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Updated: Jun 29, 2025

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
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Ancestral sequence reconstruction dissects structural and functional differences among eosinophil ribonucleases.

Thi Thanh Quynh Tran1, Chitra Narayanan2, Andrea N Loes3

  • 1Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, Laval, Quebec, Canada.

The Journal of Biological Chemistry
|April 8, 2024
PubMed
Summary

Scientists engineered a novel enzyme by reconstructing ancestral ribonuclease (AncRNase) sequences. This engineered enzyme exhibits antimicrobial and cytotoxic properties, demonstrating targeted modulation of ribonuclease functions.

Keywords:
RNase 2RNase 3X-ray crystallographyancestral RNaseancestral sequence reconstructionchimeragenesiseosinophileosinophil cationic proteineosinophil-derived neurotoxinmolecular dynamicsprotein evolutionstructural biology

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Area of Science:

  • Biochemistry
  • Evolutionary Biology
  • Structural Biology

Background:

  • Conserved protein folds can evolve diverse functions, but predicting atomic-level interactions driving new activities is difficult.
  • Pancreatic-type ribonucleases (RNases) share a core structure that has adapted for varied biological roles.
  • Eosinophil RNase 2 and RNase 3 subfamilies exemplify functional divergence within a conserved structural fold.

Purpose of the Study:

  • To investigate the evolutionary and molecular factors distinguishing biological activities within the eosinophil RNase 2/3 subfamily.
  • To understand the functional, structural, and dynamical differences between ancestral and contemporary eosinophil RNases.
  • To engineer novel RNase functions using insights from ancestral sequence reconstruction.

Main Methods:

  • Ancestral sequence reconstruction to infer evolutionary pathways.
  • Comparative analysis of functional, structural, and dynamical properties of ancestral and contemporary RNases.
  • Protein engineering based on ancestral sequence predictions to create chimeric enzymes.

Main Results:

  • Identified distinct functional, structural, and dynamical behaviors differentiating ancestral ribonuclease (AncRNase) from contemporary orthologs.
  • Demonstrated that AncRNase predictions can guide protein engineering efforts.
  • Successfully designed a 4-residue variant that confers RNase 3-like antimicrobial and cytotoxic activities to human RNase 2.

Conclusions:

  • Elucidated evolutionary pathways governing structure-function relationships in eosinophil RNases.
  • Provided insights into the mutational basis for functional divergence within the RNase 2/3 subfamily.
  • Showcased the potential of ancestral reconstruction for designing enzymes with novel, targeted functions.