Architecture and folding mechanism of the Azoarcus group I pre-tRNA

Prashanth Rangan, Benoît Masquida, Eric Westhof, Sarah A. Woodson

Research output: Contribution to journalArticle

Abstract

Self-splicing RNAs must evolve to function in their specific exon context. The conformation of a group I pre-tRNAile from the bacterium Azoarcus was probed by ribonuclease T1 and hydroxyl radical cleavage, and by native gel electrophoresis. Biochemical data and three-dimensional models of the pre-tRNA showed that the tRNA is folded, and that the tRNA and intron sequences form separate tertiary domains. Models of the active site before steps 1 and 2 of the splicing reaction predict that exchange of the external G-cofactor and the 3′-terminal G is accomplished by a slight conformational change in P9.0 of the Azoarcus group I intron. Kinetic assays showed that the pre-tRNA folds in minutes, much more slowly than the intron alone. The dependence of the folding kinetics on Mg2+ and the concentration of urea, and RNase T1 experiments showed that formation of native pre-tRNA is delayed by misfolding of P3-P9, including mispairing beween residues in P9 and the tRNA. Thus, although the intron and tRNA sequences form separate domains in the native pre-tRNA, their folding is coupled via metastable non-native base-pairs. This could help prevent premature processing of the 5′ and 3′ ends of unspliced pre-tRNA.

Original languageEnglish (US)
Pages (from-to)41-51
Number of pages11
JournalJournal of molecular biology
Volume339
Issue number1
DOIs
StatePublished - May 21 2004

Keywords

  • RNA modelling
  • RNase, ribonuclease
  • exoG, external G-cofactor
  • group I ribozyme
  • hydroxyl radical footprinting
  • tRNA splicing

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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