Preferential interaction of the his pause RNA hairpin with RNA polymerase beta subunit residues 904-950 correlates with strong transcriptional pausing.
RNA secondary structures (hairpins) that form as the nascent RNA emerges from RNA polymerase are important components of many signals that regulate transcription, including some pause sites, all rho-independent terminators, and some antiterminators. At the his leader pause site, a 5-bp-stem, 8-nt-loop pause RNA hairpin forms 11 nt from the RNA 3' end and stabilizes a transcription complex conformation slow to react with NTP substrate. This stabilization appears to depend at least in part on an interaction with RNA polymerase. We tested for RNA hairpin interaction with the paused polymerase by crosslinking 5-iodoUMP positioned specifically in the hairpin loop. In the paused conformation, strong and unusual crosslinking of the pause hairpin to beta904-950 replaced crosslinking to beta' and to other parts of beta that occurred in nonpaused complexes prior to hairpin formation. These changes in nascent RNA interactions may inhibit reactive alignment of the RNA 3' end in the paused complex and be related to events at rho-independent terminators.
Wang
D
D
Division of Biology and Biomedical Sciences, Washington University, St. Louis, MO 63130, USA.
Severinov
K
K
Landick
R
R
D000595:Amino Acid Sequence; D003432:Cross-Linking Reagents; D012321:DNA-Directed RNA Polymerases / Q000235:genetics* / Q000378:metabolism; D006632:Histamine / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D016415:Sequence Alignment; D014158:Transcription, Genetic
D003432:Cross-Linking Reagents; D012313:RNA; D006632:Histamine; D012321:DNA-Directed RNA Polymerases