Forward translocation is the natural pathway of RNA release at an intrinsic terminator.
Intrinsic terminators of bacterial RNA polymerase are small (< approximately 30 bp) sequences containing a dyad symmetry that encodes a hairpin in the RNA, followed immediately by a uridine-rich stretch of 5-9 nucleotides just before the site of RNA release. Formation of the RNA hairpin destabilizes the elongation complex, leading to transcript release. We test a model in which hair-pin formation drives RNA polymerase and the melted DNA bubble downstream without transcript elongation, thus releasing the transcript from its enclosure within the enzyme as an RNA/DNA hybrid. We show that blocking downstream translocation of RNAP and preventing downstream DNA unwinding both inhibit transcript release. We argue that translocation of RNA polymerase is essential and that translocation of the bubble stimulates, but is not required, for RNA release; we conclude that forward translocation is the natural pathway of RNA release at an intrinsic terminator.
Santangelo
Thomas J
TJ
Department of Molecular Biology and Genetics, 349 Biotechnology Building, Cornell University, Ithaca, NY 14853, USA.
Roberts
Jeffrey W
JW
D001426:Bacterial Proteins / Q000378:metabolism*; D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry / Q000378:metabolism*; D013728:Terminator Regions, Genetic; D014158:Transcription, Genetic
D001426:Bacterial Proteins; D012329:RNA, Bacterial; D004247:DNA; D012321:DNA-Directed RNA Polymerases