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PreprintCited by 7Bioinformatics and Genomic NetworksBiotin and Related StudiesFungal and yeast genetics research

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Barcode Fusion Genetics-Protein-fragment Complementation Assay (BFG-PCA): tools and resources that expand the potential for binary protein interaction discovery

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Evans-Yamamoto, Daniel, Rouleau, François D., Nanda, Piyush, Makanae, Koji, Liu, Yin, Després, Philippe C., Matsuo, Hitoshi, Seki, Motoaki, Dube, Alexandre K., Ascencio, Diana, Yachie, Nozomu, Landry, Christian R.·2021·Nucleic Acids Research
DOI 10.1101/2021.07.27.453987PMC PMC9122585

Preprint — published as 10.1093/nar/gkac045

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Abstract

Barcode fusion genetics (BFG) utilizes deep sequencing to improve the throughput of protein-protein interaction (PPI) screening in pools. BFG has been implemented in Yeast two-hybrid (Y2H) screens (BFG-Y2H). While Y2H requires test protein pairs to localize in the nucleus for reporter reconstruction, Dihydrofolate Reductase Protein-Fragment Complementation Assay (DHFR-PCA) allows proteins to localize in broader subcellular contexts and proves to be largely orthogonal to Y2H. Here, we implemented BFG to DHFR-PCA (BFG-PCA). This plasmid-based system can leverage ORF collections across model organisms to perform comparative analysis, unlike the original DHFR-PCA that requires yeast genomic integration. The scalability and quality of BFG-PCA were demonstrated by screening human and yeast interactions for >11,000 protein pairs. BFG-PCA showed high-sensitivity and high-specificity for capturing known interactions for both species. BFG-Y2H and BFG-PCA capture distinct sets of PPIs, which can partially be explained based on the domain orientation of the reporter tags. BFG-PCA is a high-throughput protein interaction technology to interrogate binary PPIs that exploits clone collections from any species of interest, expanding the scope of PPI assays.

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Metadata

Authors
Evans-Yamamoto, D., Rouleau, F. D., Nanda, P., Makanae, K., Liu, Y., Després, P. C., Matsuo, H., Seki, M., Dube, A. K., Ascencio, D., Yachie, N., & Landry, C. R.
Affiliations
  • Keio University (JP)
  • PROTEO (CA)
  • Research Center for Advanced Science and Technology, The University of Tokyo (JP)
Corresponding author
  • Yachie, Nozomu
  • Landry, Christian R.
ORCID
Venue
Nucleic Acids Research
Publisher
openRxiv
Published
2021-07-27
Volume
50
Issue
9
Pages
e54-e54
ISSN
0305-1048 (ISSN-L)
DOI
10.1101/2021.07.27.453987
PMC
PMC9122585
OpenAlex
W4206302690
Cited by
7
References
1
Citations by year
2025: 3 · 2024: 3 · 2023: 1
FWCI
0.57
Type
journal article
Language
en
Open access
Licence
cc-by-nc
Locations
  • Nucleic Acids Research (publishedVersion, cc-by-nc)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
Funders
  • Watanabe Foundation
  • Sylff Association
  • Keio University
  • Canada Research Chairs
  • Astellas Pharma
  • Daiichi Sankyo Foundation of Life Science
  • Astellas Foundation for Research on Metabolic Disorders
  • Canadian Institutes of Health Research (387697)
  • Japan Society for the Promotion of Science (18H02428, 21K07934, DC1 Fellowship, 20J21144)
  • Fonds de recherche du Québec – Nature et technologies
  • Ube Foundation
  • Daiichi Sankyo Europe
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Biotin and Related Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
Keywords
protein-fragment complementation assay, dihydrofolate reductase, protein-protein interaction screening, yeast two-hybrid
MeSH terms
Biological Assay, Humans, Proteins, Saccharomyces cerevisiae, Tetrahydrofolate Dehydrogenase, Two-Hybrid System Techniques, Protein Interaction Mapping

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