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A functional ribosomal RNA tertiary structure involves a base triple interaction

G L Conn1, R R Gutell, D E Draper

  • 1Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA.

Biochemistry
|August 26, 1998
PubMed
Summary
This summary is machine-generated.

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Evolutionary analysis reveals a conserved base triple in ribosomal RNA. This RNA structure is crucial for maintaining tertiary folding and interactions with ribosomal protein L11 and thiostrepton.

Area of Science:

  • Molecular Biology
  • Structural Biology
  • Evolutionary Biology

Background:

  • The L11 binding domain of 23S ribosomal RNA plays a critical role in protein synthesis.
  • Understanding the structural dynamics and evolutionary conservation of this domain is key to deciphering its function.

Purpose of the Study:

  • To investigate the functional significance of a conserved nucleotide exchange pattern at positions (1092/1099)1072 in the 23S ribosomal RNA L11 binding domain.
  • To elucidate the role of this pattern in RNA tertiary structure formation and ligand binding.

Main Methods:

  • Comparative sequence analysis to identify evolutionary patterns.
  • RNA variant analysis using UV melting to assess tertiary structure.
  • Ribosomal protein L11 and thiostrepton binding assays to evaluate functional impact.

Related Experiment Videos

Main Results:

  • A coordinated nucleotide exchange at positions (1092/1099)1072, occurring at least 4 times during evolution, suggests a base triple formation.
  • Alteration of the unpaired nucleotide C1072 to U abolished tertiary structure and reduced ligand binding by 10-fold.
  • Substitution of the base pair CG1092/1099 to UA allowed tertiary structure formation but altered pH dependence.
  • A fully compensated mutation (CG)C to (UA)U restored wild-type like tertiary structure and ligand binding.

Conclusions:

  • The identified base triple at (1092/1099)1072 is essential for the proper tertiary folding of the 23S ribosomal RNA L11 binding domain.
  • This base triple significantly influences the interaction with ribosomal protein L11 and the antibiotic thiostrepton.
  • The findings provide insights into RNA folding mechanisms and the evolution of functional RNA structures.