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PARPAL: PARalog Protein redistribution using Abundance and Localization in yeast database.

Brittany M Greco1,2, Gerardo Zapata3,4, Rohan Dandage1,2

  • 1Department of Biology, Concordia University, 7141 Sherbrooke St W, Montreal, QC, Canada H4B 1R6.

G3 (Bethesda, Md.)
|June 28, 2025
PubMed
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This summary is machine-generated.

Whole-genome duplication (WGD) drives gene evolution. The PARPAL database tracks protein redistribution after paralog deletion in yeast, revealing insights into gene retention mechanisms and paralog evolution.

Area of Science:

  • Evolutionary Biology
  • Genomics
  • Cell Biology

Background:

  • Whole-genome duplication (WGD) is a significant evolutionary force.
  • Understanding the retention and evolution of genes duplicated via WGD is crucial.
  • Protein redistribution offers insights into gene retention mechanisms.

Purpose of the Study:

  • To develop a resource for studying paralog protein redistribution after WGD.
  • To analyze changes in protein abundance and subcellular localization in response to paralog deletion.
  • To provide a quantitative measure of gene retention and evolution.

Main Methods:

  • High-content screening of protein redistribution in yeast.
  • Deep learning neural network analysis of protein localization and abundance.
Keywords:
Saccharomyces cerevisiaebudding yeastdeep neural networkduplicated geneshigh-content screeningparalogsphenomicsprotein abundanceprotein subcellular localization

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  • Interrogation of 82 paralog pairs across two genetic backgrounds in Saccharomyces cerevisiae.

    • Main Results:

    • The PARPAL database catalogs redistribution data for 164 proteins.
    • Observed dependent and compensatory redistribution patterns between paralogs (e.g., Skn7-Hms2, Cue1-Cue4).
    • Data links to studies on gene interactions and protein abundance.

    Conclusions:

    • PARPAL serves as a valuable resource for yeast genetics and evolutionary studies.
    • The database facilitates research into paralog retention and evolution.
    • Enables investigation of protein dynamics and paralog interactions in other organisms.