Print Email Facebook Twitter Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria Title Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria Author Dulin, D. (University of Oxford; Friedrich-Alexander-Universität Erlangen-Nürnberg) Bauer, David L.V. (University of Oxford) Malinen, Anssi M. (University of Oxford; University of Turku) Bakermans, Jacob J.W. (University of Oxford) Kaller, Martin (University of Oxford) Morichaud, Zakia (CNRS/Université de Montpellier II) Petushkov, Ivan (Russian Academy of Sciences) Depken, S.M. (TU Delft BN/Martin Depken Lab; Kavli institute of nanoscience Delft) Brodolin, Konstantin (CNRS/Université de Montpellier II) Kulbachinskiy, Andrey (Russian Academy of Sciences) Kapanidis, Achillefs N. (University of Oxford) Date 2018-04-16 Abstract Transcription in bacteria is controlled by multiple molecular mechanisms that precisely regulate gene expression. It has been recently shown that initial RNA synthesis by the bacterial RNA polymerase (RNAP) is interrupted by pauses; however, the pausing determinants and the relationship of pausing with productive and abortive RNA synthesis remain poorly understood. Using single-molecule FRET and biochemical analysis, here we show that the pause encountered by RNAP after the synthesis of a 6-nt RNA (ITC6) renders the promoter escape strongly dependent on the NTP concentration. Mechanistically, the paused ITC6 acts as a checkpoint that directs RNAP to one of three competing pathways: productive transcription, abortive RNA release, or a new unscrunching/scrunching pathway. The cyclic unscrunching/scrunching of the promoter generates a long-lived, RNA-bound paused state; the abortive RNA release and DNA unscrunching are thus not as tightly linked as previously thought. Finally, our new model couples the pausing with the abortive and productive outcomes of initial transcription. To reference this document use: http://resolver.tudelft.nl/uuid:7c953849-4b2e-4bda-bd67-484821ce59b9 DOI https://doi.org/10.1038/s41467-018-03902-9 ISSN 2041-1723 Source Nature Communications, 9 (1) Part of collection Institutional Repository Document type journal article Rights © 2018 D. Dulin, David L.V. Bauer, Anssi M. Malinen, Jacob J.W. Bakermans, Martin Kaller, Zakia Morichaud, Ivan Petushkov, S.M. Depken, Konstantin Brodolin, Andrey Kulbachinskiy, Achillefs N. Kapanidis Files PDF s41467_018_03902_9.pdf 1.54 MB Close viewer /islandora/object/uuid:7c953849-4b2e-4bda-bd67-484821ce59b9/datastream/OBJ/view