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Distribution of ADAT-Dependent Codons in the Human Transcriptome.

Àlbert Rafels-Ybern1, Camille Stephan-Otto Attolini2, Lluís Ribas de Pouplana3,4

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Summary

Adenosine deaminases acting on tRNAs (ADAT) modify transfer RNAs (tRNA) to influence protein translation. ADAT-modified tRNAs preferentially recognize specific codons, impacting the amino acid composition of proteins.

Keywords:
ADAT2-ADAT3codon degeneracytRNA gene copy numbertRNA modification enzymes

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • Nucleotide modifications in transfer RNA (tRNA) anticodons are crucial for translation efficiency, fidelity, and regulation.
  • The specific functions of most tRNA modifications remain largely unknown.
  • Adenosine deaminases acting on tRNAs (ADAT2-ADAT3, or ADAT) are eukaryotic enzymes that convert adenine (A) to inosine (I) at the first anticodon position (34) via hydrolytic deamination.

Purpose of the Study:

  • To investigate the influence of ADAT activity on mammalian translation.
  • To characterize the human transcriptome and proteome concerning ADAT-related codon frequency and distribution.

Main Methods:

  • Analysis of human transcriptome and proteome data.
  • Identification and quantification of ADAT-modified tRNAs and their corresponding codons.
  • Correlation of codon usage with protein amino acid composition.

Main Results:

  • Eight distinct tRNAs are substrates for ADAT modification.
  • ADAT-modified tRNAs recognize NNC, NNU, and NNA codons, but not NNG codons.
  • Transcripts encoding proteins rich in ADAT-recognized amino acids (ADAT-aa) exhibit enrichment in NNC, NNU, and NNA codons.
  • Proteins with high ADAT-aa content are preferentially composed of threonine, alanine, proline, and serine (TAPS).

Conclusions:

  • ADAT activity shapes codon usage in the human transcriptome.
  • The enrichment of ADAT-codons in TAPS-rich proteins suggests a mechanism for translational regulation based on tRNA modification.
  • This finding provides insights into the functional significance of nucleotide modifications in tRNA anticodons.