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Abstract
Sulfur assimilation and the biosynthesis of methionine, cysteine and S-adenosylmethionine (SAM) are critical to life. As a cofactor, SAM is required for the activity of most methyltransferases (MTases) and as such has broad impact on diverse cellular processes. Assigning function to MTases remains a challenge however, as many MTases are partially redundant, they often have multiple cellular roles and these activities can be condition-dependent. To address these challenges, we performed a systematic synthetic genetic analysis of all pairwise MTase double mutations in normal and stress conditions (16°C, 37°C, and LiCl) resulting in an unbiased comprehensive overview of the complexity and plasticity of the methyltransferome. Based on this network, we performed biochemical analysis of members of the histone H3K4 COMPASS complex and the phospholipid methyltransferase OPI3 to reveal a new role for a phospholipid methyltransferase in mediating histone methylation (H3K4) which underscores a potential link between lipid homeostasis and histone methylation. Our findings provide a valuable resource to study methyltransferase function, the dynamics of the methyltransferome, genetic crosstalk between biological processes and the dynamics of the methyltransferome in response to cellular stress.
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Affiliation(s)
- Guri Giaever
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Elena Lissina
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Corey Nislow
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
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Lee AY, St Onge RP, Proctor MJ, Wallace IM, Nile AH, Spagnuolo PA, Jitkova Y, Gronda M, Wu Y, Kim MK, Cheung-Ong K, Torres NP, Spear ED, Han MKL, Schlecht U, Suresh S, Duby G, Heisler LE, Surendra A, Fung E, Urbanus ML, Gebbia M, Lissina E, Miranda M, Chiang JH, Aparicio AM, Zeghouf M, Davis RW, Cherfils J, Boutry M, Kaiser CA, Cummins CL, Trimble WS, Brown GW, Schimmer AD, Bankaitis VA, Nislow C, Bader GD, Giaever G. Mapping the cellular response to small molecules using chemogenomic fitness signatures. Science 2014; 344:208-11. [PMID: 24723613 DOI: 10.1126/science.1250217] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Genome-wide characterization of the in vivo cellular response to perturbation is fundamental to understanding how cells survive stress. Identifying the proteins and pathways perturbed by small molecules affects biology and medicine by revealing the mechanisms of drug action. We used a yeast chemogenomics platform that quantifies the requirement for each gene for resistance to a compound in vivo to profile 3250 small molecules in a systematic and unbiased manner. We identified 317 compounds that specifically perturb the function of 121 genes and characterized the mechanism of specific compounds. Global analysis revealed that the cellular response to small molecules is limited and described by a network of 45 major chemogenomic signatures. Our results provide a resource for the discovery of functional interactions among genes, chemicals, and biological processes.
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Affiliation(s)
- Anna Y Lee
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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Lissina E, Weiss D, Young B, Rella A, Cheung-Ong K, Del Poeta M, Clarke SG, Giaever G, Nislow C. A novel small molecule methyltransferase is important for virulence in Candida albicans. ACS Chem Biol 2013; 8:2785-93. [PMID: 24083538 DOI: 10.1021/cb400607h] [Citation(s) in RCA: 6] [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: 12/30/2022]
Abstract
Candida albicans is an opportunistic pathogen capable of causing life-threatening infections in immunocompromised individuals. Despite its significant health impact, our understanding of C. albicans pathogenicity is limited, particularly at the molecular level. One of the largely understudied enzyme families in C. albicans are small molecule AdoMet-dependent methyltransferases (smMTases), which are important for maintenance of cellular homeostasis by clearing toxic chemicals, generating novel cellular intermediates, and regulating intra- and interspecies interactions. In this study, we demonstrated that C. albicans Crg1 (CaCrg1) is a bona fide smMTase that interacts with the toxin in vitro and in vivo. We report that CaCrg1 is important for virulence-related processes such as adhesion, hyphal elongation, and membrane trafficking. Biochemical and genetic analyses showed that CaCrg1 plays a role in the complex sphingolipid pathway: it binds to exogenous short-chain ceramides in vitro and interacts genetically with genes of glucosylceramide pathway, and the deletion of CaCRG1 leads to significant changes in the abundance of phytoceramides. Finally we found that this novel lipid-related smMTase is required for virulence in the waxmoth Galleria mellonella, a model of infection.
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Affiliation(s)
- Elena Lissina
- Department
of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, 160 College St., Toronto, M5S 3E1, Canada
| | - David Weiss
- Department
of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Brian Young
- Department
of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Antonella Rella
- Department
of Molecular Genetics and Microbiology, Stony Brook University, 150 Life Sciences Building, Stony Brook, New York 11794-5222, United States
| | - Kahlin Cheung-Ong
- Department
of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, 160 College St., Toronto, M5S 3E1, Canada
| | - Maurizio Del Poeta
- Department
of Molecular Genetics and Microbiology, Stony Brook University, 150 Life Sciences Building, Stony Brook, New York 11794-5222, United States
| | - Steven G. Clarke
- Department
of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Guri Giaever
- Department
of Pharmaceutical Sciences, University of British Columbia, 2405
Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Corey Nislow
- Department
of Pharmaceutical Sciences, University of British Columbia, 2405
Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
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Wan LCK, Mao DYL, Neculai D, Strecker J, Chiovitti D, Kurinov I, Poda G, Thevakumaran N, Yuan F, Szilard RK, Lissina E, Nislow C, Caudy AA, Durocher D, Sicheri F. Reconstitution and characterization of eukaryotic N6-threonylcarbamoylation of tRNA using a minimal enzyme system. Nucleic Acids Res 2013; 41:6332-46. [PMID: 23620299 PMCID: PMC3695523 DOI: 10.1093/nar/gkt322] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [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] [Indexed: 11/29/2022] Open
Abstract
The universally conserved Kae1/Qri7/YgjD and Sua5/YrdC protein families have been implicated in growth, telomere homeostasis, transcription and the N6-threonylcarbamoylation (t6A) of tRNA, an essential modification required for translational fidelity by the ribosome. In bacteria, YgjD orthologues operate in concert with the bacterial-specific proteins YeaZ and YjeE, whereas in archaeal and eukaryotic systems, Kae1 operates as part of a larger macromolecular assembly called KEOPS with Bud32, Cgi121, Gon7 and Pcc1 subunits. Qri7 orthologues function in the mitochondria and may represent the most primitive member of the Kae1/Qri7/YgjD protein family. In accordance with previous findings, we confirm that Qri7 complements Kae1 function and uncover that Qri7 complements the function of all KEOPS subunits in growth, t6A biosynthesis and, to a partial degree, telomere maintenance. These observations suggest that Kae1 provides a core essential function that other subunits within KEOPS have evolved to support. Consistent with this inference, Qri7 alone is sufficient for t6A biosynthesis with Sua5 in vitro. In addition, the 2.9 Å crystal structure of Qri7 reveals a simple homodimer arrangement that is supplanted by the heterodimerization of YgjD with YeaZ in bacteria and heterodimerization of Kae1 with Pcc1 in KEOPS. The partial complementation of telomere maintenance by Qri7 hints that KEOPS has evolved novel functions in higher organisms.
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Affiliation(s)
- Leo C K Wan
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
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Lissina E, Young B, Urbanus ML, Guan XL, Lowenson J, Hoon S, Baryshnikova A, Riezman I, Michaut M, Riezman H, Cowen LE, Wenk MR, Clarke SG, Giaever G, Nislow C. A systems biology approach reveals the role of a novel methyltransferase in response to chemical stress and lipid homeostasis. PLoS Genet 2011; 7:e1002332. [PMID: 22028670 PMCID: PMC3197675 DOI: 10.1371/journal.pgen.1002332] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 08/19/2011] [Indexed: 11/24/2022] Open
Abstract
Using small molecule probes to understand gene function is an attractive approach that allows functional characterization of genes that are dispensable in standard laboratory conditions and provides insight into the mode of action of these compounds. Using chemogenomic assays we previously identified yeast Crg1, an uncharacterized SAM-dependent methyltransferase, as a novel interactor of the protein phosphatase inhibitor cantharidin. In this study we used a combinatorial approach that exploits contemporary high-throughput techniques available in Saccharomyces cerevisiae combined with rigorous biological follow-up to characterize the interaction of Crg1 with cantharidin. Biochemical analysis of this enzyme followed by a systematic analysis of the interactome and lipidome of CRG1 mutants revealed that Crg1, a stress-responsive SAM-dependent methyltransferase, methylates cantharidin in vitro. Chemogenomic assays uncovered that lipid-related processes are essential for cantharidin resistance in cells sensitized by deletion of the CRG1 gene. Lipidome-wide analysis of mutants further showed that cantharidin induces alterations in glycerophospholipid and sphingolipid abundance in a Crg1-dependent manner. We propose that Crg1 is a small molecule methyltransferase important for maintaining lipid homeostasis in response to drug perturbation. This approach demonstrates the value of combining chemical genomics with other systems-based methods for characterizing proteins and elucidating previously unknown mechanisms of action of small molecule inhibitors.
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Affiliation(s)
- Elena Lissina
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Brian Young
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Malene L. Urbanus
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Xue Li Guan
- Department of Biological Sciences, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Jonathan Lowenson
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Shawn Hoon
- Molecular Engineering Lab, Agency for Science, Technology, and Research, Singapore, Singapore
| | - Anastasia Baryshnikova
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Isabelle Riezman
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Magali Michaut
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Howard Riezman
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Leah E. Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Markus R. Wenk
- Department of Biological Sciences, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Steven G. Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Guri Giaever
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
- Department of Pharmacy and Pharmaceutical Sciences, University of Toronto, Toronto, Canada
| | - Corey Nislow
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
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