Targeting plant UBX proteins: AI-enhanced lessons from distant cousins

Trends Plant Sci. 2022 Nov;27(11):1099-1108. doi: 10.1016/j.tplants.2022.05.012. Epub 2022 Jun 16.

Abstract

Across all eukaryotic kingdoms, ubiquitin regulatory X (UBX) domain-containing adaptor proteins control the segregase cell division control protein 48 (CDC48), and thereby also control cellular proteostasis and adaptation. The structures and biological roles of UBX proteins in animals and fungi have garnered considerable attention. However, their counterparts in plants remain markedly understudied. Since 2021, the artificial intelligence (AI)-based algorithm AlphaFold has provided predictions of protein structural features that can be highly accurate. Predictions of the proteomes of all major model organisms are now freely accessible to the entire research community through user-friendly web interfaces. We propose that the combination of cross-kingdom comparison with AF analysis produces a wealth of testable hypotheses to inspire and guide experimental research on plant UBX domain-containing (PUX) proteins.

Keywords: AAA-ATPase; AlphaFold; adaptor proteins; bioinformatics; evolution; protein interactions.

Publication types

  • Review
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphatases* / chemistry
  • Adenosine Triphosphatases* / metabolism
  • Animals
  • Artificial Intelligence
  • Cell Cycle Proteins* / chemistry
  • Cell Cycle Proteins* / metabolism
  • Plant Proteins / genetics
  • Plant Proteins / metabolism
  • Proteome / metabolism
  • Ubiquitin / metabolism
  • Valosin Containing Protein / metabolism

Substances

  • Cell Cycle Proteins
  • Plant Proteins
  • Proteome
  • Ubiquitin
  • Adenosine Triphosphatases
  • Valosin Containing Protein