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The archaeology of coding RNA.

Ascensión Ariza-Mateos1,2, Carlos Briones3,4, Celia Perales2,4,5

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Researchers used an "RNA archaeology" method to find ancient RNA structures. They discovered tRNA-like elements and dsRNA motifs in viral and human liver mRNA, suggesting their role in early RNA evolution and the origin of coding RNAs.

Keywords:
RNA worldRNase IIIRNase Pbiocommunicationbiosemioticsquasispecies

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Area of Science:

  • Molecular Biology
  • Evolutionary Biology
  • Biochemistry

Background:

  • Theories on RNA origin suggest proto-tRNA-like structures concatenated and expanded.
  • Identifying ancient RNA elements is challenging due to sequence alterations during mRNA evolution.

Purpose of the Study:

  • To apply an "RNA archaeology" method to discover evolutionary patterns in RNA.
  • To identify ancient RNA elements and motifs in viral and cellular mRNAs.

Main Methods:

  • Utilized biochemical and biophysical tools to search for ancient-like RNA structures.
  • Examined genomic viral RNAs (Hepatitis C virus) and human liver mRNA populations.
  • Employed a nonphylogenetic and nonrepresentational strategy termed "RNA archaeology".

Main Results:

  • Discovered tRNA-like elements in functionally relevant positions within viral RNA and IFNA5 mRNA.
  • Found a high representation of tRNA-like elements in hepatic mRNA, suggesting their role in coding RNA formation.
  • Observed recurring double-stranded RNA (dsRNA)-like motifs adjacent to tRNA-like elements in viral and IFNA5 RNAs.

Conclusions:

  • The findings suggest tRNA-like elements and dsRNA motifs were important in the RNA world for RNA concatenation and expansion.
  • The RNA archaeology method aids in understanding the structural and functional versatility of RNA elements predating protein synthesis.
  • These ancient RNA elements may represent evolutionary "losers" that adapted to selective pressures favoring longer coding mRNAs.