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Related Experiment Video

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Nonradioactive Assay to Measure Polynucleotide Phosphorylation of Small Nucleotide Substrates
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Evolutionary dynamics of Polynucelotide phosphorylases.

Upneet K Sokhi1, Rob DeSalle2, Manny D Bacolod1

  • 1Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States.

Molecular Phylogenetics and Evolution
|February 8, 2014
PubMed
Summary
This summary is machine-generated.

Polynucleotide phosphorylase (PNPase) and RNase PH (RPH) evolved from a common ancestor. Phylogenetic analysis reveals PNP2 and RPH arose from PNP1 duplication, with significant sequence changes in vertebrate evolution.

Keywords:
Positive selectionPurifying selectiondN/dS ratio

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Area of Science:

  • Evolutionary biology
  • Molecular biology
  • Biochemistry

Background:

  • Polynucleotide phosphorylase (PNPase) is a conserved exoribonuclease with RNase PH (RPH) homology.
  • PNPase comprises two catalytic RNase PH domains (PNP1, PNP2), an α-helical domain, and RNA-binding domains.
  • PNP1, PNP2, and RPH share homology, suggesting a common ancestral origin within the PDX protein family.

Purpose of the Study:

  • To investigate the evolutionary history of PNPase and RNase PH domains.
  • To understand the evolutionary events shaping these domains in vertebrates, particularly mammals.

Main Methods:

  • Phylogenetic analysis of PNPase/RNase PH sequences from 43 vertebrate taxa.
  • Branch and site-specific dN/dS analyses to detect directional sequence change.
  • Identification of conserved and variable regions within protein domains.

Main Results:

  • Phylogenetic analysis indicates PNP2 and RPH are sister taxa, originating from PNP1 domain duplication.
  • All three domains (PNP1, PNP2, RPH), plus KH and S1 domains, show significant directional sequence evolution.
  • Codons with high dN/dS ratios (>1.0) are located in disordered protein regions, while functionally important sites show low dN/dS ratios (≈0.0).

Conclusions:

  • The study elucidates the evolutionary trajectory of PNPase and RPH domains.
  • Domain duplication and subsequent sequence divergence played key roles in refining these proteins in the vertebrate lineage.
  • Understanding evolutionary pressures on protein domains aids in predicting functional constraints and evolutionary adaptations.