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Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System
Published on: August 1, 2016
RNA-amino acid binding: a stereochemical era for the genetic code
Michael Yarus1, Jeremy Joseph Widmann, Rob Knight
1Department of MCD Biology and Chemistry/Biochemistry, University of Colorado, Boulder, CO 80309-0347, USA. yarus@stripe.colorado.edu
Journal of Molecular Evolution
|October 2, 2009
Summary
This study reveals a strong link between amino acids and their genetic code triplets within RNA binding sites, suggesting a stereochemical origin for the genetic code during evolution. This chemical interaction era likely incorporated most amino acids into the code.
Area of Science:
- Structural Biology
- Origin of Life
- Genetics
Background:
- Understanding the chemical principles of RNA-amino acid interactions is key to deciphering the origins of the genetic code.
- Previous studies have explored RNA-amino acid binding but lacked a comprehensive analysis of coding triplet correlations.
- Riboswitches, aptamers, and RNA-protein complexes (RNPs) provide structural insights into these interactions.
Purpose of the Study:
- To deduce chemical principles governing specific RNA-amino acid interactions using structural data.
- To investigate the correlation between RNA binding sites, amino acids, and their cognate coding triplets.
- To explore the potential role of stereochemical interactions in the evolution of the genetic code.
Main Methods:
- Combined crystallographic and Nuclear Magnetic Resonance (NMR) structural data of RNA-amino acid complexes.
- Analyzed sequences from 337 independent binding sites for 8 amino acids (18,551 nucleotides).
- Calculated the probability of cognate triplets appearing by chance in RNA binding sites.
Main Results:
- A 'polar profile' summarizes chemical principles of RNA-amino acid binding.
- A highly robust connection was found between amino acids and cognate coding triplets within RNA binding sites.
- The probability of cognate triplets being unrelated to binding sites is extremely low (P ≈ 5.3 x 10⁻⁴⁵ for codons).
Conclusions:
- A stereochemical era, driven by RNA-amino acid chemical interactions, likely shaped the early genetic code.
- Most modern amino acids (≈75%) may have entered the code during this era.
- A Direct RNA Template model provides a plausible early history for coded peptide synthesis based on these findings.
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