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Ólafsson G, Haase MAB, Boeke JD. Humanization reveals pervasive incompatibility of yeast and human kinetochore components. G3 (BETHESDA, MD.) 2023; 14:jkad260. [PMID: 37962556 PMCID: PMC10755175 DOI: 10.1093/g3journal/jkad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 06/29/2023] [Accepted: 11/06/2023] [Indexed: 11/15/2023]
Abstract
Kinetochores assemble on centromeres to drive chromosome segregation in eukaryotic cells. Humans and budding yeast share most of the structural subunits of the kinetochore, whereas protein sequences have diverged considerably. The conserved centromeric histone H3 variant, CenH3 (CENP-A in humans and Cse4 in budding yeast), marks the site for kinetochore assembly in most species. A previous effort to complement Cse4 in yeast with human CENP-A was unsuccessful; however, co-complementation with the human core nucleosome was not attempted. Previously, our lab successfully humanized the core nucleosome in yeast; however, this severely affected cellular growth. We hypothesized that yeast Cse4 is incompatible with humanized nucleosomes and that the kinetochore represented a limiting factor for efficient histone humanization. Thus, we argued that including the human CENP-A or a Cse4-CENP-A chimera might improve histone humanization and facilitate kinetochore function in humanized yeast. The opposite was true: CENP-A expression reduced histone humanization efficiency, was toxic to yeast, and disrupted cell cycle progression and kinetochore function in wild-type (WT) cells. Suppressors of CENP-A toxicity included gene deletions of subunits of 3 conserved chromatin remodeling complexes, highlighting their role in CenH3 chromatin positioning. Finally, we attempted to complement the subunits of the NDC80 kinetochore complex, individually and in combination, without success, in contrast to a previous study indicating complementation by the human NDC80/HEC1 gene. Our results suggest that limited protein sequence similarity between yeast and human components in this very complex structure leads to failure of complementation.
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Affiliation(s)
- Guðjón Ólafsson
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Max A B Haase
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Vilcek Institute of Graduate Biomedical Sciences, NYU School of Medicine, New York, NY 10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 14 11201, USA
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Klemm C, Wood H, Thomas GH, Ólafsson G, Torres MT, Thorpe PH. Forced association of SARS-CoV-2 proteins with the yeast proteome perturb vesicle trafficking. MICROBIAL CELL (GRAZ, AUSTRIA) 2021; 8:280-296. [PMID: 34909432 PMCID: PMC8642885 DOI: 10.15698/mic2021.12.766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/07/2021] [Accepted: 10/15/2021] [Indexed: 11/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the highly infectious coronavirus disease COVID-19. Extensive research has been performed in recent months to better understand how SARS-CoV-2 infects and manipulates its host to identify potential drug targets and support patient recovery from COVID-19. However, the function of many SARS-CoV-2 proteins remains uncharacterised. Here we used the Synthetic Physical Interactions (SPI) method to recruit SARS-CoV-2 proteins to most of the budding yeast proteome to identify conserved pathways which are affected by SARS-CoV-2 proteins. The set of yeast proteins that result in growth defects when associated with the viral proteins have homologous functions that overlap those identified in studies performed in mammalian cells. Specifically, we were able to show that recruiting the SARS-CoV-2 NSP1 protein to HOPS, a vesicle-docking complex, is sufficient to perturb membrane trafficking in yeast consistent with the hijacking of the endoplasmic-reticulum-Golgi intermediate compartment trafficking pathway during viral infection of mammalian cells. These data demonstrate that the yeast SPI method is a rapid way to identify potential functions of ectopic viral proteins.
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Affiliation(s)
- Cinzia Klemm
- School of Biological and Behavioural Sciences, Queen Mary University of London, E1 4NS, UK
| | - Henry Wood
- School of Biological and Behavioural Sciences, Queen Mary University of London, E1 4NS, UK
| | - Grace Heredge Thomas
- School of Biological and Behavioural Sciences, Queen Mary University of London, E1 4NS, UK
| | - Guðjón Ólafsson
- School of Biological and Behavioural Sciences, Queen Mary University of London, E1 4NS, UK
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Mara Teixeira Torres
- School of Biological and Behavioural Sciences, Queen Mary University of London, E1 4NS, UK
| | - Peter H. Thorpe
- School of Biological and Behavioural Sciences, Queen Mary University of London, E1 4NS, UK
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Mishra PK, Wood H, Stanton J, Au WC, Eisenstatt JR, Boeckmann L, Sclafani RA, Weinreich M, Bloom KS, Thorpe PH, Basrai MA. Cdc7-mediated phosphorylation of Cse4 regulates high-fidelity chromosome segregation in budding yeast. Mol Biol Cell 2021; 32:ar15. [PMID: 34432494 PMCID: PMC8693968 DOI: 10.1091/mbc.e21-06-0323] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/11/2021] [Accepted: 08/18/2021] [Indexed: 12/21/2022] Open
Abstract
Faithful chromosome segregation maintains chromosomal stability as errors in this process contribute to chromosomal instability (CIN), which has been observed in many diseases including cancer. Epigenetic regulation of kinetochore proteins such as Cse4 (CENP-A in humans) plays a critical role in high-fidelity chromosome segregation. Here we show that Cse4 is a substrate of evolutionarily conserved Cdc7 kinase, and that Cdc7-mediated phosphorylation of Cse4 prevents CIN. We determined that Cdc7 phosphorylates Cse4 in vitro and interacts with Cse4 in vivo in a cell cycle-dependent manner. Cdc7 is required for kinetochore integrity as reduced levels of CEN-associated Cse4, a faster exchange of Cse4 at the metaphase kinetochores, and defects in chromosome segregation, are observed in a cdc7-7 strain. Phosphorylation of Cse4 by Cdc7 is important for cell survival as constitutive association of a kinase-dead variant of Cdc7 (cdc7-kd) with Cse4 at the kinetochore leads to growth defects. Moreover, phospho-deficient mutations of Cse4 for consensus Cdc7 target sites contribute to CIN phenotype. In summary, our results have defined a role for Cdc7-mediated phosphorylation of Cse4 in faithful chromosome segregation.
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Affiliation(s)
- Prashant K. Mishra
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Henry Wood
- Queen Mary University of London, London E1 4NS, UK
| | - John Stanton
- University of North Carolina, Chapel Hill, NC 27599
| | - Wei-Chun Au
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Jessica R. Eisenstatt
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Lars Boeckmann
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | | | | | | | | | - Munira A. Basrai
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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Howell RSM, Csikász-Nagy A, Thorpe PH. Synthetic Physical Interactions with the Yeast Centrosome. G3 (BETHESDA, MD.) 2019; 9:2183-2194. [PMID: 31076383 PMCID: PMC6643875 DOI: 10.1534/g3.119.400117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/02/2019] [Indexed: 12/30/2022]
Abstract
The yeast centrosome or Spindle Pole Body (SPB) is an organelle situated in the nuclear membrane, where it nucleates spindle microtubules and acts as a signaling hub. Various studies have explored the effects of forcing individual proteins to interact with the yeast SPB, however no systematic study has been performed. We used synthetic physical interactions to detect proteins that inhibit growth when forced to associate with the SPB. We found the SPB to be especially sensitive to relocalization, necessitating a novel data analysis approach. This novel analysis of SPI screening data shows that regions of the cell are locally more sensitive to forced relocalization than previously thought. Furthermore, we found a set of associations that result in elevated SPB number and, in some cases, multi-polar spindles. Since hyper-proliferation of centrosomes is a hallmark of cancer cells, these associations point the way for the use of yeast models in the study of spindle formation and chromosome segregation in cancer.
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Affiliation(s)
- Rowan S M Howell
- The Francis Crick Institute, London, NW1 1AT UK
- Randall Division of Cell and Molecular Biophysics, King's College, London, SE1 1UL UK
| | - Attila Csikász-Nagy
- Randall Division of Cell and Molecular Biophysics, King's College, London, SE1 1UL UK
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, 1083 Hungary
| | - Peter H Thorpe
- School of Biological and Chemical Sciences, Queen Mary University, London, E1 4NS UK
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Mishra PK, Olafsson G, Boeckmann L, Westlake TJ, Jowhar ZM, Dittman LE, Baker RE, D’Amours D, Thorpe PH, Basrai MA. Cell cycle-dependent association of polo kinase Cdc5 with CENP-A contributes to faithful chromosome segregation in budding yeast. Mol Biol Cell 2019; 30:1020-1036. [PMID: 30726152 PMCID: PMC6589903 DOI: 10.1091/mbc.e18-09-0584] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/04/2019] [Accepted: 01/30/2019] [Indexed: 12/18/2022] Open
Abstract
Evolutionarily conserved polo-like kinase, Cdc5 (Plk1 in humans), associates with kinetochores during mitosis; however, the role of cell cycle-dependent centromeric ( CEN) association of Cdc5 and its substrates that exclusively localize to the kinetochore have not been characterized. Here we report that evolutionarily conserved CEN histone H3 variant, Cse4 (CENP-A in humans), is a substrate of Cdc5, and that the cell cycle-regulated association of Cse4 with Cdc5 is required for cell growth. Cdc5 contributes to Cse4 phosphorylation in vivo and interacts with Cse4 in mitotic cells. Mass spectrometry analysis of in vitro kinase assays showed that Cdc5 phosphorylates nine serine residues clustered within the N-terminus of Cse4. Strains with cse4-9SA exhibit increased errors in chromosome segregation, reduced levels of CEN-associated Mif2 and Mcd1/Scc1 when combined with a deletion of MCM21. Moreover, the loss of Cdc5 from the CEN chromatin contributes to defects in kinetochore integrity and reduction in CEN-associated Cse4. The cell cycle-regulated association of Cdc5 with Cse4 is essential for cell viability as constitutive association of Cdc5 with Cse4 at the kinetochore leads to growth defects. In summary, our results have defined a role for Cdc5-mediated Cse4 phosphorylation in faithful chromosome segregation.
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Affiliation(s)
- Prashant K. Mishra
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Gudjon Olafsson
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Lars Boeckmann
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Timothy J. Westlake
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Ziad M. Jowhar
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Lauren E. Dittman
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Richard E. Baker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655
| | - Damien D’Amours
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Peter H. Thorpe
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Munira A. Basrai
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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