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Elmore JM, Velásquez-Zapata V, Wise RP. Next-Generation Yeast Two-Hybrid Screening to Discover Protein-Protein Interactions. Methods Mol Biol 2023; 2690:205-222. [PMID: 37450150 DOI: 10.1007/978-1-0716-3327-4_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Yeast two-hybrid is a powerful approach to discover new protein-protein interactions. Traditional methods involve screening a target protein against a cDNA expression library and assaying individual positive colonies to identify interacting partners. Here we describe a simple approach to perform yeast two-hybrid screens of a cDNA expression library in batch liquid culture. Positive yeast cell populations are enriched under selection and then harvested en masse. Prey cDNAs are amplified and used as input for next-generation sequencing libraries for identification, quantification, and ranking.
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Affiliation(s)
- J Mitch Elmore
- USDA-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN, USA.
- USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research, Ames, IA, USA.
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA, USA.
| | - Valeria Velásquez-Zapata
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA, USA
- Program in Bioinformatics & Computational Biology, Iowa State University, Ames, IA, USA
| | - Roger P Wise
- USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research, Ames, IA, USA
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA, USA
- Program in Bioinformatics & Computational Biology, Iowa State University, Ames, IA, USA
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Fibrillarin RNA methylase is an interacting protein of Cryptosporidium parvum calmodulin-like protein (CpCML). Microb Pathog 2022; 170:105679. [PMID: 35843442 DOI: 10.1016/j.micpath.2022.105679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 11/23/2022]
Abstract
Cryptosporidium parvum is an obligate protozoan parasite invading epithelial cells of small intestine of human and animals, and causing diarrheal disease. In apicomplexan parasites, calcium signaling can regulate many essential biological processes such as invasion and migration. As the main intracellular receptor for calcium ions, calmodulins control the activities of hundreds of enzymes and proteins. Calmodulin-like protein (CML) is an important member of the calmodulin family and may play a key role in C. parvum, however, the actual situation is still not clear. The present study aimed to identify the parasite interaction partner proteins of C. parvum calmodulin-like protein (CpCML). By constructing the cpcml bait plasmid, 5 potential CpCML - interacting proteins in C. parvum oocyst were screened by yeast-two-hybrid system (Y2H). Bimolecular fluorescence complementation (BiFC) and Co-immunoprecipitation (Co-IP) were performed as subsequent validations. Fibrillarin RNA methylase (FBL) was identified via this screening method as CpCML interacting protein in C. parvum. The identification of this interaction made it possible to get a further understanding of the function of CpCML and its contribution to the pathogenicity of C. parvum.
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Gu Y, Li G, Wang P, Guo Y, Li J. A simple and precise method (Y2H-in-frame-seq) improves yeast two-hybrid screening with cDNA libraries. J Genet Genomics 2021; 49:595-598. [PMID: 34864215 DOI: 10.1016/j.jgg.2021.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 10/19/2022]
Affiliation(s)
- Yinghui Gu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Guannan Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Ping Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yan Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jingrui Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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Hu Y, Yu Q, Chen Y, Zhang L, Fu X, Ding L, Liu Y, Guan Z, Fang W, Chen F, Song A. Labour-saving construction of a target protein interaction network by selective culture and high-throughput sequencing. Biotechnol J 2021; 16:e2100204. [PMID: 34328672 DOI: 10.1002/biot.202100204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 12/14/2022]
Abstract
Yeast two-hybrid (Y2H) is a classic method of screening for protein-protein interactions. However, the operation process is labor intensive and time consuming, and there is a high possibility of false positives and false negatives. Combined with wet lab operation and bioinformatics analysis, we developed a novel method of Y2H library screening using Chrysanthemum morifolium CmMPK3 as an example. The protocol can not only greatly simplify the steps of traditional Y2H library screening but also identify as many interacting proteins as possible. Furthermore, this protocol is applicable to any species, even if no genomic information is available yet.
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Affiliation(s)
- Yueheng Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Qi Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yu Chen
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Luyao Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xianrong Fu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Lian Ding
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ye Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhiyong Guan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Weimin Fang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Aiping Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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