101/199307
A1 David Dulin
A1 David L. V. Bauer
A1 Anssi M. Malinen
A1 Jacob J. W. Bakermans
A1 Martin Kaller
A1 Zakia Morichaud
A1 Ivan Petushkov
A1 Martin Depken
A1 Konstantin Brodolin
A1 Andrey Kulbachinskiy
A1 Achillefs N. Kapanidis
YR 2017
UL http://biorxiv.org/content/early/2017/10/06/199307.abstract
AB Transcription in bacteria is controlled by multiple molecular mechanisms that precisely regulate gene expression. Recently, initial RNA synthesis by the bacterial RNA polymerase (RNAP) has been shown to be interrupted by pauses; however, the pausing determinants and the relationship of pausing with productive and abortive RNA synthesis remain poorly understood. Here, we employed single-molecule FRET and biochemical analysis to disentangle the pausing-related pathways of bacterial initial transcription. We present further evidence that region σ3.2 constitutes a barrier after the initial transcribing complex synthesizes a 6-nt RNA (ITC6), halting transcription. We also show that the paused ITC6 state acts as a checkpoint that directs RNAP, in an NTP-dependent manner, to one of three competing pathways: productive transcription, abortive RNA release, or a new unscrunching/scrunching pathway that blocks transcription initiation. Our results show that abortive RNA release and DNA unscrunching are not as tightly coupled as previously thought.