Journal
NATURE COMMUNICATIONS
Volume 9, Issue -, Pages -Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/s41467-018-03902-9
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Funding
- European Research Council [261227]
- Wellcome Trust [110164/Z/15/Z]
- UK BBSRC [BB/H01795X/1, BB/J00054X/1]
- US National Science Foundation grant [1309306]
- EPA Cephalosporin Junior Research Fellowship at Linacre College, Oxford
- Interdisciplinary Center for Clinical Research (IZKF) at the University Hospital of the University of Erlangen-Nuremberg
- Instrumentarium Science Foundation
- Finnish Cultural Foundation
- Alfred Kordelin Foundation
- Russian Foundation for Basic Research grant [17-54-150009]
- BBSRC [BB/H01795X/1, BB/J00054X/1] Funding Source: UKRI
- Div Of Biological Infrastructure
- Direct For Biological Sciences [1309306] Funding Source: National Science Foundation
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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.
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