Nature Communications (Apr 2023)

Next-generation large-scale binary protein interaction network for Drosophila melanogaster

  • Hong-Wen Tang,
  • Kerstin Spirohn,
  • Yanhui Hu,
  • Tong Hao,
  • István A. Kovács,
  • Yue Gao,
  • Richard Binari,
  • Donghui Yang-Zhou,
  • Kenneth H. Wan,
  • Joel S. Bader,
  • Dawit Balcha,
  • Wenting Bian,
  • Benjamin W. Booth,
  • Atina G. Coté,
  • Steffi de Rouck,
  • Alice Desbuleux,
  • Kah Yong Goh,
  • Dae-Kyum Kim,
  • Jennifer J. Knapp,
  • Wen Xing Lee,
  • Irma Lemmens,
  • Cathleen Li,
  • Mian Li,
  • Roujia Li,
  • Hyobin Julianne Lim,
  • Yifang Liu,
  • Katja Luck,
  • Dylan Markey,
  • Carl Pollis,
  • Sudharshan Rangarajan,
  • Jonathan Rodiger,
  • Sadie Schlabach,
  • Yun Shen,
  • Dayag Sheykhkarimli,
  • Bridget TeeKing,
  • Frederick P. Roth,
  • Jan Tavernier,
  • Michael A. Calderwood,
  • David E. Hill,
  • Susan E. Celniker,
  • Marc Vidal,
  • Norbert Perrimon,
  • Stephanie E. Mohr

DOI
https://doi.org/10.1038/s41467-023-37876-0
Journal volume & issue
Vol. 14, no. 1
pp. 1 – 16

Abstract

Read online

Abstract Generating reference maps of interactome networks illuminates genetic studies by providing a protein-centric approach to finding new components of existing pathways, complexes, and processes. We apply state-of-the-art methods to identify binary protein-protein interactions (PPIs) for Drosophila melanogaster. Four all-by-all yeast two-hybrid (Y2H) screens of > 10,000 Drosophila proteins result in the ‘FlyBi’ dataset of 8723 PPIs among 2939 proteins. Testing subsets of data from FlyBi and previous PPI studies using an orthogonal assay allows for normalization of data quality; subsequent integration of FlyBi and previous data results in an expanded binary Drosophila reference interaction network, DroRI, comprising 17,232 interactions among 6511 proteins. We use FlyBi data to generate an autophagy network, then validate in vivo using autophagy-related assays. The deformed wings (dwg) gene encodes a protein that is both a regulator and a target of autophagy. Altogether, these resources provide a foundation for building new hypotheses regarding protein networks and function.