Preferential interaction of the his pause RNA hairpin with RNA polymerase β subunit residues 904-950 correlates with strong transcriptional pausing

Daguang Wang, Konstantin Severinov, Robert Landick

Research output: Contribution to journalArticlepeer-review

29 Citations (Scopus)

Abstract

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 p-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 β904-950 replaced crosslinking to β and to other parts of β 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 p-independent terminators.

Original languageEnglish
Pages (from-to)8433-8438
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume94
Issue number16
DOIs
Publication statusPublished - 5 Aug 1997
Externally publishedYes

Keywords

  • Crosslinking
  • RNA polymerase
  • RNA secondary structure
  • Transcription complex
  • Transcriptional pausing

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