Steric complementarity in the decoding center is important for tRNA selection by the ribosome

Area of Science:

• Molecular Biology
• Structural Biology
• Biochemistry

Background:

• Ribosome fidelity in protein synthesis relies on accurate transfer RNA (tRNA) selection.
• Universally conserved ribosomal RNA bases (G530, A1492, A1493) were thought to monitor codon-anticodon helix geometry via hydrogen bonds.
• Recent studies challenged the role of these hydrogen bonds in discriminating cognate from near-cognate tRNAs.

Purpose of the Study:

• To investigate the precise molecular mechanisms underlying tRNA selection by the ribosome.
• To determine the relative importance of hydrogen bonding versus steric interactions in the decoding center.

Main Methods:

• Synthesized messenger RNAs (mRNAs) with 2'-deoxynucleotide or 2'-fluoro substitutions in the codon-anticodon helix binding site.
• Assessed the impact of these substitutions on tRNA selection fidelity.
• Evaluated the effect of antibiotics paromomycin and streptomycin on tRNA selection with modified mRNAs.

Main Results:

• Multiple 2'-deoxynucleotide substitutions in mRNA significantly impaired tRNA selection.
• Multiple 2'-fluoro substitutions had only minor effects on tRNA selection.
• The antibiotics paromomycin and streptomycin restored tRNA selection efficiency with 2'-deoxynucleotide substituted mRNAs.

Conclusions:

• Steric complementarity within the ribosomal decoding center plays a more critical role than previously appreciated in tRNA selection.
• Hydrogen bonds involving G530, A1492, and A1493 may not be the primary determinants for distinguishing cognate from near-cognate tRNAs.
• The findings provide new insights into the fidelity mechanisms of translation and potential targets for antibiotic action.