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 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 () and Stephanie E. Mohr ()
Additional contact information
Hong-Wen Tang: Harvard Medical School
Kerstin Spirohn: Harvard Medical School
Yanhui Hu: Harvard Medical School
Tong Hao: Harvard Medical School
István A. Kovács: Dana-Farber Cancer Institute
Yue Gao: Harvard Medical School
Richard Binari: Harvard Medical School
Donghui Yang-Zhou: Harvard Medical School
Kenneth H. Wan: Lawrence Berkeley National Laboratory
Joel S. Bader: Whiting School of Engineering, Johns Hopkins University
Dawit Balcha: Harvard Medical School
Wenting Bian: Harvard Medical School
Benjamin W. Booth: Lawrence Berkeley National Laboratory
Atina G. Coté: Dana-Farber Cancer Institute
Steffi Rouck: Cytokine Receptor Lab, VIB Center for Medical Biotechnology
Alice Desbuleux: Harvard Medical School
Kah Yong Goh: Duke-NUS Medical School
Dae-Kyum Kim: Roswell Park Comprehensive Cancer Center
Jennifer J. Knapp: University of Toronto
Wen Xing Lee: Duke-NUS Medical School
Irma Lemmens: Cytokine Receptor Lab, VIB Center for Medical Biotechnology
Cathleen Li: Harvard Medical School
Mian Li: Harvard Medical School
Roujia Li: Dana-Farber Cancer Institute
Hyobin Julianne Lim: Roswell Park Comprehensive Cancer Center
Yifang Liu: Harvard Medical School
Katja Luck: Harvard Medical School
Dylan Markey: Harvard Medical School
Carl Pollis: Harvard Medical School
Sudharshan Rangarajan: Harvard Medical School
Jonathan Rodiger: Harvard Medical School
Sadie Schlabach: Harvard Medical School
Yun Shen: Harvard Medical School
Dayag Sheykhkarimli: Dana-Farber Cancer Institute
Bridget TeeKing: Harvard Medical School
Frederick P. Roth: Dana-Farber Cancer Institute
Jan Tavernier: Cytokine Receptor Lab, VIB Center for Medical Biotechnology
Michael A. Calderwood: Harvard Medical School
David E. Hill: Harvard Medical School
Susan E. Celniker: Lawrence Berkeley National Laboratory
Marc Vidal: Harvard Medical School
Norbert Perrimon: Harvard Medical School
Stephanie E. Mohr: Harvard Medical School

Nature Communications, 2023, vol. 14, issue 1, 1-16

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41467-023-37876-0

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