1
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Milholland KL, Waddey BT, Velázquez-Marrero KG, Lihon MV, Danzeisen EL, Naughton NH, Adams TJ, Schwartz JL, Liu X, Hall MC. Cdc14 phosphatases use an intramolecular pseudosubstrate motif to stimulate and regulate catalysis. J Biol Chem 2024; 300:107644. [PMID: 39122012 DOI: 10.1016/j.jbc.2024.107644] [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: 04/22/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024] Open
Abstract
Cdc14 phosphatases are related structurally and mechanistically to protein tyrosine phosphatases (PTPs) but evolved a unique specificity for phosphoSer-Pro-X-Lys/Arg sites primarily deposited by cyclin-dependent kinases. This specialization is widely conserved in eukaryotes. The evolutionary reconfiguration of the Cdc14 active site to selectively accommodate phosphoSer-Pro likely required modification to the canonical PTP catalytic cycle. While studying Saccharomyces cerevisiae Cdc14, we discovered a short sequence in the disordered C terminus, distal to the catalytic domain, which mimics an optimal substrate. Kinetic analyses demonstrated this pseudosubstrate binds the active site and strongly stimulates rate-limiting phosphoenzyme hydrolysis, and we named it "substrate-like catalytic enhancer" (SLiCE). The SLiCE motif is found in all Dikarya fungal Cdc14 orthologs and contains an invariant glutamine, which we propose is positioned via substrate-like contacts to assist orientation of the hydrolytic water, similar to a conserved active site glutamine in other PTPs that Cdc14 lacks. AlphaFold2 predictions revealed vertebrate Cdc14 orthologs contain a conserved C-terminal alpha helix bound to the active site. Although apparently unrelated to the fungal sequence, this motif also makes substrate-like contacts and has an invariant glutamine in the catalytic pocket. Altering these residues in human Cdc14A and Cdc14B demonstrated that it functions by the same mechanism as the fungal motif. However, the fungal and vertebrate SLiCE motifs were not functionally interchangeable, illuminating potential active site differences during catalysis. Finally, we show that the fungal SLiCE motif is a target for phosphoregulation of Cdc14 activity. Our study uncovered evolution of an unusual stimulatory pseudosubstrate motif in Cdc14 phosphatases.
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Affiliation(s)
| | - Benjamin T Waddey
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | | | - Michelle V Lihon
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Emily L Danzeisen
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Noelle H Naughton
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Timothy J Adams
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Jack L Schwartz
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Xing Liu
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA; Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Mark C Hall
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA; Institute for Cancer Research, Purdue University, West Lafayette, Indiana, USA; Institute for Drug Discovery, Purdue University, West Lafayette, Indiana, USA; Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana, USA.
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2
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Milholland KL, Gregor JB, Hoda S, Píriz-Antúnez S, Dueñas-Santero E, Vu BG, Patel KP, Moye-Rowley WS, Vázquez de Aldana CR, Correa-Bordes J, Briggs SD, Hall MC. Rapid, efficient auxin-inducible protein degradation in Candida pathogens. mSphere 2023; 8:e0028323. [PMID: 37594261 PMCID: PMC10597344 DOI: 10.1128/msphere.00283-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 06/30/2023] [Indexed: 08/19/2023] Open
Abstract
A variety of inducible protein degradation (IPD) systems have been developed as powerful tools for protein functional characterization. IPD systems provide a convenient mechanism for rapid inactivation of almost any target protein of interest. Auxin-inducible degradation (AID) is one of the most common IPD systems and has been established in diverse eukaryotic research model organisms. Thus far, IPD tools have not been developed for use in pathogenic fungal species. Here, we demonstrate that the original AID and the second generation, AID2, systems work efficiently and rapidly in the human pathogenic yeasts, Candida albicans and Candida glabrata. We developed a collection of plasmids that support AID system use in laboratory strains of these pathogens. These systems can induce >95% degradation of target proteins within minutes. In the case of AID2, maximal degradation was achieved at low nanomolar concentrations of the synthetic auxin analog 5-adamantyl-indole-3-acetic acid. Auxin-induced target degradation successfully phenocopied gene deletions in both species. The system should be readily adaptable to other fungal species and to clinical pathogen strains. Our results define the AID system as a powerful and convenient functional genomics tool for protein characterization in fungal pathogens. IMPORTANCE Life-threatening fungal infections are an escalating human health problem, complicated by limited treatment options and the evolution of drug resistant pathogen strains. Identification of new targets for therapeutics to combat invasive fungal infections, including those caused by Candida species, is an urgent need. In this report, we establish and validate an inducible protein degradation methodology in Candida albicans and Candida glabrata that provides a new tool for protein functional characterization in these, and likely other, fungal pathogen species. We expect this tool will ultimately be useful for the identification and characterization of promising drug targets and factors involved in virulence and drug resistance.
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Affiliation(s)
| | - Justin B. Gregor
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Smriti Hoda
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | | | - Encarnación Dueñas-Santero
- Institute of Functional Biology and Genomics, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca (USAL), Salamanca, Spain
| | - Bao Gia Vu
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Krishna P. Patel
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - W. Scott Moye-Rowley
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Carlos R. Vázquez de Aldana
- Institute of Functional Biology and Genomics, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca (USAL), Salamanca, Spain
| | - Jaime Correa-Bordes
- Department of Biomedical Sciences, Universidad de Extremadura, Badajoz, Spain
| | - Scott D. Briggs
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
- Institute for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Mark C. Hall
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
- Institute for Cancer Research, Purdue University, West Lafayette, Indiana, USA
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3
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Milholland KL, Gregor JB, Hoda S, Píriz-Antúnez S, Dueñas-Santero E, Vu BG, Patel KP, Moye-Rowley WS, de Aldana CRV, Correa-Bordes J, Briggs SD, Hall MC. Rapid, efficient auxin-inducible protein degradation in Candida pathogens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.17.541235. [PMID: 37293017 PMCID: PMC10245712 DOI: 10.1101/2023.05.17.541235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A variety of inducible protein degradation (IPD) systems have been developed as powerful tools for protein functional characterization. IPD systems provide a convenient mechanism for rapid inactivation of almost any target protein of interest. Auxin-inducible degradation (AID) is one of the most common IPD systems and has been established in diverse eukaryotic research model organisms. Thus far, IPD tools have not been developed for use in pathogenic fungal species. Here, we demonstrate that the original AID and the second generation AID2 systems work efficiently and rapidly in the human pathogenic yeasts Candida albicans and Candida glabrata . We developed a collection of plasmids that support AID system use in laboratory strains of these pathogens. These systems can induce >95% degradation of target proteins within minutes. In the case of AID2, maximal degradation was achieved at low nanomolar concentrations of the synthetic auxin analog 5-adamantyl-indole-3-acetic acid (5-Ad-IAA). Auxin-induced target degradation successfully phenocopied gene deletions in both species. The system should be readily adaptable to other fungal species and to clinical pathogen strains. Our results define the AID system as a powerful and convenient functional genomics tool for protein characterization in fungal pathogens.
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Affiliation(s)
- Kedric L. Milholland
- Department of Biochemistry and Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Justin B. Gregor
- Department of Biochemistry and Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Smriti Hoda
- Department of Biochemistry and Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | | | - Encarnación Dueñas-Santero
- Institute of Functional Biology and Genomics, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca (USAL), Salamanca, Spain
| | - Bao Gia Vu
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Krishna P. Patel
- Department of Biochemistry and Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - W. Scott Moye-Rowley
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Carlos R. Vázquez de Aldana
- Institute of Functional Biology and Genomics, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca (USAL), Salamanca, Spain
| | - Jaime Correa-Bordes
- Department of Biomedical Sciences, Universidad de Extremadura, Badajoz, Spain
| | - Scott D. Briggs
- Department of Biochemistry and Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Mark C. Hall
- Department of Biochemistry and Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
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4
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Milholland KL, AbdelKhalek A, Baker KM, Hoda S, DeMarco AG, Naughton NH, Koeberlein AN, Lorenz GR, Anandasothy K, Esperilla-Muñoz A, Narayanan SK, Correa-Bordes J, Briggs SD, Hall MC. Cdc14 phosphatase contributes to cell wall integrity and pathogenesis in Candida albicans. Front Microbiol 2023; 14:1129155. [PMID: 36876065 PMCID: PMC9977832 DOI: 10.3389/fmicb.2023.1129155] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/26/2023] [Indexed: 02/18/2023] Open
Abstract
The Cdc14 phosphatase family is highly conserved in fungi. In Saccharomyces cerevisiae, Cdc14 is essential for down-regulation of cyclin-dependent kinase activity at mitotic exit. However, this essential function is not broadly conserved and requires only a small fraction of normal Cdc14 activity. Here, we identified an invariant motif in the disordered C-terminal tail of fungal Cdc14 enzymes that is required for full enzyme activity. Mutation of this motif reduced Cdc14 catalytic rate and provided a tool for studying the biological significance of high Cdc14 activity. A S. cerevisiae strain expressing the reduced-activity hypomorphic mutant allele (cdc14hm ) as the sole source of Cdc14 proliferated like the wild-type parent strain but exhibited an unexpected sensitivity to cell wall stresses, including chitin-binding compounds and echinocandin antifungal drugs. Sensitivity to echinocandins was also observed in Schizosaccharomyces pombe and Candida albicans strains lacking CDC14, suggesting this phenotype reflects a novel and conserved function of Cdc14 orthologs in mediating fungal cell wall integrity. In C. albicans, the orthologous cdc14hm allele was sufficient to elicit echinocandin hypersensitivity and perturb cell wall integrity signaling. It also caused striking abnormalities in septum structure and the same cell separation and hyphal differentiation defects previously observed with cdc14 gene deletions. Since hyphal differentiation is important for C. albicans pathogenesis, we assessed the effect of reduced Cdc14 activity on virulence in Galleria mellonella and mouse models of invasive candidiasis. Partial reduction in Cdc14 activity via cdc14hm mutation severely impaired C. albicans virulence in both assays. Our results reveal that high Cdc14 activity is important for C. albicans cell wall integrity and pathogenesis and suggest that Cdc14 may be worth future exploration as an antifungal drug target.
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Affiliation(s)
- Kedric L Milholland
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Ahmed AbdelKhalek
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States
| | - Kortany M Baker
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Smriti Hoda
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Andrew G DeMarco
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Noelle H Naughton
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Angela N Koeberlein
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Gabrielle R Lorenz
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Kartikan Anandasothy
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | | | - Sanjeev K Narayanan
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States
| | - Jaime Correa-Bordes
- Department of Biomedical Sciences, Universidad de Extremadura, Badajoz, Spain
| | - Scott D Briggs
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States.,Institute for Cancer Research, Purdue University, West Lafayette, IN, United States
| | - Mark C Hall
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States.,Institute for Cancer Research, Purdue University, West Lafayette, IN, United States
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5
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Nicoletti G, White K. The Anti-Fungal Activity of Nitropropenyl Benzodioxole (NPBD), a Redox-Thiol Oxidant and Tyrosine Phosphatase Inhibitor. Antibiotics (Basel) 2022; 11:antibiotics11091188. [PMID: 36139967 PMCID: PMC9495065 DOI: 10.3390/antibiotics11091188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Phylogenetically diverse fungal species are an increasing cause of severe disease and mortality. Identification of new targets and development of new fungicidal drugs are required to augment the effectiveness of current chemotherapy and counter increasing resistance in pathogens. Nitroalkenyl benzene derivatives are thiol oxidants and inhibitors of cysteine-based molecules, which show broad biological activity against microorganisms. Nitropropenyl benzodioxole (NPBD), one of the most active antimicrobial derivatives, shows high activity in MIC assays for phylogenetically diverse saprophytic, commensal and parasitic fungi. NPBD was fungicidal to all species except the dermatophytic fungi, with an activity profile comparable to that of Amphotericin B and Miconazole. NPBD showed differing patterns of dynamic kill rates under different growth conditions for Candida albicans and Aspergillus fumigatus and was rapidly fungicidal for non-replicating vegetative forms and microconidia. It did not induce resistant or drug tolerant strains in major pathogens on long term exposure. A literature review highlights the complexity and interactivity of fungal tyrosine phosphate and redox signaling pathways, their differing metabolic effects in fungal species and identifies some targets for inhibition. A comparison of the metabolic activities of Amphotericin B, Miconazole and NPBD highlights the multiple cellular functions of these agents and the complementarity of many mechanisms. The activity profile of NPBD illustrates the functional diversity of fungal tyrosine phosphatases and thiol-based redox active molecules and contributes to the validation of tyrosine phosphatases and redox thiol molecules as related and complementary selective targets for antimicrobial drug development. NPBD is a selective antifungal agent with low oral toxicity which would be suitable for local treatment of skin and mucosal infections.
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6
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Touati SA, Hofbauer L, Jones AW, Snijders AP, Kelly G, Uhlmann F. Cdc14 and PP2A Phosphatases Cooperate to Shape Phosphoproteome Dynamics during Mitotic Exit. Cell Rep 2020; 29:2105-2119.e4. [PMID: 31722221 PMCID: PMC6857435 DOI: 10.1016/j.celrep.2019.10.041] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 09/27/2019] [Accepted: 10/10/2019] [Indexed: 12/22/2022] Open
Abstract
Temporal control over protein phosphorylation and dephosphorylation is crucial for accurate chromosome segregation and for completion of the cell division cycle during exit from mitosis. In budding yeast, the Cdc14 phosphatase is thought to be a major regulator at this time, while in higher eukaryotes PP2A phosphatases take a dominant role. Here, we use time-resolved phosphoproteome analysis in budding yeast to evaluate the respective contributions of Cdc14, PP2ACdc55, and PP2ARts1. This reveals an overlapping requirement for all three phosphatases during mitotic progression. Our time-resolved phosphoproteome resource reveals how Cdc14 instructs the sequential pattern of phosphorylation changes, in part through preferential recognition of serine-based cyclin-dependent kinase (Cdk) substrates. PP2ACdc55 and PP2ARts1 in turn exhibit a broad substrate spectrum with some selectivity for phosphothreonines and a role for PP2ARts1 in sustaining Aurora kinase activity. These results illustrate synergy and coordination between phosphatases as they orchestrate phosphoproteome dynamics during mitotic progression. Cdc14, PP2ACdc55, and PP2ARts1 phosphatases cooperate during budding yeast mitosis Cdc14 targets serine Cdk motifs for rapid dephosphorylation PP2ACdc55 dephosphorylates Cdk and Plk substrates on threonine residues PP2ARts1 displays regulatory crosstalk with Aurora kinase
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Affiliation(s)
- Sandra A Touati
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
| | - Lorena Hofbauer
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Andrew W Jones
- Mass Spectrometry Proteomics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Ambrosius P Snijders
- Mass Spectrometry Proteomics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Gavin Kelly
- Bioinformatics & Biostatistics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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7
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DeMarco AG, Milholland KL, Pendleton AL, Whitney JJ, Zhu P, Wesenberg DT, Nambiar M, Pepe A, Paula S, Chmielewski J, Wisecaver JH, Tao WA, Hall MC. Conservation of Cdc14 phosphatase specificity in plant fungal pathogens: implications for antifungal development. Sci Rep 2020; 10:12073. [PMID: 32694511 PMCID: PMC7374715 DOI: 10.1038/s41598-020-68921-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/24/2020] [Indexed: 11/08/2022] Open
Abstract
Cdc14 protein phosphatases play an important role in plant infection by several fungal pathogens. This and other properties of Cdc14 enzymes make them an intriguing target for development of new antifungal crop treatments. Active site architecture and substrate specificity of Cdc14 from the model fungus Saccharomyces cerevisiae (ScCdc14) are well-defined and unique among characterized phosphatases. Cdc14 appears absent from some model plants. However, the extent of conservation of Cdc14 sequence, structure, and specificity in fungal plant pathogens is unknown. We addressed this by performing a comprehensive phylogenetic analysis of the Cdc14 family and comparing the conservation of active site structure and specificity among a sampling of plant pathogen Cdc14 homologs. We show that Cdc14 was lost in the common ancestor of angiosperm plants but is ubiquitous in ascomycete and basidiomycete fungi. The unique substrate specificity of ScCdc14 was invariant in homologs from eight diverse species of dikarya, suggesting it is conserved across the lineage. A synthetic substrate mimetic inhibited diverse fungal Cdc14 homologs with similar low µM Ki values, but had little effect on related phosphatases. Our results justify future exploration of Cdc14 as a broad spectrum antifungal target for plant protection.
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Affiliation(s)
- Andrew G DeMarco
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Kedric L Milholland
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Amanda L Pendleton
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - John J Whitney
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Peipei Zhu
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Daniel T Wesenberg
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Monessha Nambiar
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Antonella Pepe
- Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY, 11794-3400, USA
| | - Stefan Paula
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
- Department of Chemistry, California State University, 6000 J Street, Sacramento, CA, 95819, USA
| | - Jean Chmielewski
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
- Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA
| | - Jennifer H Wisecaver
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
- Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA
| | - Mark C Hall
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA.
- Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA.
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8
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Rincón AM, Monje-Casas F. A guiding torch at the poles: the multiple roles of spindle microtubule-organizing centers during cell division. Cell Cycle 2020; 19:1405-1421. [PMID: 32401610 DOI: 10.1080/15384101.2020.1754586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
The spindle constitutes the cellular machinery that enables the segregation of the chromosomes during eukaryotic cell division. The microtubules that form this fascinating and complex genome distribution system emanate from specialized structures located at both its poles and known as microtubule-organizing centers (MTOCs). Beyond their structural function, the spindle MTOCs play fundamental roles in cell cycle control, the activation and functionality of the mitotic checkpoints and during cellular aging. This review highlights the pivotal importance of spindle-associated MTOCs in multiple cellular processes and their central role as key regulatory hubs where diverse intracellular signals are integrated and coordinated to ensure the successful completion of cell division and the maintenance of the replicative lifespan.
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Affiliation(s)
- Ana M Rincón
- Centro Andaluz de Biología Molecular Y Medicina Regenerativa (CABIMER) / CSIC - Universidad de Sevilla - Universidad Pablo de Olavide , Sevilla, Spain.,Dpto. de Genética / Universidad de Sevilla , Sevilla, Spain
| | - Fernando Monje-Casas
- Centro Andaluz de Biología Molecular Y Medicina Regenerativa (CABIMER) / CSIC - Universidad de Sevilla - Universidad Pablo de Olavide , Sevilla, Spain.,Consejo Superior de Investigaciones Científicas (CSIC) , Sevilla, Spain
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9
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James K, Olson PD. The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma. BMC Genomics 2020; 21:346. [PMID: 32380953 PMCID: PMC7204028 DOI: 10.1186/s12864-020-6710-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 03/30/2020] [Indexed: 12/14/2022] Open
Abstract
Background Reference genome and transcriptome assemblies of helminths have reached a level of completion whereby secondary analyses that rely on accurate gene estimation or syntenic relationships can be now conducted with a high level of confidence. Recent public release of the v.3 assembly of the mouse bile-duct tapeworm, Hymenolepis microstoma, provides chromosome-level characterisation of the genome and a stabilised set of protein coding gene models underpinned by bioinformatic and empirical data. However, interactome data have not been produced. Conserved protein-protein interactions in other organisms, termed interologs, can be used to transfer interactions between species, allowing systems-level analysis in non-model organisms. Results Here, we describe a probabilistic, integrated network of interologs for the H. microstoma proteome, based on conserved protein interactions found in eukaryote model species. Almost a third of the 10,139 gene models in the v.3 assembly could be assigned interaction data and assessment of the resulting network indicates that topologically-important proteins are related to essential cellular pathways, and that the network clusters into biologically meaningful components. Moreover, network parameters are similar to those of single-species interaction networks that we constructed in the same way for S. cerevisiae, C. elegans and H. sapiens, demonstrating that information-rich, system-level analyses can be conducted even on species separated by a large phylogenetic distance from the major model organisms from which most protein interaction evidence is based. Using the interolog network, we then focused on sub-networks of interactions assigned to discrete suites of genes of interest, including signalling components and transcription factors, germline multipotency genes, and genes differentially-expressed between larval and adult worms. Results show not only an expected bias toward highly-conserved proteins, such as components of intracellular signal transduction, but in some cases predicted interactions with transcription factors that aid in identifying their target genes. Conclusions With key helminth genomes now complete, systems-level analyses can provide an important predictive framework to guide basic and applied research on helminths and will become increasingly informative as new protein-protein interaction data accumulate.
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Affiliation(s)
- Katherine James
- Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne, UK. .,Department of Life Sciences, The Natural History Museum, Cromwell Road, London, UK.
| | - Peter D Olson
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, UK
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10
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Warren NJH, Eastman A. Comparison of the different mechanisms of cytotoxicity induced by checkpoint kinase I inhibitors when used as single agents or in combination with DNA damage. Oncogene 2020; 39:1389-1401. [PMID: 31659257 PMCID: PMC7023985 DOI: 10.1038/s41388-019-1079-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 12/31/2022]
Abstract
Inhibition of the DNA damage response is an emerging strategy to treat cancer. Understanding how DNA damage response inhibitors cause cytotoxicity in cancer cells is crucial to their further clinical development. This review focuses on three different mechanisms of cell killing by checkpoint kinase I inhibitors (CHK1i). DNA damage induced by chemotherapy drugs, such as topoisomerase I inhibitors, results in S and G2 phase arrest. Addition of CHK1i promotes cell cycle progression before repair is completed resulting in mitotic catastrophe. Ribonucleotide reductase inhibitors such as gemcitabine also arrest cells in S phase by preventing dNTP synthesis. Addition of CHK1i re-activates the DNA helicase to unwind DNA, but in the absence of dNTPs, this leads to excessive single-strand DNA that exceeds the protective capacity of the single-strand-binding protein RPA. Unprotected DNA is subjected to nuclease cleavage, resulting in replication catastrophe. CHK1i alone also kills a subset of cell lines through MRE11 and MUS81-mediated DNA cleavage in S phase cells. The choice of mechanism depends on the activation state of CDK2. Low level activation of CDK2 mediates helicase activation, cell cycle progression, and both replication and mitotic catastrophe. In contrast, high CDK2 activity is required for sensitivity to CHK1i as monotherapy. This high CDK2 activity threshold usually occurs late in the cell cycle to prepare for mitosis, but in CHK1i-sensitive cells, high activity can be attained in early S phase, resulting in DNA cleavage and cell death. This sensitivity to CHK1i has previously been associated with endogenous replication stress, but the dependence on high CDK2 activity, as well as MRE11, contradicts this hypothesis. The major unresolved question is why some cell lines fail to restrain their high CDK2 activity and hence succumb to CHK1i in S phase. Resolving this question will facilitate stratification of patients for treatment with CHK1i as monotherapy.
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Affiliation(s)
- Nicholas J H Warren
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756, USA
| | - Alan Eastman
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756, USA.
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756, USA.
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11
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Wasserman D, Nachum S, Cohen M, Enrico TP, Noach-Hirsh M, Parasol J, Zomer-Polak S, Auerbach N, Sheinberger-Chorni E, Nevenzal H, Levi-Dadon N, Wang X, Lahmi R, Michaely E, Gerber D, Emanuele MJ, Tzur A. Cell cycle oscillators underlying orderly proteolysis of E2F8. Mol Biol Cell 2020; 31:725-740. [PMID: 31995441 PMCID: PMC7185961 DOI: 10.1091/mbc.e19-12-0725] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
E2F8 is a transcriptional repressor that antagonizes E2F1 at the crossroads of the cell cycle, apoptosis, and cancer. Previously, we discovered that E2F8 is a direct target of the APC/C ubiquitin ligase. Nevertheless, it remains unknown how E2F8 is dynamically controlled throughout the entirety of the cell cycle. Here, using newly developed human cell-free systems that recapitulate distinct inter-mitotic and G1 phases and a continuous transition from prometaphase to G1, we reveal an interlocking dephosphorylation switch coordinating E2F8 degradation with mitotic exit and the activation of APC/CCdh1. Further, we uncover differential proteolysis rates for E2F8 at different points within G1 phase, accounting for its accumulation in late G1 while APC/CCdh1 is still active. Finally, we demonstrate that the F-box protein Cyclin F regulates E2F8 in G2-phase. Altogether, our data define E2F8 regulation throughout the cell cycle, illuminating an extensive coordination between phosphorylation, ubiquitination and transcription in mammalian cell cycle.
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Affiliation(s)
- Danit Wasserman
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Sapir Nachum
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Meital Cohen
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Taylor P Enrico
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Meirav Noach-Hirsh
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Jasmin Parasol
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Sarit Zomer-Polak
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Naomi Auerbach
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Evelin Sheinberger-Chorni
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Hadas Nevenzal
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Nofar Levi-Dadon
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Xianxi Wang
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Roxane Lahmi
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Efrat Michaely
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Doron Gerber
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Michael J Emanuele
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Amit Tzur
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
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12
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The Multiple Roles of the Cdc14 Phosphatase in Cell Cycle Control. Int J Mol Sci 2020; 21:ijms21030709. [PMID: 31973188 PMCID: PMC7038166 DOI: 10.3390/ijms21030709] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 12/20/2022] Open
Abstract
The Cdc14 phosphatase is a key regulator of mitosis in the budding yeast Saccharomyces cerevisiae. Cdc14 was initially described as playing an essential role in the control of cell cycle progression by promoting mitotic exit on the basis of its capacity to counteract the activity of the cyclin-dependent kinase Cdc28/Cdk1. A compiling body of evidence, however, has later demonstrated that this phosphatase plays other multiple roles in the regulation of mitosis at different cell cycle stages. Here, we summarize our current knowledge about the pivotal role of Cdc14 in cell cycle control, with a special focus in the most recently uncovered functions of the phosphatase.
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13
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Ramos F, Villoria MT, Alonso-Rodríguez E, Clemente-Blanco A. Role of protein phosphatases PP1, PP2A, PP4 and Cdc14 in the DNA damage response. Cell Stress 2019; 3:70-85. [PMID: 31225502 PMCID: PMC6551743 DOI: 10.15698/cst2019.03.178] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Maintenance of genome integrity is fundamental for cellular physiology. Our hereditary information encoded in the DNA is intrinsically susceptible to suffer variations, mostly due to the constant presence of endogenous and environmental genotoxic stresses. Genomic insults must be repaired to avoid loss or inappropriate transmission of the genetic information, a situation that could lead to the appearance of developmental anomalies and tumorigenesis. To safeguard our genome, cells have evolved a series of mechanisms collectively known as the DNA damage response (DDR). This surveillance system regulates multiple features of the cellular response, including the detection of the lesion, a transient cell cycle arrest and the restoration of the broken DNA molecule. While the role of multiple kinases in the DDR has been well documented over the last years, the intricate roles of protein dephosphorylation have only recently begun to be addressed. In this review, we have compiled recent information about the function of protein phosphatases PP1, PP2A, PP4 and Cdc14 in the DDR, focusing mainly on their capacity to regulate the DNA damage checkpoint and the repair mechanism encompassed in the restoration of a DNA lesion.
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Affiliation(s)
- Facundo Ramos
- Cell Cycle and Genome Stability Group. Institute of Functional Biology and Genomics (IBFG). Spanish National Research Council (CSIC), University of Salamanca (USAL), C/Zacarías González 2, Salamanca 37007, SPAIN
| | - María Teresa Villoria
- Cell Cycle and Genome Stability Group. Institute of Functional Biology and Genomics (IBFG). Spanish National Research Council (CSIC), University of Salamanca (USAL), C/Zacarías González 2, Salamanca 37007, SPAIN
| | - Esmeralda Alonso-Rodríguez
- Cell Cycle and Genome Stability Group. Institute of Functional Biology and Genomics (IBFG). Spanish National Research Council (CSIC), University of Salamanca (USAL), C/Zacarías González 2, Salamanca 37007, SPAIN
| | - Andrés Clemente-Blanco
- Cell Cycle and Genome Stability Group. Institute of Functional Biology and Genomics (IBFG). Spanish National Research Council (CSIC), University of Salamanca (USAL), C/Zacarías González 2, Salamanca 37007, SPAIN
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14
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Control of Eukaryotic DNA Replication Initiation-Mechanisms to Ensure Smooth Transitions. Genes (Basel) 2019; 10:genes10020099. [PMID: 30700044 PMCID: PMC6409694 DOI: 10.3390/genes10020099] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 01/25/2019] [Accepted: 01/25/2019] [Indexed: 02/06/2023] Open
Abstract
DNA replication differs from most other processes in biology in that any error will irreversibly change the nature of the cellular progeny. DNA replication initiation, therefore, is exquisitely controlled. Deregulation of this control can result in over-replication characterized by repeated initiation events at the same replication origin. Over-replication induces DNA damage and causes genomic instability. The principal mechanism counteracting over-replication in eukaryotes is a division of replication initiation into two steps—licensing and firing—which are temporally separated and occur at distinct cell cycle phases. Here, we review this temporal replication control with a specific focus on mechanisms ensuring the faultless transition between licensing and firing phases.
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15
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Ovejero S, Ayala P, Malumbres M, Pimentel-Muiños FX, Bueno A, Sacristán MP. Biochemical analyses reveal amino acid residues critical for cell cycle-dependent phosphorylation of human Cdc14A phosphatase by cyclin-dependent kinase 1. Sci Rep 2018; 8:11871. [PMID: 30089874 PMCID: PMC6082843 DOI: 10.1038/s41598-018-30253-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 07/24/2018] [Indexed: 12/20/2022] Open
Abstract
Cdc14 enzymes compose a family of highly conserved phosphatases that are present in a wide range of organisms, including yeast and humans, and that preferentially reverse the phosphorylation of Cyclin-Dependent Kinase (Cdk) substrates. The budding yeast Cdc14 orthologue has essential functions in the control of late mitosis and cytokinesis. In mammals, however, the two Cdc14 homologues, Cdc14A and Cdc14B, do not play a prominent role in controlling late mitotic events, suggesting that some Cdc14 functions are not conserved across species. Moreover, in yeast, Cdc14 is regulated by changes in its subcellular location and by phosphorylation events. In contrast, little is known about the regulation of human Cdc14 phosphatases. Here, we have studied how the human Cdc14A orthologue is regulated during the cell cycle. We found that Cdc14A is phosphorylated on Ser411, Ser453 and Ser549 by Cdk1 early in mitosis and becomes dephosphorylated during late mitotic stages. Interestingly, in vivo and in vitro experiments revealed that, unlike in yeast, Cdk1-mediated phosphorylation of human Cdc14A did not control its catalytic activity but likely modulated its interaction with other proteins in early mitosis. These findings point to differences in Cdk1-mediated mechanisms of regulation between human and yeast Cdc14 orthologues.
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Affiliation(s)
- Sara Ovejero
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC), Universidad de Salamanca-CSIC, Campus Miguel de Unamuno, 37007, Salamanca, Spain.,Institute of Human Genetics, CNRS, Université de Montpellier, Montpellier, France
| | - Patricia Ayala
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC), Universidad de Salamanca-CSIC, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Marcos Malumbres
- Centro Nacional de Investigaciones Oncológicas (CNIO), E-28029, Madrid, Spain
| | - Felipe X Pimentel-Muiños
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC), Universidad de Salamanca-CSIC, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Avelino Bueno
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC), Universidad de Salamanca-CSIC, Campus Miguel de Unamuno, 37007, Salamanca, Spain.,Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - María P Sacristán
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC), Universidad de Salamanca-CSIC, Campus Miguel de Unamuno, 37007, Salamanca, Spain. .,Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
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16
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Candida albicans Cdc15 is essential for mitotic exit and cytokinesis. Sci Rep 2018; 8:8899. [PMID: 29891974 PMCID: PMC5995815 DOI: 10.1038/s41598-018-27157-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/30/2018] [Indexed: 12/21/2022] Open
Abstract
Candida albicans displays a variety of morphological forms, and the ability to switch forms must be linked with cell cycle control. In budding yeast the Mitotic Exit Network (MEN) acts to drive mitotic exit and signal for cytokinesis and cell separation. However, previous reports on the MEN in C. albicans have raised questions on its role in this organism, with the components analysed to date demonstrating differing levels of importance in the processes of mitotic exit, cytokinesis and cell separation. This work focuses on the role of the Cdc15 kinase in C. albicans and demonstrates that, similar to Saccharomyces cerevisiae, it plays an essential role in signalling for mitotic exit and cytokinesis. Cells depleted of Cdc15 developed into elongated filaments, a common response to cell cycle arrest in C. albicans. These filaments emerged exclusively from large budded cells, contained two nuclear bodies and exhibited a hyper-extended spindle, all characteristic of these cells failing to exit mitosis. Furthermore these filaments displayed a clear cytokinesis defect, and CDC15 over-expression led to aberrant cell separation following hyphal morphogenesis. Together, these results are consistent with Cdc15 playing an essential role in signalling for mitotic exit, cytokinesis and cell separation in C. albicans.
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