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Overlapping Peptide Library to Map Qa-1 Epitopes in a Protein
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Overlapping genes and the proteins they encode differ significantly in their sequence composition from

Angelo Pavesi1, Alberto Vianelli2, Nicola Chirico2

  • 1Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.

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Overlapping genes, which encode multiple proteins from one DNA sequence, are abundant in viruses and eukaryotes. A new dataset reveals these genes have a distinct amino acid composition, potentially easing evolutionary constraints.

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Overlapping genes encode multiple proteins from a single DNA sequence, posing evolutionary challenges.
  • These genes are common in viruses and increasingly recognized in eukaryotes, but often missed in genome annotation.
  • Accurate detection is crucial for understanding viral infection and evolutionary studies.

Purpose of the Study:

  • To create a high-quality benchmark dataset of experimentally proven viral overlapping genes.
  • To analyze the evolutionary and compositional characteristics of overlapping genes.
  • To investigate the potential role of amino acid composition in the prevalence and evolution of overlapping genes.

Main Methods:

  • Assembled a dataset of 80 experimentally validated viral overlapping genes.
  • Analyzed nucleotide and amino acid composition of overlapping versus non-overlapping genes.
  • Utilized principal component analysis to identify compositional biases.

Main Results:

  • Overlapping genes exhibit significantly different nucleotide and amino acid compositions compared to non-overlapping genes.
  • Proteins encoded by overlapping genes are enriched in high-degeneracy amino acids and depleted in low-degeneracy ones.
  • A consistent composition bias was observed across most overlapping genes, including six mammalian examples.

Conclusions:

  • A near-universal amino acid composition bias may facilitate the origin or evolution of overlapping genes.
  • The findings highlight the importance of identifying overlapping genes for accurate genomic and evolutionary analyses.
  • This study provides a valuable resource for future research on overlapping genes in various organisms.