ArticleProteome science2010
Improving the yeast two-hybrid system with permutated fusions proteins: the Varicella Zoster Virus interactome.
Article in Proteome science, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
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Who cites it
77 citing papers in PubMed.
- Comprehensive review and assessment of machine learning approaches for host-pathogen protein-protein interaction prediction.Briefings in bioinformatics · 2026Review
- Serial innovations by Asgard archaea shaped the DNA replication machinery of the early eukaryotic ancestor.Nature ecology & evolution · 2025Article
- The TRAPPC8/TRS85 subunit of the Arabidopsis TRAPPIII tethering complex regulates endoplasmic reticulum function and autophagy.Plant physiology · 2025Article
- The complex I subunit B22 contains a LYR domain that is crucial for an interaction with the mitochondrial acyl carrier protein SDAP1.The Plant journal : for cell and molecular biology · 2025Article
- High-Throughput Yeast Two-Hybrid Technology for Investigating Molecular Virology.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Structural insights into the disulfide isomerase and chaperone activity of TrbB of the F plasmid type IV secretion system.Current research in structural biology · 2024Article
- FTSH PROTEASE 3 facilitates Complex I degradation through a direct interaction with the Complex I subunit PSST.The Plant cell · 2023Article
- Combinatorial interactions between viral proteins expand the potential functional landscape of the tomato yellow leaf curl virus proteome.PLoS pathogens · 2022Article
- The mitochondrial LYR protein SDHAF1 is required for succinate dehydrogenase activity in Arabidopsis.The Plant journal : for cell and molecular biology · 2022Article
- Unraveling Protein Interactions between the Temperate Virus Bam35 and ItsInternational journal of molecular sciences · 2021Article
- Conservation and divergence of meiotic DNA double strand break forming mechanisms in Arabidopsis thaliana.Nucleic acids research · 2021Article
- Screening of the HBx transactivation domain interacting proteins and the function of interactor Pin1 in HBV replication.Scientific reports · 2021Article
- Varicella-zoster virus early infection but not complete replication is required for the induction of chronic hypersensitivity in rat models of postherpetic neuralgia.PLoS pathogens · 2021Article
- Imaging of multiple fluorescent proteins in canopies enables synthetic biology in plants.Plant biotechnology journal · 2021Article
- Near-atomic cryo-electron microscopy structures of varicella-zoster virus capsids.Nature microbiology · 2020Article
- Five enzymes of the Arg/N-degron pathway form a targeting complex: The concept of superchanneling.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Evolution of Substrates and Components of the Pro/N-Degron Pathway.Biochemistry · 2020Article
- Construction and characterization of a high-quality cDNA library of Cymbidium faberi suitable for yeast one- and two-hybrid assays.BMC biotechnology · 2020Article
- A Mitochondrial LYR Protein Is Required for Complex I Assembly.Plant physiology · 2019Article
- Conserved Central Intraviral Protein Interactome of themSystems · 2019Article
17 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
backgroundYeast two-hybrid (Y2H) screens have been among the most powerful methods to detect and analyze protein-protein interactions. However, they suffer from a significant degree of false negatives, i.e. true interactions that are not detected, and to a certain degree from false positives, i.e. interactions that appear to take place only in the context of the Y2H assay. While the fraction of false positives remains difficult to estimate, the fraction of false negatives in typical Y2H screens is on the order of 70-90%. Here we present novel Y2H vectors that significantly decrease the number of false negatives and help to mitigate the false positive problem.
resultsWe have constructed two new vectors (pGBKCg and pGADCg) that allow us to make both C-terminal fusion proteins of DNA-binding and activation domains. Both vectors can be combined with existing vectors for N-terminal fusions and thus allow four different bait-prey combinations: NN, CC, NC, and CN. We have tested all approximately 4,900 pairwise combinations of the 70 Varicella-Zoster-Virus (VZV) proteins for interactions, using all possible combinations. About approximately 20,000 individual Y2H tests resulted in 182 NN, 89 NC, 149 CN, and 144 CC interactions. Overlap between screens ranged from 17% (NC-CN) to 43% (CN-CC). Performing four screens (i.e. permutations) instead of one resulted in about twice as many interactions and thus much fewer false negatives. In addition, interactions that are found in multiple combinations confirm each other and thus provide a quality score. This study is the first systematic analysis of such N- and C-terminal Y2H vectors.
conclusionsPermutations of C- and N-terminal Y2H vectors dramatically increase the coverage of interactome studies and thus significantly reduce the number of false negatives. We suggest that future interaction screens should use such vector combinations on a routine basis, not the least because they provide a built-in quality score for Y2H interactions that can provide a measure of reproducibility without additional assays.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.