NusG controls transcription pausing and RNA polymerase translocation throughout the <i>Bacillus subtilis</i> genome
Alexander V. Yakhnin, Peter Fitzgerald, Carl McIntosh, Helen Yakhnin, Maria L. Kireeva, Joshua Turek-Herman, Zachary F. Mandell, Mikhail Kashlev, Paul Babitzke
Abstract
Significance Transcription can be transiently halted by pausing of RNAP, which provides additional time for gene regulatory events to occur. NusG is a universally conserved transcription elongation factor that was known to stimulate pausing at two positions in the Bacillus subtilis genome, both of which regulated expression of the downstream gene. Using genome-wide sequencing of nascent RNA, we identified thousands of pause sites in B. subtilis including 1,600 NusG-dependent pause sites. NusG induces pausing of RNAP in response to a conserved TTNTTT sequence motif in the nontemplate DNA strand within the paused transcription bubble. NusG-dependent pausing was confirmed at several pause sites in vitro. NusG-dependent pausing in the ribD riboswitch decreases the concentration of flavin mononucleotide required to regulate ribD expression.