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Adaptive evolution: Eukaryotic enzyme's specificity shift to a bacterial substrate.

Emi Latifah1, Indira Rizqita Ivanesthi1, Yi-Kuan Tseng2

  • 1Department of Life Sciences, National Central University, Taoyuan, Taiwan.

Protein Science : a Publication of the Protein Society
|May 17, 2024
PubMed
Summary
This summary is machine-generated.

Prolyl-tRNA synthetase (ProRS) enzymes are E-type or P-type. Thermus thermophilus ProRS, an E-type enzyme, uniquely charges P-type tRNA, demonstrating enzyme adaptability.

Keywords:
aminoacyl‐tRNA synthetasehalofuginoneidentity elementprotein synthesistRNAthermophilic bacterium

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Enzymology

Background:

  • Aminoacyl-tRNA synthetases (aaRS) are essential enzymes that attach specific amino acids to their cognate tRNAs.
  • Prolyl-tRNA synthetase (ProRS) exists in eukaryote/archaeon-like (E-type) and prokaryote-like (P-type) forms, distinguished by their tRNA recognition.
  • The bacterium Thermus thermophilus ProRS (TtProRS) presents a unique case, exhibiting E-type characteristics while interacting with P-type tRNA.

Purpose of the Study:

  • To investigate the paradoxical substrate specificity of Thermus thermophilus ProRS (TtProRS).
  • To elucidate the molecular mechanisms underlying TtProRS's recognition of P-type tRNAPro.
  • To understand the enzyme's resilience to halofuginone and its implications for ProRS evolution.

Main Methods:

  • Biochemical assays to assess tRNA charging activity.
  • Inhibitor sensitivity assays using halofuginone.
  • Structural and sequence analysis of TtProRS and its cognate tRNAPro.
  • Mutagenesis studies to identify key recognition elements.

Main Results:

  • TtProRS, an E-type enzyme, selectively charges P-type tRNAPro, which possesses bacterium-specific acceptor-stem elements (G72 and A73).
  • TtProRS exhibits resilience to halofuginone, a characteristic shared with P-type ProRS.
  • TtProRS recognizes tRNAPro via acceptor-stem elements (G72/A73) and anticodon elements (G35/G36).
  • Unlike P-type ProRS, TtProRS utilizes a non-conserved RTR sequence in its eukaryote-like motif 2 loop for G72/A73 recognition, bypassing the conserved R residue typical of P-type enzymes.

Conclusions:

  • TtProRS demonstrates remarkable adaptive plasticity, accommodating a novel substrate despite its E-type classification.
  • The study highlights alternative molecular strategies for tRNA recognition, expanding our understanding of enzyme evolution.
  • The findings offer insights into the functional convergence and divergence of housekeeping enzymes across different domains of life.