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Michnick SW, Levy ED, Landry CR, Kowarzyk J, Messier V. Corrigendum: The Dihydrofolate Reductase Protein-Fragment Complementation Assay: A Survival-Selection Assay for Large-Scale Analysis of Protein-Protein Interactions. Cold Spring Harb Protoc 2022; 2022:pdb.corr107812. [PMID: 34983863 DOI: 10.1101/pdb.corr107812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Ear PH, Kowarzyk J, Michnick SW. Corrigendum: Dissecting the Contingent Interactions of Protein Complexes with the Optimized Yeast Cytosine Deaminase Protein-Fragment Complementation Assay. Cold Spring Harb Protoc 2022; 2022:pdb.corr107814. [PMID: 34983865 DOI: 10.1101/pdb.corr107814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Stynen B, Abd-Rabbo D, Kowarzyk J, Miller-Fleming L, Aulakh SK, Garneau P, Ralser M, Michnick SW. Changes of Cell Biochemical States Are Revealed in Protein Homomeric Complex Dynamics. Cell 2018; 175:1418-1429.e9. [PMID: 30454649 PMCID: PMC6242466 DOI: 10.1016/j.cell.2018.09.050] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 09/04/2018] [Accepted: 09/24/2018] [Indexed: 01/22/2023]
Abstract
We report here a simple and global strategy to map out gene functions and target pathways of drugs, toxins, or other small molecules based on "homomer dynamics" protein-fragment complementation assays (hdPCA). hdPCA measures changes in self-association (homomerization) of over 3,500 yeast proteins in yeast grown under different conditions. hdPCA complements genetic interaction measurements while eliminating the confounding effects of gene ablation. We demonstrate that hdPCA accurately predicts the effects of two longevity and health span-affecting drugs, the immunosuppressant rapamycin and the type 2 diabetes drug metformin, on cellular pathways. We also discovered an unsuspected global cellular response to metformin that resembles iron deficiency and includes a change in protein-bound iron levels. This discovery opens a new avenue to investigate molecular mechanisms for the prevention or treatment of diabetes, cancers, and other chronic diseases of aging.
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Affiliation(s)
- Bram Stynen
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Diala Abd-Rabbo
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada; Centre Robert-Cedergren, Bio-Informatique et Génomique, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, QC H3C 3J7, Canada
| | - Jacqueline Kowarzyk
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Leonor Miller-Fleming
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Simran Kaur Aulakh
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Philippe Garneau
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Markus Ralser
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Biochemistry, Charité University Medicine, Berlin, Germany
| | - Stephen W Michnick
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada; Centre Robert-Cedergren, Bio-Informatique et Génomique, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, QC H3C 3J7, Canada.
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Weill U, Yofe I, Sass E, Stynen B, Davidi D, Natarajan J, Ben-Menachem R, Avihou Z, Goldman O, Harpaz N, Chuartzman S, Kniazev K, Knoblach B, Laborenz J, Boos F, Kowarzyk J, Ben-Dor S, Zalckvar E, Herrmann JM, Rachubinski RA, Pines O, Rapaport D, Michnick SW, Levy ED, Schuldiner M. Genome-wide SWAp-Tag yeast libraries for proteome exploration. Nat Methods 2018; 15:617-622. [PMID: 29988094 PMCID: PMC6076999 DOI: 10.1038/s41592-018-0044-9] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 05/10/2018] [Indexed: 12/31/2022]
Abstract
Yeast libraries revolutionized the systematic study of cell biology. To extensively increase the number of such libraries and the type of information that can be gleaned from them, we previously devised the SWAp-Tag (SWAT) approach that enables rapid, easy and efficient creation of yeast strain collections. Here we present the construction and investigation of a full genome library of ~5500 strains carrying the SWAT NOP1promoter-GFP module at the N terminus of proteins, as well as its use in creating six additional libraries that either restore the native regulation, create an overexpression library with a Cherry tag or enable protein complementation assays from two fragments of an enzyme or fluorophore. We show methods to utilize these SWAT collections to systematically characterize the yeast proteome on multiple levels spanning protein abundance, localization, topology and interactions. Our findings demonstrate how diverse full-genome SWAT libraries facilitate obtaining insights into numerous aspects of the proteome.
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Affiliation(s)
- Uri Weill
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ido Yofe
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ehud Sass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Bram Stynen
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montreal, QC, Canada
| | - Dan Davidi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Janani Natarajan
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Reut Ben-Menachem
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Zohar Avihou
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Omer Goldman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Nofar Harpaz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Silvia Chuartzman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Kiril Kniazev
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Barbara Knoblach
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Janina Laborenz
- Department of Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Felix Boos
- Department of Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Jacqueline Kowarzyk
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montreal, QC, Canada
| | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Johannes M Herrmann
- Department of Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | | | - Ophry Pines
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Stephen W Michnick
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montreal, QC, Canada
| | - Emmanuel D Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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Stynen B, Abd-Rabbo D, Kowarzyk J, Miller-Fleming L, Ralser M, Michnick SW. A Novel Yeast Global Genetic Screen Reveals That Metformin Induces an Iron Deficiency-Like State. SSRN Journal 2018. [DOI: 10.2139/ssrn.3155883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Stynen B, Abd-rabbo D, Kowarzyk J, Miller-fleming L, Ralser M, Michnick S. A Yeast Global Genetic Screen Reveals that Metformin Induces an Iron Deficiency-Like State.. [DOI: 10.1101/190389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
AbstractWe report here a simple and global strategy to map out gene functions and target pathways of drugs, toxins or other small molecules based on “homomer dynamics” Protein-fragment Complementation Assays (hdPCA). hdPCA measures changes in self-association (homomerization) of over 3,500 yeast proteins in yeast grown under different conditions. hdPCA complements genetic interaction measurements while eliminating confounding effects of gene ablation. We demonstrate that hdPCA accurately predicts the effects of two longevity and health-span-affecting drugs, immunosuppressant rapamycin and type II diabetes drug metformin, on cellular pathways. We also discovered an unsuspected global cellular response to metformin that resembles iron deficiency. This discovery opens a new avenue to investigate molecular mechanisms for the prevention or treatments of diabetes, cancers and other chronic diseases of aging.
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Michnick SW, Landry CR, Levy ED, Diss G, Ear PH, Kowarzyk J, Malleshaiah MK, Messier V, Tchekanda E. Protein-Fragment Complementation Assays for Large-Scale Analysis, Functional Dissection, and Spatiotemporal Dynamic Studies of Protein-Protein Interactions in Living Cells. Cold Spring Harb Protoc 2016; 2016:2016/11/pdb.top083543. [PMID: 27803260 DOI: 10.1101/pdb.top083543] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Protein-fragment complementation assays (PCAs) comprise a family of assays that can be used to study protein-protein interactions (PPIs), conformation changes, and protein complex dimensions. We developed PCAs to provide simple and direct methods for the study of PPIs in any living cell, subcellular compartments or membranes, multicellular organisms, or in vitro. Because they are complete assays, requiring no cell-specific components other than reporter fragments, they can be applied in any context. PCAs provide a general strategy for the detection of proteins expressed at endogenous levels within appropriate subcellular compartments and with normal posttranslational modifications, in virtually any cell type or organism under any conditions. Here we introduce a number of applications of PCAs in budding yeast, Saccharomyces cerevisiae These applications represent the full range of PPI characteristics that might be studied, from simple detection on a large scale to visualization of spatiotemporal dynamics.
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Affiliation(s)
- Stephen W Michnick
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Christian R Landry
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO-Québec Research Network on Protein Function, Structure and Engineering, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Emmanuel D Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Guillaume Diss
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO-Québec Research Network on Protein Function, Structure and Engineering, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Po Hien Ear
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Jacqueline Kowarzyk
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Mohan K Malleshaiah
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Vincent Messier
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada.,Department of Medical Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Emmanuelle Tchekanda
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
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Ear PH, Kowarzyk J, Michnick SW. Dissecting the Contingent Interactions of Protein Complexes with the Optimized Yeast Cytosine Deaminase Protein-Fragment Complementation Assay. Cold Spring Harb Protoc 2016; 2016:2016/11/pdb.prot090043. [PMID: 27803254 DOI: 10.1101/pdb.prot090043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Here, we present a detailed protocol for studying in yeast cells the contingent interaction between a substrate and its multisubunit enzyme complex by using a death selection technique known as the optimized yeast cytosine deaminase protein-fragment complementation assay (OyCD PCA). In yeast, the enzyme cytosine deaminase (encoded by FCY1) is involved in pyrimidine metabolism. The PCA is based on an engineered form of yeast cytosine deaminase optimized by directed evolution for maximum activity (OyCD), which acts as a reporter converting the pro-drug 5-fluorocytosine (5-FC) to 5-fluorouracil (5-FU), a toxic compound that kills the cell. Cells that have OyCD PCA activity convert 5-FC to 5-FU and die. Using this assay, it is possible to assess how regulatory subunits of an enzyme contribute to the overall interaction between the catalytic subunit and the potential substrates. Furthermore, OyCD PCA can be used to dissect different functions of mutant forms of a protein as a mutant can disrupt interaction with one partner, while retaining interaction with others. As it is scalable to a medium- or high-throughput format, OyCD PCA can be used to study hundreds to thousands of pairwise protein-protein interactions in different deletion strains. In addition, OyCD PCA vectors (pAG413GAL1-ccdB-OyCD-F[1] and pAG415GAL1-ccdB-OyCD-F[2]) have been designed to be compatible with the proprietary Gateway technology. It is therefore easy to generate fusion genes with the OyCD reporter fragments. As an example, we will focus on the yeast cyclin-dependent protein kinase 1 (Cdk1, encoded by CDC28), its regulatory cyclin subunits, and its substrates or binding partners.
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Affiliation(s)
- Po Hien Ear
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Jacqueline Kowarzyk
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Stephen W Michnick
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
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Michnick SW, Levy ED, Landry CR, Kowarzyk J, Messier V. The Dihydrofolate Reductase Protein-Fragment Complementation Assay: A Survival-Selection Assay for Large-Scale Analysis of Protein-Protein Interactions. Cold Spring Harb Protoc 2016; 2016:2016/11/pdb.prot090027. [PMID: 27803252 DOI: 10.1101/pdb.prot090027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Protein-fragment complementation assays (PCAs) can be used to study protein-protein interactions (PPIs) in any living cell, in vivo or in vitro, in any subcellular compartment or membranes. Here, we present a detailed protocol for performing and analyzing a high-throughput PCA screening to study PPIs in yeast, using dihydrofolate reductase (DHFR) as the reporter protein. The DHFR PCA is a simple survival-selection assay in which Saccharomyces cerevisiae DHFR (scDHFR) is inhibited by methotrexate, thus preventing nucleotide synthesis and causing arrest of cell division. Complementation of cells with a methotrexate-insensitive murine DHFR restores nucleotide synthesis, allowing cell proliferation. The methotrexate-resistant DHFR has two mutations (L22F and F31S) and is 10,000 times less sensitive to methotrexate than wild-type scDHFR, but retains full catalytic activity. The DHFR PCA is sensitive enough for PPIs to be detected for open reading frame (ORF)-PCA fragments expressed off of their endogenous promoters.
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Affiliation(s)
- Stephen W Michnick
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Emmanuel D Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100 Israel
| | - Christian R Landry
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO-Québec Research Network on Protein Function, Structure and Engineering, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Jacqueline Kowarzyk
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Vincent Messier
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada.,Department of Medical Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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Ear PH, Kowarzyk J, Booth MJ, Abd-Rabbo D, Shulist K, Hall C, Vogel J, Michnick SW. Erratum to: Combining the Optimized Yeast Cytosine Deaminase Protein Fragment Complementation Assay and an In Vitro Cdk1 Targeting Assay to Study the Regulation of the γ-Tubulin Complex. Methods Mol Biol 2016; 1342:E1. [PMID: 27240595 DOI: 10.1007/978-1-4939-2957-3_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Affiliation(s)
- Po Hien Ear
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, Canada, H3C 3J7
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jacqueline Kowarzyk
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, Canada, H3C 3J7
| | - Michael J Booth
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, Canada, H3C 3J7
- Merton College, University of Oxford, Merton Street, Oxford, OX1 4JD, UK
| | - Diala Abd-Rabbo
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, Canada, H3C 3J7
- Centre Robert-Cedergren, Bio-Informatique et Génomique, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, Canada, H3C 3J7
| | - Kristian Shulist
- Department of Biology, McGill University, 3649 William Osler, Montreal, QC, Canada, H3G 0B1
| | - Conrad Hall
- Department of Biology, McGill University, 3649 William Osler, Montreal, QC, Canada, H3G 0B1
| | - Jackie Vogel
- Department of Biology, McGill University, 3649 William Osler, Montreal, QC, Canada, H3G 0B1.
| | - Stephen W Michnick
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, Canada, H3C 3J7.
- Centre Robert-Cedergren, Bio-Informatique et Génomique, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, Canada, H3C 3J7.
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Ear PH, Kowarzyk J, Booth MJ, Abd-Rabbo D, Shulist K, Hall C, Vogel J, Michnick SW. Combining the Optimized Yeast Cytosine Deaminase Protein Fragment Complementation Assay and an In Vitro Cdk1 Targeting Assay to Study the Regulation of the γ-Tubulin Complex. Methods Mol Biol 2016; 1342:237-57. [PMID: 26254928 DOI: 10.1007/978-1-4939-2957-3_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Cdk1 is the essential cyclin-dependent kinase in the budding yeast Saccharomyces cerevisiae. Cdk1 orchestrates cell cycle control by phosphorylating target proteins with extraordinary temporal and spatial specificity by complexing with one of the nine cyclin regulatory subunits. The identification of the cyclin required for targeting Cdk1 to a substrate can help to place the regulation of that protein at a specific time point during the cell cycle and reveal information needed to elucidate the biological significance of the regulation. Here, we describe a combination of strategies to identify interaction partners of Cdk1, and associate these complexes to the appropriate cyclins using a cell-based protein-fragment complementation assay. Validation of the specific reliance of the OyCD interaction between Cdk1 and budding yeast γ-tubulin on the Clb3 cyclin, relative to the mitotic Clb2 cyclin, was performed by an in vitro kinase assay using the γ-tubulin complex as a substrate.
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Affiliation(s)
- Po Hien Ear
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, Canada, H3C 3J7
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