Unusual metal specificity and structure of the group I ribozyme from Chlamydomonas reinhardtii 23S rRNA

Tai Chih Kuo, Obed W. Odom, David L. Herrin

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Group I intron ribozymes require cations for folding and catalysis, and the current literature indicates that a number of cations can promote folding, but only Mg2+ and Mn2+ support both processes. However, some group I introns are active only with Mg2+, e.g. three of the five group I introns in Chlamydomonas reinhardtii. We have investigated one of these ribozymes, an intron from the 23S LSU rRNA gene of Chlamydomonas reinhardtii (Cr.LSU), by determining if the inhibition by Mn2+ involves catalysis, folding, or both. Kinetic analysis of guanosine-dependent cleavage by a Cr.LSU ribozyme, 23S.5ΔGb, that lacks the 3′ exon and intron-terminal G shows that Mn2+ does not affect guanosine binding or catalysis, but instead promotes misfolding of the ribozyme. Surprisingly, ribozyme misfolding induced by Mn2+ is highly cooperative, with a Hill coefficient larger than that of native folding induced by Mg2+. At lower Mn2+ concentrations, metal inhibition is largely alleviated by the guanosine cosubstrate (GMP). The concentration dependence of guanosine cosubstrate-induced folding suggests that it functions by interacting with the G binding site, perhaps by displacing an inhibitory Mn2+. Because of these and other properties of Cr.LSU, the tertiary structure of the intron from 23S.5ΔGb was examined using Fe2+-EDTA cleavage. The ground-state structure shows evidence of an unusually open ribozyme core: the catalytic P3-P7 domain and the nucleotides that connect it to the P4-P5-P6 domain are exposed to solvent. The implications of this structure for the in vitro and in vivo properties of this intron ribozyme are discussed.

Original languageEnglish
Pages (from-to)2631-2644
Number of pages14
JournalFEBS Journal
Volume273
Issue number12
DOIs
Publication statusPublished - Jun 2006

Fingerprint

Chlamydomonas reinhardtii
Catalytic RNA
Introns
Metals
Guanosine
Catalysis
Cations
GIR1 ribozyme
rRNA Genes
Edetic Acid
Ground state
Exons
Catalytic Domain
Nucleotides
Genes
Binding Sites
Kinetics

Keywords

  • Fe-EDTA
  • Group I intron
  • Mn
  • RNA structure
  • RNA-metal interactions

ASJC Scopus subject areas

  • Biochemistry

Cite this

Unusual metal specificity and structure of the group I ribozyme from Chlamydomonas reinhardtii 23S rRNA. / Kuo, Tai Chih; Odom, Obed W.; Herrin, David L.

In: FEBS Journal, Vol. 273, No. 12, 06.2006, p. 2631-2644.

Research output: Contribution to journalArticle

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