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Related Experiment Videos

A protonated base pair participating in rRNA tertiary structural interactions.

A V Kubarenko1, P V Sergiev, A A Bogdanov

  • 1Department of Chemistry, Moscow State University, Moscow 119899, Russia.

Nucleic Acids Research
|January 29, 2002
PubMed
Summary

Protonated bases in Escherichia coli 23S ribosomal RNA were identified using chemical probing. These charged base pairs are essential for ribosomal subunit structure and function.

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • Ribosomes are essential molecular machines responsible for protein synthesis.
  • The 50S ribosomal subunit contains 23S ribosomal RNA (rRNA), a key structural and catalytic component.
  • Previous studies revealed non-Watson-Crick base pairing in archaeal ribosomes.

Purpose of the Study:

  • To investigate the presence and structural role of charged base pairs in Escherichia coli 23S rRNA.
  • To confirm the protonation state of specific residues predicted to form isostructural base pairs with archaeal counterparts.
  • To identify novel charged base pairs within the E. coli ribosome.

Main Methods:

  • X-ray crystallography of Haloarcula marismortui ribosomes.
  • Comparative analysis of rRNA secondary structures between H. marismortui and E. coli.

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  • Chemical probing using sodium borohydride reduction.
  • Primer extension analysis to detect modified bases and block reverse transcription.

    • Main Results:

    • A protonated base pair, U2511-CH(+)2575, was identified in E. coli 23S rRNA, isostructural to a pair in H. marismortui.
    • A second charged base pair, AH(+)1528-G1543, was discovered in the E. coli 23S rRNA.
    • Both identified charged base pairs were dependent on the intact ribosomal subunit and absent in deproteinized rRNA.

    Conclusions:

    • Protonated bases play a critical role in maintaining the structural integrity of the E. coli 50S ribosomal subunit.
    • The presence of these charged base pairs is context-dependent, requiring the complete ribosomal assembly.
    • These findings highlight the importance of specific base modifications and interactions in ribosome function.