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Gutierrez-Morton E, Haluska C, Collins L, Rizkallah R, Tomko RJ, Wang Y. The polySUMOylation axis promotes nucleolar release of Tof2 for mitotic exit. Cell Rep 2024; 43:114492. [PMID: 39002125 PMCID: PMC11298248 DOI: 10.1016/j.celrep.2024.114492] [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: 12/22/2023] [Revised: 05/02/2024] [Accepted: 06/26/2024] [Indexed: 07/15/2024] Open
Abstract
In budding yeast, the nucleolus serves as the site to sequester Cdc14, a phosphatase essential for mitotic exit. Nucleolar proteins Tof2, Net1, and Fob1 are required for this sequestration. Although it is known that these nucleolar proteins are SUMOylated, how SUMOylation regulates their activity remains unknown. Here, we show that Tof2 exhibits cell-cycle-regulated nucleolar delocalization and turnover. Depletion of the nuclear small ubiquitin-like modifier (SUMO) protease Ulp2 not only causes Tof2 polySUMOylation, nucleolar delocalization, and degradation but also leads to Cdc14 nucleolar release and activation. This outcome depends on polySUMOylation and the activity of downstream enzymes, including SUMO-targeted ubiquitin ligase and Cdc48/p97 segregase. We further developed a system to tether SUMO machinery to Tof2 and generated a SUMO-deficient tof2 mutant, and the results indicate that Tof2 polySUMOylation is necessary and sufficient for its nucleolar delocalization and degradation. Together, our work reveals a polySUMO-dependent mechanism that delocalizes Tof2 from the nucleolus to facilitate mitotic exit.
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Affiliation(s)
- Emily Gutierrez-Morton
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306, USA
| | - Cory Haluska
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Liam Collins
- College of Arts and Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Raed Rizkallah
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306, USA
| | - Robert J Tomko
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306, USA
| | - Yanchang Wang
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306, USA.
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2
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Iribarren PA, Di Marzio LA, Berazategui MA, Saura A, Coria L, Cassataro J, Rojas F, Navarro M, Alvarez VE. Depolymerization of SUMO chains induces slender to stumpy differentiation in T. brucei bloodstream parasites. PLoS Pathog 2024; 20:e1012166. [PMID: 38635823 PMCID: PMC11060531 DOI: 10.1371/journal.ppat.1012166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/30/2024] [Accepted: 04/01/2024] [Indexed: 04/20/2024] Open
Abstract
Trypanosoma brucei are protozoan parasites that cause sleeping sickness in humans and nagana in cattle. Inside the mammalian host, a quorum sensing-like mechanism coordinates its differentiation from a slender replicative form into a quiescent stumpy form, limiting growth and activating metabolic pathways that are beneficial to the parasite in the insect host. The post-translational modification of proteins with the Small Ubiquitin-like MOdifier (SUMO) enables dynamic regulation of cellular metabolism. SUMO can be conjugated to its targets as a monomer but can also form oligomeric chains. Here, we have investigated the role of SUMO chains in T. brucei by abolishing the ability of SUMO to polymerize. We have found that parasites able to conjugate only SUMO monomers are primed for differentiation. This was demonstrated for monomorphic lines that are normally unable to produce stumpy forms in response to quorum sensing signaling in mice, and also for pleomorphic cell lines in which stumpy cells were observed at unusually low parasitemia levels. SUMO chain mutants showed a stumpy compatible transcriptional profile and better competence to differentiate into procyclics. Our study indicates that SUMO depolymerization may represent a coordinated signal triggered during stumpy activation program.
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Affiliation(s)
- Paula Ana Iribarren
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo Ugalde”–IIBIO (UNSAM-CONICET), San Martin, Buenos Aires, Argentina
| | - Lucía Ayelén Di Marzio
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo Ugalde”–IIBIO (UNSAM-CONICET), San Martin, Buenos Aires, Argentina
| | - María Agustina Berazategui
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo Ugalde”–IIBIO (UNSAM-CONICET), San Martin, Buenos Aires, Argentina
| | - Andreu Saura
- Instituto de Parasitología y Biomedicina “López-Neyra”, CSIC (IPBLN-CSIC), Granada, Spain
| | - Lorena Coria
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo Ugalde”–IIBIO (UNSAM-CONICET), San Martin, Buenos Aires, Argentina
| | - Juliana Cassataro
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo Ugalde”–IIBIO (UNSAM-CONICET), San Martin, Buenos Aires, Argentina
| | - Federico Rojas
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom
| | - Miguel Navarro
- Instituto de Parasitología y Biomedicina “López-Neyra”, CSIC (IPBLN-CSIC), Granada, Spain
| | - Vanina Eder Alvarez
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo Ugalde”–IIBIO (UNSAM-CONICET), San Martin, Buenos Aires, Argentina
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Antoniuk-Majchrzak J, Enkhbaatar T, Długajczyk A, Kaminska J, Skoneczny M, Klionsky DJ, Skoneczna A. Stability of Rad51 recombinase and persistence of Rad51 DNA repair foci depends on post-translational modifiers, ubiquitin and SUMO. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119526. [PMID: 37364618 DOI: 10.1016/j.bbamcr.2023.119526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/02/2023] [Accepted: 06/19/2023] [Indexed: 06/28/2023]
Abstract
The DNA double-strand breaks are particularly deleterious, especially when an error-free repair pathway is unavailable, enforcing the error-prone recombination pathways to repair the lesion. Cells can resume the cell cycle but at the expense of decreased viability due to genome rearrangements. One of the major players involved in recombinational repair of DNA damage is Rad51 recombinase, a protein responsible for presynaptic complex formation. We previously showed that an increased level of this protein promotes the usage of illegitimate recombination. Here we show that the level of Rad51 is regulated via the ubiquitin-dependent proteolytic pathway. The ubiquitination of Rad51 depends on multiple E3 enzymes, including SUMO-targeted ubiquitin ligases. We also demonstrate that Rad51 can be modified by both ubiquitin and SUMO. Moreover, its modification with ubiquitin may lead to opposite effects: degradation dependent on Rad6, Rad18, Slx8, Dia2, and the anaphase-promoting complex, or stabilization dependent on Rsp5. We also show that post-translational modifications with SUMO and ubiquitin affect Rad51's ability to form and disassemble DNA repair foci, respectively, influencing cell cycle progression and cell viability in genotoxic stress conditions. Our data suggest the existence of a complex E3 ligases network that regulates Rad51 recombinase's turnover, its molecular activity, and access to DNA, limiting it to the proportions optimal for the actual cell cycle stage and growth conditions, e.g., stress. Dysregulation of this network would result in a drop in cell viability due to uncontrolled genome rearrangement in the yeast cells. In mammals would promote the development of genetic diseases and cancer.
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Affiliation(s)
| | - Tuguldur Enkhbaatar
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Anna Długajczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Joanna Kaminska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Marek Skoneczny
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Daniel J Klionsky
- Life Sciences Institute, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Adrianna Skoneczna
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland.
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4
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Tsirkas I, Zur T, Dovrat D, Cohen A, Ravkaie L, Aharoni A. Protein fluorescent labeling in live yeast cells using scFv-based probes. CELL REPORTS METHODS 2022; 2:100357. [PMID: 36590693 PMCID: PMC9795370 DOI: 10.1016/j.crmeth.2022.100357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/19/2022] [Accepted: 11/10/2022] [Indexed: 12/12/2022]
Abstract
The fusion of fluorescent proteins (FPs) to endogenous proteins is a widespread approach for microscopic examination of protein function, expression, and localization in the cell. However, proteins that are sensitive to FP fusion or expressed at low levels are difficult to monitor using this approach. Here, we develop a single-chain fragment variable (scFv)-FP approach to efficiently label Saccharomyces cerevisiae proteins that are tagged with repeats of hemagglutinin (HA)-tag sequences. We demonstrate the successful labeling of DNA-binding proteins and proteins localized to different cellular organelles including the nuclear membrane, peroxisome, Golgi apparatus, and mitochondria. This approach can lead to a significant increase in fluorescence intensity of the labeled protein, allows C'-terminal labeling of difficult-to-tag proteins and increased detection sensitivity of DNA-damage foci. Overall, the development of a scFv-FP labeling approach in yeast provides a general and simple tool for the function and localization analysis of the yeast proteome.
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Affiliation(s)
- Ioannis Tsirkas
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Tomer Zur
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Daniel Dovrat
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Amit Cohen
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Lior Ravkaie
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Amir Aharoni
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
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5
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Bonnet A, Chaput C, Palmic N, Palancade B, Lesage P. A nuclear pore sub-complex restricts the propagation of Ty retrotransposons by limiting their transcription. PLoS Genet 2021; 17:e1009889. [PMID: 34723966 PMCID: PMC8585004 DOI: 10.1371/journal.pgen.1009889] [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: 12/22/2020] [Revised: 11/11/2021] [Accepted: 10/18/2021] [Indexed: 11/19/2022] Open
Abstract
Beyond their canonical function in nucleocytoplasmic exchanges, nuclear pore complexes (NPCs) regulate the expression of protein-coding genes. Here, we have implemented transcriptomic and molecular methods to specifically address the impact of the NPC on retroelements, which are present in multiple copies in genomes. We report a novel function for the Nup84 complex, a core NPC building block, in specifically restricting the transcription of LTR-retrotransposons in yeast. Nup84 complex-dependent repression impacts both Copia and Gypsy Ty LTR-retrotransposons, all over the S. cerevisiae genome. Mechanistically, the Nup84 complex restricts the transcription of Ty1, the most active yeast retrotransposon, through the tethering of the SUMO-deconjugating enzyme Ulp1 to NPCs. Strikingly, the modest accumulation of Ty1 RNAs caused by Nup84 complex loss-of-function is sufficient to trigger an important increase of Ty1 cDNA levels, resulting in massive Ty1 retrotransposition. Altogether, our study expands our understanding of the complex interactions between retrotransposons and the NPC, and highlights the importance for the cells to keep retrotransposons under tight transcriptional control.
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Affiliation(s)
- Amandine Bonnet
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U944, CNRS UMR 7212, Paris, France
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Carole Chaput
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U944, CNRS UMR 7212, Paris, France
| | - Noé Palmic
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U944, CNRS UMR 7212, Paris, France
| | - Benoit Palancade
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Pascale Lesage
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U944, CNRS UMR 7212, Paris, France
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6
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Mercurio K, Singh D, Walden E, Baetz K. Global analysis of Saccharomyces cerevisiae growth in mucin. G3 (BETHESDA, MD.) 2021; 11:jkab294. [PMID: 34849793 PMCID: PMC8527512 DOI: 10.1093/g3journal/jkab294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/03/2021] [Indexed: 11/12/2022]
Abstract
Metagenomic profiling of the human gut microbiome has discovered DNA from dietary yeasts like Saccharomyces cerevisiae. However, it is unknown if the S. cerevisiae detected by common metagenomic methods are from dead dietary sources, or from live S. cerevisiae colonizing the gut similar to their close relative Candida albicans. While S. cerevisiae can adapt to minimal oxygen and acidic environments, it has not been explored whether this yeast can metabolize mucin, the large, gel-forming, highly glycosylated proteins representing a major source of carbon in the gut mucosa. We reveal that S. cerevisiae can utilize mucin as their main carbon source, as well as perform both a transcriptome analysis and a chemogenomic screen to identify biological pathways required for this yeast to grow optimally in mucin. In total, 739 genes demonstrate significant differential expression in mucin culture, and deletion of 21 genes impact growth in mucin. Both screens suggest that mitochondrial function is required for proper growth in mucin, and through secondary assays we determine that mucin exposure induces mitogenesis and cellular respiration. We further show that deletion of an uncharacterized ORF, YCR095W-A, led to dysfunction in mitochondrial morphology and oxygen consumption in mucin. Finally, we demonstrate that Yps7, an aspartyl protease and homolog to mucin-degrading proteins in C. albicans, is important for growth on mucin. Collectively, our work serves as the initial step toward establishing how this common dietary fungus can survive in the mucus environment of the human gut.
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Affiliation(s)
- Kevin Mercurio
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Dylan Singh
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Elizabeth Walden
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Kristin Baetz
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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7
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Yin R, Song J, Esquela-Kerscher A, Kerscher O. Detection of rapidly accumulating stress-induced SUMO in prostate cancer cells by a fluorescent SUMO biosensor. Mol Carcinog 2021; 60:886-897. [PMID: 34559929 DOI: 10.1002/mc.23353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 11/11/2022]
Abstract
SUMO conjugates and SUMO chains form when SUMO, a small ubiquitin-like modifier protein, is covalently linked to other cellular proteins or itself. During unperturbed growth, cells maintain balanced levels of SUMO conjugates. In contrast, eukaryotic cells that are exposed to proteotoxic and genotoxic insults mount a cytoprotective SUMO stress response (SSR). One hallmark of the SSR is a rapid and massive increase of SUMO conjugates in response to oxidative, thermal, and osmotic stress. Here, we use a recombinant fluorescent SUMO biosensor, KmUTAG-fl, to investigate differences in the SSR in a normal human prostate epithelial cell line immortalized with SV40 (PNT2) and two human prostate cancer cell lines that differ in aggressiveness and response to androgen (LNCaP and PC3). In cells that grow unperturbed, SUMO is enriched in the nuclei of all three cell lines. However, upon 30 min of exposure to ultraviolet radiation or oxidative stress, we detected significant cytosolic enrichment of SUMO as measured by KmUTAG-fl staining. This rapid enrichment in cytosolic SUMO levels was on average fivefold higher in the LNCaP and PC3 prostate cancer cell lines compared to normal immortalized PNT2 cells. Additionally, this enhanced enrichment of cytosolic SUMO was reversible as cells recovered from stress exposure. Our study validates the use of the fluorescent KmUTAG-fl SUMO biosensor to detect differences of SUMO levels and localization between normal and cancer cells and provides new evidence that cancer cells may exhibit an enhanced SSR.
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Affiliation(s)
- Rui Yin
- Department of Biology, University of Maryland College Park, College Park, Maryland, USA
| | | | - Aurora Esquela-Kerscher
- Department of Microbiology and Molecular Cell Biology, Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, Virginia, USA
| | - Oliver Kerscher
- Department of Biology, College of William & Mary, Williamsburg, Virginia, USA
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8
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Nucleolar release of rDNA repeats for repair involves SUMO-mediated untethering by the Cdc48/p97 segregase. Nat Commun 2021; 12:4918. [PMID: 34389719 PMCID: PMC8363623 DOI: 10.1038/s41467-021-25205-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 07/20/2021] [Indexed: 12/12/2022] Open
Abstract
Ribosomal RNA genes (rDNA) are highly unstable and susceptible to rearrangement due to their repetitive nature and active transcriptional status. Sequestration of rDNA in the nucleolus suppresses uncontrolled recombination. However, broken repeats must be first released to the nucleoplasm to allow repair by homologous recombination. Nucleolar release of broken rDNA repeats is conserved from yeast to humans, but the underlying molecular mechanisms are currently unknown. Here we show that DNA damage induces phosphorylation of the CLIP-cohibin complex, releasing membrane-tethered rDNA from the nucleolus in Saccharomyces cerevisiae. Downstream of phosphorylation, SUMOylation of CLIP-cohibin is recognized by Ufd1 via its SUMO-interacting motif, which targets the complex for disassembly through the Cdc48/p97 chaperone. Consistent with a conserved mechanism, UFD1L depletion in human cells impairs rDNA release. The dynamic and regulated assembly and disassembly of the rDNA-tethering complex is therefore a key determinant of nucleolar rDNA release and genome integrity.
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9
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Bhagwat NR, Owens SN, Ito M, Boinapalli JV, Poa P, Ditzel A, Kopparapu S, Mahalawat M, Davies OR, Collins SR, Johnson JR, Krogan NJ, Hunter N. SUMO is a pervasive regulator of meiosis. eLife 2021; 10:57720. [PMID: 33502312 PMCID: PMC7924959 DOI: 10.7554/elife.57720] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 01/26/2021] [Indexed: 02/06/2023] Open
Abstract
Protein modification by SUMO helps orchestrate the elaborate events of meiosis to faithfully produce haploid gametes. To date, only a handful of meiotic SUMO targets have been identified. Here, we delineate a multidimensional SUMO-modified meiotic proteome in budding yeast, identifying 2747 conjugation sites in 775 targets, and defining their relative levels and dynamics. Modified sites cluster in disordered regions and only a minority match consensus motifs. Target identities and modification dynamics imply that SUMOylation regulates all levels of chromosome organization and each step of meiotic prophase I. Execution-point analysis confirms these inferences, revealing functions for SUMO in S-phase, the initiation of recombination, chromosome synapsis and crossing over. K15-linked SUMO chains become prominent as chromosomes synapse and recombine, consistent with roles in these processes. SUMO also modifies ubiquitin, forming hybrid oligomers with potential to modulate ubiquitin signaling. We conclude that SUMO plays diverse and unanticipated roles in regulating meiotic chromosome metabolism. Most mammalian, yeast and other eukaryote cells have two sets of chromosomes, one from each parent, which contain all the cell’s DNA. Sex cells – like the sperm and egg – however, have half the number of chromosomes and are formed by a specialized type of cell division known as meiosis. At the start of meiosis, each cell replicates its chromosomes so that it has twice the amount of DNA. The cell then undergoes two rounds of division to form sex cells which each contain only one set of chromosomes. Before the cell divides, the two duplicated sets of chromosomes pair up and swap sections of their DNA. This exchange allows each new sex cell to have a unique combination of DNA, resulting in offspring that are genetically distinct from their parents. This complex series of events is tightly regulated, in part, by a protein called the 'small ubiquitin-like modifier' (or SUMO for short), which attaches itself to other proteins and modifies their behavior. This process, known as SUMOylation, can affect a protein’s stability, where it is located in the cell and how it interacts with other proteins. However, despite SUMO being known as a key regulator of meiosis, only a handful of its protein targets have been identified. To gain a better understanding of what SUMO does during meiosis, Bhagwat et al. set out to find which proteins are targeted by SUMO in budding yeast and to map the specific sites of modification. The experiments identified 2,747 different sites on 775 different proteins, suggesting that SUMO regulates all aspects of meiosis. Consistently, inactivating SUMOylation at different times revealed SUMO plays a role at every stage of meiosis, including the replication of DNA and the exchanges between chromosomes. In depth analysis of the targeted proteins also revealed that SUMOylation targets different groups of proteins at different stages of meiosis and interacts with other protein modifications, including the ubiquitin system which tags proteins for destruction. The data gathered by Bhagwat et al. provide a starting point for future research into precisely how SUMO proteins control meiosis in yeast and other organisms. In humans, errors in meiosis are the leading cause of pregnancy loss and congenital diseases. Most of the proteins identified as SUMO targets in budding yeast are also present in humans. So, this research could provide a platform for medical advances in the future. The next step is to study mammalian models, such as mice, to confirm that the regulation of meiosis by SUMO is the same in mammals as in yeast.
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Affiliation(s)
- Nikhil R Bhagwat
- Howard Hughes Medical Institute, University of California Davis, Davis, United States.,Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Shannon N Owens
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Masaru Ito
- Howard Hughes Medical Institute, University of California Davis, Davis, United States.,Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Jay V Boinapalli
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Philip Poa
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Alexander Ditzel
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Srujan Kopparapu
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Meghan Mahalawat
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Owen Richard Davies
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, United Kingdom
| | - Sean R Collins
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Jeffrey R Johnson
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, United States
| | - Nevan J Krogan
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, United States
| | - Neil Hunter
- Howard Hughes Medical Institute, University of California Davis, Davis, United States.,Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States.,Department of Molecular & Cellular Biology, University of California Davis, Davis, United States
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10
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Ryu HY, Zhao D, Li J, Su D, Hochstrasser M. Histone sumoylation promotes Set3 histone-deacetylase complex-mediated transcriptional regulation. Nucleic Acids Res 2020; 48:12151-12168. [PMID: 33231641 PMCID: PMC7708062 DOI: 10.1093/nar/gkaa1093] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 10/12/2020] [Accepted: 10/27/2020] [Indexed: 12/02/2022] Open
Abstract
Histones are substrates of the SUMO (small ubiquitin-like modifier) conjugation pathway. Several reports suggest histone sumoylation affects transcription negatively, but paradoxically, our genome-wide analysis shows the modification concentrated at many active genes. We find that trans-tail regulation of histone-H2B ubiquitylation and H3K4 di-methylation potentiates subsequent histone sumoylation. Consistent with the known control of the Set3 histone deacetylase complex (HDAC) by H3K4 di-methylation, histone sumoylation directly recruits the Set3 complex to both protein-coding and noncoding RNA (ncRNA) genes via a SUMO-interacting motif in the HDAC Cpr1 subunit. The altered gene expression profile caused by reducing histone sumoylation matches well to the profile in cells lacking Set3. Histone H2B sumoylation and the Set3 HDAC coordinately suppress cryptic ncRNA transcription initiation internal to mRNA genes. Our results reveal an elaborate co-transcriptional histone crosstalk pathway involving the consecutive ubiquitylation, methylation, sumoylation and deacetylation of histones, which maintains transcriptional fidelity by suppressing spurious transcription.
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Affiliation(s)
- Hong-Yeoul Ryu
- Correspondence may also be addressed to Hong-Yeoul Ryu. Tel: +82 53 950 6352;
| | - Dejian Zhao
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06520, USA
| | - Jianhui Li
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Dan Su
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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11
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Jansen NS, Vertegaal ACO. A Chain of Events: Regulating Target Proteins by SUMO Polymers. Trends Biochem Sci 2020; 46:113-123. [PMID: 33008689 DOI: 10.1016/j.tibs.2020.09.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/21/2020] [Accepted: 09/04/2020] [Indexed: 02/07/2023]
Abstract
Small ubiquitin-like modifiers (SUMOs) regulate virtually all nuclear processes. The fate of the target protein is determined by the architecture of the attached SUMO protein, which can be of polymeric nature. Here, we highlight the multifunctional aspects of dynamic signal transduction by SUMO polymers. The SUMO-targeted ubiquitin ligases (STUbLs) RING-finger protein 4 (RNF4) and RNF111 recognize SUMO polymers in a chain-architecture-dependent manner, leading to the formation of hybrid chains, which could enable proteasomal destruction of proteins. Recent publications have highlighted essential roles for SUMO chain disassembly by the mammalian SUMO proteases SENP6 and SENP7 and the yeast SUMO protease Ulp2. SENP6 is particularly important for centromere assembly. These recent findings demonstrate the diversity of SUMO polymer signal transduction for proteolytic and nonproteolytic purposes.
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Affiliation(s)
- Nicolette S Jansen
- Department of Cell and Chemical Biology, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands.
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12
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Chen X, Yi J, Song W, Liu J, Luo Q, Liu L. Chassis engineering of Escherichia coli for trans-4-hydroxy-l-proline production. Microb Biotechnol 2020; 14:392-402. [PMID: 32396278 PMCID: PMC7936311 DOI: 10.1111/1751-7915.13573] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/16/2020] [Accepted: 03/23/2020] [Indexed: 02/06/2023] Open
Abstract
Microbial production of trans-4-hydroxy-l-proline (Hyp) offers significant advantages over conventional chemical extraction. However, it is still challenging for industrial production of Hyp due to its low production efficiency. Here, chassis engineering was used for tailoring Escherichia coli cellular metabolism to enhance enzymatic production of Hyp. Specifically, four proline 4-hydroxylases (P4H) were selected to convert l-proline to Hyp, and the recombinant strain overexpressing DsP4H produced 32.5 g l-1 Hyp with α-ketoglutarate addition. To produce Hyp without α-ketoglutarate addition, α-ketoglutarate supply was enhanced by rewiring the TCA cycle and l-proline degradation pathway, and oxygen transfer was improved by fine-tuning heterologous haemoglobin expression. In a 5-l fermenter, the engineered strain E. coliΔsucCDΔputA-VHb(L) -DsP4H showed a significant increase in Hyp titre, conversion rate and productivity up to 49.8 g l-1 , 87.4% and 1.38 g l-1 h-1 respectively. This strategy described here provides an efficient method for production of Hyp, and it has a great potential in industrial application.
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Affiliation(s)
- Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China
| | - Juyang Yi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Shaoxing Baiyin Biotechnology Co. Ltd, Shaoxing, 312000, China
| | - Wei Song
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China
| | - Qiuling Luo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China
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13
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Muellner J, Schmidt KH. Yeast Genome Maintenance by the Multifunctional PIF1 DNA Helicase Family. Genes (Basel) 2020; 11:genes11020224. [PMID: 32093266 PMCID: PMC7073672 DOI: 10.3390/genes11020224] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 12/04/2022] Open
Abstract
The two PIF1 family helicases in Saccharomyces cerevisiae, Rrm3, and ScPif1, associate with thousands of sites throughout the genome where they perform overlapping and distinct roles in telomere length maintenance, replication through non-histone proteins and G4 structures, lagging strand replication, replication fork convergence, the repair of DNA double-strand break ends, and transposable element mobility. ScPif1 and its fission yeast homolog Pfh1 also localize to mitochondria where they protect mitochondrial genome integrity. In addition to yeast serving as a model system for the rapid functional evaluation of human Pif1 variants, yeast cells lacking Rrm3 have proven useful for elucidating the cellular response to replication fork pausing at endogenous sites. Here, we review the increasingly important cellular functions of the yeast PIF1 helicases in maintaining genome integrity, and highlight recent advances in our understanding of their roles in facilitating fork progression through replisome barriers, their functional interactions with DNA repair, and replication stress response pathways.
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Affiliation(s)
- Julius Muellner
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA;
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Kristina H. Schmidt
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA;
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
- Correspondence:
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14
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Recruitment of the Ulp2 protease to the inner kinetochore prevents its hyper-sumoylation to ensure accurate chromosome segregation. PLoS Genet 2019; 15:e1008477. [PMID: 31747400 PMCID: PMC6892545 DOI: 10.1371/journal.pgen.1008477] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 12/04/2019] [Accepted: 10/14/2019] [Indexed: 01/15/2023] Open
Abstract
The kinetochore is the central molecular machine that drives chromosome segregation in all eukaryotes. Genetic studies have suggested that protein sumoylation plays a role in regulating the inner kinetochore; however, the mechanism remains elusive. Here, we show that Saccharomyces cerevisiae Ulp2, an evolutionarily conserved SUMO specific protease, contains a previously uncharacterized kinetochore-targeting motif that recruits Ulp2 to the kinetochore via the Ctf3CENP-I-Mcm16CENP-H-Mcm22CENP-K complex (CMM). Once recruited, Ulp2 selectively targets multiple subunits of the kinetochore, specifically the Constitutive Centromere-Associated Network (CCAN), via its SUMO-interacting motif (SIM). Mutations that impair the kinetochore recruitment of Ulp2 or its binding to SUMO result in an elevated rate of chromosome loss, while mutations that affect both result in a synergistic increase of chromosome loss rate, hyper-sensitivity to DNA replication stress, along with a dramatic accumulation of hyper-sumoylated CCAN. Notably, sumoylation of CCAN occurs at the kinetochore and is perturbed by DNA replication stress. These results indicate that Ulp2 utilizes its dual substrate recognition to prevent hyper-sumoylation of CCAN, ensuring accurate chromosome segregation during cell division.
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15
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Peng Y, Wang Z, Wang Z, Yu F, Li J, Wong J. SUMOylation down-regulates rDNA transcription by repressing expression of upstream-binding factor and proto-oncogene c-Myc. J Biol Chem 2019; 294:19155-19166. [PMID: 31694914 DOI: 10.1074/jbc.ra119.010624] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/29/2019] [Indexed: 11/06/2022] Open
Abstract
Ribosome biogenesis is critical for proliferating cells and requires the coordinated activities of three eukaryotic RNA polymerases. We recently showed that the small ubiquitin-like modifier (SUMO) system controls the global level of RNA polymerase II (Pol II)-controlled transcription in mammalian cells by regulating cyclin-dependent kinase 9 activity. Here, we present evidence that the SUMO system also plays a critical role in the control of Pol I transcription. Using an siRNA-based knockdown approach, we found that multiple SUMO E3 ligases of the PIAS (protein inhibitor of activated STAT) family are involved in SUMO-mediated repression of ribosomal DNA (rDNA) gene transcription. We demonstrate that endogenous SUMO represses rDNA transcription primarily by repressing upstream-binding factor and proto-oncogene c-Myc expression and that ectopic overexpression of SUMO-associated enzymes additionally represses rDNA transcription via c-Myc SUMOylation and its subsequent degradation. The results of our study reveal a critical role of SUMOylation in the control of rDNA transcription, uncover the underlying mechanisms involved, and indicate that the SUMO system coordinates Pol I- and Pol II-mediated transcription in mammalian cells.
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Affiliation(s)
- Yu Peng
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-East China Normal University Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Zhenxing Wang
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-East China Normal University Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Zhiqiang Wang
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-East China Normal University Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Fang Yu
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-East China Normal University Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.,Department of Medicine, University of Florida, Gainesville, Florida 32610
| | - Jiwen Li
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-East China Normal University Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-East China Normal University Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China .,State Key Laboratory of Oncogene and Related Genes, Shanghai Cancer Institute and Shanghai Jiao Tong University, Shanghai 200240, China
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16
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Kumar R, Sabapathy K. RNF4—A Paradigm for SUMOylation‐Mediated Ubiquitination. Proteomics 2019; 19:e1900185. [DOI: 10.1002/pmic.201900185] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/13/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Ramesh Kumar
- Cancer & Stem Cell Biology Program Duke–NUS Medical School 8 College Road Singapore 169857 Singapore
| | - Kanaga Sabapathy
- Cancer & Stem Cell Biology Program Duke–NUS Medical School 8 College Road Singapore 169857 Singapore
- Laboratory of Molecular Carcinogenesis Division of Cellular & Molecular Research Humphrey Oei Institute of Cancer Research National Cancer Centre Singapore 11 Hospital Drive Singapore 169610 Singapore
- Department of Biochemistry National University of Singapore 8 Medical Drive Singapore 117597 Singapore
- Institute of Molecular and Cellular Biology 61 Biopolis Drive Singapore 138673 Singapore
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17
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Psakhye I, Castellucci F, Branzei D. SUMO-Chain-Regulated Proteasomal Degradation Timing Exemplified in DNA Replication Initiation. Mol Cell 2019; 76:632-645.e6. [PMID: 31519521 PMCID: PMC6891891 DOI: 10.1016/j.molcel.2019.08.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 07/01/2019] [Accepted: 08/01/2019] [Indexed: 11/18/2022]
Abstract
Similar to ubiquitin, SUMO forms chains, but the identity of SUMO-chain-modified factors and the purpose of this modification remain largely unknown. Here, we identify the budding yeast SUMO protease Ulp2, able to disassemble SUMO chains, as a DDK interactor enriched at replication origins that promotes DNA replication initiation. Replication-engaged DDK is SUMOylated on chromatin, becoming a degradation-prone substrate when Ulp2 no longer protects it against SUMO chain assembly. Specifically, SUMO chains channel DDK for SUMO-targeted ubiquitin ligase Slx5/Slx8-mediated and Cdc48 segregase-assisted proteasomal degradation. Importantly, the SUMOylation-defective ddk-KR mutant rescues inefficient replication onset and MCM activation in cells lacking Ulp2, suggesting that SUMO chains time DDK degradation. Using two unbiased proteomic approaches, we further identify subunits of the MCM helicase and other factors as SUMO-chain-modified degradation-prone substrates of Ulp2 and Slx5/Slx8. We thus propose SUMO-chain/Ulp2-protease-regulated proteasomal degradation as a mechanism that times the availability of functionally engaged SUMO-modified protein pools during replication and beyond.
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Affiliation(s)
- Ivan Psakhye
- IFOM, FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | | | - Dana Branzei
- IFOM, FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy; Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, 27100 Pavia, Italy.
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18
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Chhunchha B, Singh P, Singh DP, Kubo E. Ginkgolic Acid Rescues Lens Epithelial Cells from Injury Caused by Redox Regulated-Aberrant Sumoylation Signaling by Reviving Prdx6 and Sp1 Expression and Activities. Int J Mol Sci 2018; 19:E3520. [PMID: 30413111 PMCID: PMC6274983 DOI: 10.3390/ijms19113520] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/04/2018] [Accepted: 11/06/2018] [Indexed: 12/11/2022] Open
Abstract
Sumoylation is a downstream effector of aging/oxidative stress; excess oxidative stress leads to dysregulation of a specificity protein1 (Sp1) and its target genes, such as Peroxiredoxin 6 (Prdx6), resulting in cellular damage. To cope with oxidative stress, cells rely on a signaling pathway involving redox-sensitive genes. Herein, we examined the therapeutic efficacy of the small molecule Ginkgolic acid (GA), a Sumoylation antagonist, to disrupt aberrant Sumoylation signaling in human and mouse lens epithelial cells (LECs) facing oxidative stress or aberrantly expressing Sumo1 (small ubiquitin-like modifier). We found that GA globally reduced aberrant Sumoylation of proteins. In contrast, Betulinic acid (BA), a Sumoylation agonist, augmented the process. GA increased Sp1 and Prdx6 expression by disrupting the Sumoylation signaling, while BA repressed the expression of both molecules. In vitro DNA binding, transactivation, Sumoylation and expression assays revealed that GA enhanced Sp1 binding to GC-boxes in the Prdx6 promoter and upregulated its transcription. Cell viability and intracellular redox status assays showed that LECs pretreated with GA gained resistance against oxidative stress-driven aberrant Sumoylation signaling. Overall, our study revealed an unprecedented role for GA in LECs and provided new mechanistic insights into the use of GA in rescuing LECs from aging/oxidative stress-evoked dysregulation of Sp1/Prdx6 protective molecules.
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Affiliation(s)
- Bhavana Chhunchha
- Department of Ophthalmology and Visual Science, University of Nebraska Medical Center, Omaha, NE 68198, USA.
| | - Prerna Singh
- Department of Ophthalmology and Visual Science, University of Nebraska Medical Center, Omaha, NE 68198, USA.
| | - Dhirendra P Singh
- Department of Ophthalmology and Visual Science, University of Nebraska Medical Center, Omaha, NE 68198, USA.
| | - Eri Kubo
- Department of Ophthalmology, Kanazawa Medical University, Ishikawa 9200293, Japan.
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19
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Iribarren PA, Di Marzio LA, Berazategui MA, De Gaudenzi JG, Alvarez VE. SUMO polymeric chains are involved in nuclear foci formation and chromatin organization in Trypanosoma brucei procyclic forms. PLoS One 2018; 13:e0193528. [PMID: 29474435 PMCID: PMC5825156 DOI: 10.1371/journal.pone.0193528] [Citation(s) in RCA: 8] [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: 10/27/2017] [Accepted: 02/13/2018] [Indexed: 01/10/2023] Open
Abstract
SUMOylation is a post-translational modification conserved in eukaryotic organisms that involves the covalent attachment of the small ubiquitin-like protein SUMO to internal lysine residues in target proteins. This tag usually alters the interaction surface of the modified protein and can be translated into changes in its biological activity, stability or subcellular localization, among other possible outputs. SUMO can be attached as a single moiety or as SUMO polymers in case there are internal acceptor sites in SUMO itself. These chains have been shown to be important for proteasomal degradation as well as for the formation of subnuclear structures such as the synaptonemal complex in Saccharomyces cerevisiae or promyelocytic leukemia nuclear bodies in mammals. In this work, we have examined SUMO chain formation in the protozoan parasite Trypanosoma brucei. Using a recently developed bacterial strain engineered to produce SUMOylated proteins we confirmed the ability of TbSUMO to form polymers and determined the type of linkage using site-directed mutational analysis. By generating transgenic procyclic parasites unable to form chains we demonstrated that although not essential for normal growth, SUMO polymerization determines the localization of the modified proteins in the nucleus. In addition, FISH analysis of telomeres showed a differential positioning depending on the polySUMOylation abilities of the cells. Thus, our observations suggest that TbSUMO chains might play a role in establishing interaction platforms contributing to chromatin organization.
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Affiliation(s)
- Paula Ana Iribarren
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde—Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Campus Miguelete, Av. 25 de Mayo y Francia, San Martín, Buenos Aires, Argentina
| | - Lucía Ayelén Di Marzio
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde—Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Campus Miguelete, Av. 25 de Mayo y Francia, San Martín, Buenos Aires, Argentina
| | - María Agustina Berazategui
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde—Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Campus Miguelete, Av. 25 de Mayo y Francia, San Martín, Buenos Aires, Argentina
| | - Javier Gerardo De Gaudenzi
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde—Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Campus Miguelete, Av. 25 de Mayo y Francia, San Martín, Buenos Aires, Argentina
- * E-mail: (VEA); (JGDG)
| | - Vanina Eder Alvarez
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde—Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Campus Miguelete, Av. 25 de Mayo y Francia, San Martín, Buenos Aires, Argentina
- * E-mail: (VEA); (JGDG)
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20
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Peek J, Harvey C, Gray D, Rosenberg D, Kolla L, Levy-Myers R, Yin R, McMurry JL, Kerscher O. SUMO targeting of a stress-tolerant Ulp1 SUMO protease. PLoS One 2018; 13:e0191391. [PMID: 29351565 PMCID: PMC5774762 DOI: 10.1371/journal.pone.0191391] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 01/04/2018] [Indexed: 11/18/2022] Open
Abstract
SUMO proteases of the SENP/Ulp family are master regulators of both sumoylation and desumoylation and regulate SUMO homeostasis in eukaryotic cells. SUMO conjugates rapidly increase in response to cellular stress, including nutrient starvation, hypoxia, osmotic stress, DNA damage, heat shock, and other proteotoxic stressors. Nevertheless, little is known about the regulation and targeting of SUMO proteases during stress. To this end we have undertaken a detailed comparison of the SUMO-binding activity of the budding yeast protein Ulp1 (ScUlp1) and its ortholog in the thermotolerant yeast Kluyveromyces marxianus, KmUlp1. We find that the catalytic UD domains of both ScUlp1 and KmUlp1 show a high degree of sequence conservation, complement a ulp1Δ mutant in vivo, and process a SUMO precursor in vitro. Next, to compare the SUMO-trapping features of both SUMO proteases we produced catalytically inactive recombinant fragments of the UD domains of ScUlp1 and KmUlp1, termed ScUTAG and KmUTAG respectively. Both ScUTAG and KmUTAG were able to efficiently bind a variety of purified SUMO isoforms and bound immobilized SUMO1 with nanomolar affinity. However, KmUTAG showed a greatly enhanced ability to bind SUMO and SUMO-modified proteins in the presence of oxidative, temperature and other stressors that induce protein misfolding. We also investigated whether a SUMO-interacting motif (SIM) in the UD domain of KmULP1 that is not conserved in ScUlp1 may contribute to the SUMO-binding properties of KmUTAG. In summary, our data reveal important details about how SUMO proteases target and bind their sumoylated substrates, especially under stress conditions. We also show that the robust pan-SUMO binding features of KmUTAG can be exploited to detect and study SUMO-modified proteins in cell culture systems.
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Affiliation(s)
- Jennifer Peek
- Biology Department, The College of William & Mary, Williamsburg, Virginia, United States of America
| | - Catherine Harvey
- Biology Department, The College of William & Mary, Williamsburg, Virginia, United States of America
| | - Dreux Gray
- Biology Department, The College of William & Mary, Williamsburg, Virginia, United States of America
| | - Danny Rosenberg
- Biology Department, The College of William & Mary, Williamsburg, Virginia, United States of America
| | - Likhitha Kolla
- Biology Department, The College of William & Mary, Williamsburg, Virginia, United States of America
| | - Reuben Levy-Myers
- Biology Department, The College of William & Mary, Williamsburg, Virginia, United States of America
| | - Rui Yin
- Biology Department, The College of William & Mary, Williamsburg, Virginia, United States of America
| | - Jonathan L. McMurry
- Department of Molecular & Cellular Biology, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Oliver Kerscher
- Biology Department, The College of William & Mary, Williamsburg, Virginia, United States of America
- * E-mail:
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21
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Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Salas REC, Swedlow JR. The Image Data Resource: A Bioimage Data Integration and Publication Platform. Nat Methods 2017; 14:775-781. [PMID: 28775673 PMCID: PMC5536224 DOI: 10.1038/nmeth.4326] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This Resource describes the Image Data Resource (IDR), a prototype online system for biological image data that links experimental and analytic data across multiple data sets and promotes image data sharing and reanalysis. Access to primary research data is vital for the advancement of science. To extend the data types supported by community repositories, we built a prototype Image Data Resource (IDR). IDR links data from several imaging modalities, including high-content screening, multi-dimensional microscopy and digital pathology, with public genetic or chemical databases and cell and tissue phenotypes expressed using controlled ontologies. Using this integration, IDR facilitates the analysis of gene networks and reveals functional interactions that are inaccessible to individual studies. To enable reanalysis, we also established a computational resource based on Jupyter notebooks that allows remote access to the entire IDR. IDR is also an open-source platform for publishing imaging data. Thus IDR provides an online resource and a software infrastructure that promotes and extends publication and reanalysis of scientific image data.
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Affiliation(s)
- Eleanor Williams
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Josh Moore
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - Simon W Li
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - Gabriella Rustici
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - Aleksandra Tarkowska
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - Anatole Chessel
- Pharmacology & Genetics Departments and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.,LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay, Palaiseau, France
| | - Simone Leo
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK.,Center for Advanced Studies, Research, and Development in Sardinia (CRS4), Pula(CA), Italy
| | - Bálint Antal
- Pharmacology & Genetics Departments and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Richard K Ferguson
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - Ugis Sarkans
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Rafael E Carazo Salas
- Pharmacology & Genetics Departments and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.,School of Cell and Molecular Medicine, University of Bristol, Bristol, UK
| | - Jason R Swedlow
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK
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22
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A Lysine Desert Protects a Novel Domain in the Slx5-Slx8 SUMO Targeted Ub Ligase To Maintain Sumoylation Levels in Saccharomyces cerevisiae. Genetics 2017; 206:1807-1821. [PMID: 28550017 DOI: 10.1534/genetics.117.202697] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 05/23/2017] [Indexed: 01/23/2023] Open
Abstract
Protein modification by the small ubiquitin-like modifier (SUMO) plays important roles in genome maintenance. In Saccharomyces cerevisiae, proper regulation of sumoylation is known to be essential for viability in certain DNA repair mutants. Here, we find the opposite result; proper regulation of sumoylation is lethal in certain DNA repair mutants. Yeast cells lacking the repair factors TDP1 and WSS1 are synthetically lethal due to their redundant roles in removing Top1-DNA covalent complexes (Top1ccs). A screen for suppressors of tdp1∆ wss1∆ synthetic lethality isolated mutations in genes known to control global sumoylation levels including ULP1, ULP2, SIZ2, and SLX5 The results suggest that alternative pathways of repair become available when sumoylation levels are altered. Curiously, both suppressor mutations that were isolated in the Slx5 subunit of the SUMO-targeted Ub ligase created new lysine residues. These "slx5-K" mutations localize to a 398 amino acid domain that is completely free of lysine, and they result in the auto-ubiquitination and partial proteolysis of Slx5. The decrease in Slx5-K protein leads to the accumulation of high molecular weight SUMO conjugates, and the residual Ub ligase activity is needed to suppress inviability presumably by targeting polysumoylated Top1ccs. This "lysine desert" is found in the subset of large fungal Slx5 proteins, but not its smaller orthologs such as RNF4. The lysine desert solves a problem that Ub ligases encounter when evolving novel functional domains.
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23
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Nie M, Moser BA, Nakamura TM, Boddy MN. SUMO-targeted ubiquitin ligase activity can either suppress or promote genome instability, depending on the nature of the DNA lesion. PLoS Genet 2017; 13:e1006776. [PMID: 28475613 PMCID: PMC5438191 DOI: 10.1371/journal.pgen.1006776] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 05/19/2017] [Accepted: 04/24/2017] [Indexed: 11/19/2022] Open
Abstract
The posttranslational modifiers SUMO and ubiquitin critically regulate the DNA damage response (DDR). Important crosstalk between these modifiers at DNA lesions is mediated by the SUMO-targeted ubiquitin ligase (STUbL), which ubiquitinates SUMO chains to generate SUMO-ubiquitin hybrids. These SUMO-ubiquitin hybrids attract DDR proteins able to bind both modifiers, and/or are degraded at the proteasome. Despite these insights, specific roles for SUMO chains and STUbL in the DDR remain poorly defined. Notably, fission yeast defective in SUMO chain formation exhibit near wild-type resistance to genotoxins and moreover, have a greatly reduced dependency on STUbL activity for DNA repair. Based on these and other data, we propose that a critical role of STUbL is to antagonize DDR-inhibitory SUMO chain formation at DNA lesions. In this regard, we identify a SUMO-binding Swi2/Snf2 translocase called Rrp2 (ScUls1) as a mediator of the DDR defects in STUbL mutant cells. Therefore, in support of our proposal, SUMO chains attract activities that can antagonize STUbL and other DNA repair factors. Finally, we find that Taz1TRF1/TRF2-deficiency triggers extensive telomeric poly-SUMOylation. In this setting STUbL, together with its cofactor Cdc48p97, actually promotes genomic instability caused by the aberrant processing of taz1Δ telomeres by DNA repair factors. In summary, depending on the nature of the initiating DNA lesion, STUbL activity can either be beneficial or harmful. Since its discovery in 2007, SUMO-targeted ubiquitin ligase (STUbL) activity has been identified as a key regulator of diverse cellular processes such as DNA repair, mitosis and DNA replication. In each of these processes, STUbL has been shown to promote the chromatin extraction and/or degradation of SUMO chain modified proteins. However, it remains unclear whether STUbL acts as part of a "programmed" cascade to remove specific proteins, or antagonizes localized SUMO chain formation that otherwise impedes each process. Here we determine that SUMO chains, the major recruitment signal for STUbL, are largely dispensable for genotoxin resistance in fission yeast. Moreover, when SUMO chain formation is compromised, the need for STUbL activity in DNA repair is strongly reduced. These results indicate a primary role for STUbL in antagonizing localized SUMO chain formation. Interestingly, we also find that STUbL activity can be toxic at certain genomic lesions that induce extensive local SUMOylation. For example, STUbL promotes the chromosome instability and cell death caused by deprotected telomeres following Taz1TRF1/2 deletion. Together, our data suggest that STUbL limits DNA repair-inhibitory SUMO chain formation, and depending on the nature of the genomic lesion, can either suppress or cause genome instability.
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Affiliation(s)
- Minghua Nie
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States of America
| | - Bettina A. Moser
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Toru M. Nakamura
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Michael N. Boddy
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States of America
- * E-mail:
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24
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Doiron K, Goyon V, Coyaud E, Rajapakse S, Raught B, McBride HM. The dynamic interacting landscape of MAPL reveals essential functions for SUMOylation in innate immunity. Sci Rep 2017; 7:107. [PMID: 28273895 PMCID: PMC5427825 DOI: 10.1038/s41598-017-00151-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 02/13/2017] [Indexed: 01/05/2023] Open
Abstract
Activation of the innate immune response triggered by dsRNA viruses occurs through the assembly of the Mitochondrial Anti-Viral Signaling (MAVS) complex. Upon recognition of viral dsRNA, the cytosolic receptor RIG-I is activated and recruited to MAVS to activate the immune signaling response. We here demonstrate a strict requirement for a mitochondrial anchored protein ligase, MAPL (also called MUL1) in the signaling events that drive the transcriptional activation of antiviral genes downstream of Sendai virus infection, both in vivo and in vitro. A biotin environment scan of MAPL interacting polypeptides identified a series of proteins specific to Sendai virus infection; including RIG-I, IFIT1, IFIT2, HERC5 and others. Upon infection, RIG-I is SUMOylated in a MAPL-dependent manner, a conjugation step that is required for its activation. Consistent with this, MAPL was not required for signaling downstream of a constitutively activated form of RIG-I. These data highlight a critical role for MAPL and mitochondrial SUMOylation in the early steps of antiviral signaling.
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Affiliation(s)
- Karine Doiron
- Montreal Neurological Institute, McGill University, 3801 University Ave, Montreal, Quebec, H3A 2B4, Canada
| | - Vanessa Goyon
- Montreal Neurological Institute, McGill University, 3801 University Ave, Montreal, Quebec, H3A 2B4, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, 101 College St., Toronto, ON M5G 1L7, Canada
| | - Sanjeeva Rajapakse
- Montreal Neurological Institute, McGill University, 3801 University Ave, Montreal, Quebec, H3A 2B4, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, 101 College St., Toronto, ON M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Heidi M McBride
- Montreal Neurological Institute, McGill University, 3801 University Ave, Montreal, Quebec, H3A 2B4, Canada.
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25
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Pichler A, Fatouros C, Lee H, Eisenhardt N. SUMO conjugation - a mechanistic view. Biomol Concepts 2017; 8:13-36. [PMID: 28284030 DOI: 10.1515/bmc-2016-0030] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 02/06/2017] [Indexed: 02/08/2023] Open
Abstract
The regulation of protein fate by modification with the small ubiquitin-related modifier (SUMO) plays an essential and crucial role in most cellular pathways. Sumoylation is highly dynamic due to the opposing activities of SUMO conjugation and SUMO deconjugation. SUMO conjugation is performed by the hierarchical action of E1, E2 and E3 enzymes, while its deconjugation involves SUMO-specific proteases. In this review, we summarize and compare the mechanistic principles of how SUMO gets conjugated to its substrate. We focus on the interplay of the E1, E2 and E3 enzymes and discuss how specificity could be achieved given the limited number of conjugating enzymes and the thousands of substrates.
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Affiliation(s)
- Andrea Pichler
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, D-79108 Freiburg, Germany
| | - Chronis Fatouros
- Max Planck Institute of Immunobiology and Epigenetics, Department of Epigenetics, Stübeweg 51, D-79108 Freiburg, Germany
| | - Heekyoung Lee
- Max Planck Institute of Immunobiology and Epigenetics, Department of Epigenetics, Stübeweg 51, D-79108 Freiburg, Germany
| | - Nathalie Eisenhardt
- Max Planck Institute of Immunobiology and Epigenetics, Department of Epigenetics, Stübeweg 51, D-79108 Freiburg, Germany
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26
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Abstract
Post-translational protein modification by small ubiquitin-like modifier (SUMO), termed sumoylation, is an important mechanism in cellular responses to stress and one that appears to be upregulated in many cancers. Here, we examine the role of sumoylation in tumorigenesis as a possibly necessary safeguard that protects the stability and functionality of otherwise easily misregulated gene expression programmes and signalling pathways of cancer cells.
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Affiliation(s)
- Jacob-Sebastian Seeler
- Nuclear Organization and Oncogenesis Unit, INSERM U993, Institut Pasteur, 28 rue de Dr Roux, 75724 Paris Cedex 15, France
| | - Anne Dejean
- Nuclear Organization and Oncogenesis Unit, INSERM U993, Institut Pasteur, 28 rue de Dr Roux, 75724 Paris Cedex 15, France
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27
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Newman HA, Meluh PB, Lu J, Vidal J, Carson C, Lagesse E, Gray JJ, Boeke JD, Matunis MJ. A high throughput mutagenic analysis of yeast sumo structure and function. PLoS Genet 2017; 13:e1006612. [PMID: 28166236 PMCID: PMC5319795 DOI: 10.1371/journal.pgen.1006612] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 02/21/2017] [Accepted: 01/31/2017] [Indexed: 11/18/2022] Open
Abstract
Sumoylation regulates a wide range of essential cellular functions through diverse mechanisms that remain to be fully understood. Using S. cerevisiae, a model organism with a single essential SUMO gene (SMT3), we developed a library of >250 mutant strains with single or multiple amino acid substitutions of surface or core residues in the Smt3 protein. By screening this library using plate-based assays, we have generated a comprehensive structure-function based map of Smt3, revealing essential amino acid residues and residues critical for function under a variety of genotoxic and proteotoxic stress conditions. Functionally important residues mapped to surfaces affecting Smt3 precursor processing and deconjugation from protein substrates, covalent conjugation to protein substrates, and non-covalent interactions with E3 ligases and downstream effector proteins containing SUMO-interacting motifs. Lysine residues potentially involved in formation of polymeric chains were also investigated, revealing critical roles for polymeric chains, but redundancy in specific chain linkages. Collectively, our findings provide important insights into the molecular basis of signaling through sumoylation. Moreover, the library of Smt3 mutants represents a valuable resource for further exploring the functions of sumoylation in cellular stress response and other SUMO-dependent pathways.
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Affiliation(s)
- Heather A. Newman
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Pamela B. Meluh
- High Throughput Biology Center and Department of Molecular Biology and Genetics, Johns Hopkins University, School of Medicine, Baltimore, MD, United States of America
| | - Jian Lu
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Jeremy Vidal
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Caryn Carson
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Elizabeth Lagesse
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States of America
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States of America
| | - Jef D. Boeke
- High Throughput Biology Center and Department of Molecular Biology and Genetics, Johns Hopkins University, School of Medicine, Baltimore, MD, United States of America
| | - Michael J. Matunis
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, United States of America
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28
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Abstract
Thymidylate (dTMP) biosynthesis plays an essential and exclusive function in DNA synthesis and proper cell division, and therefore has been an attractive therapeutic target. Folate analogs, known as antifolates, and nucleotide analogs that inhibit the enzymatic action of the de novo thymidylate biosynthesis pathway and are commonly used in cancer treatment. In this review, we examine the mechanisms by which the antifolate 5-fluorouracil, as well as other dTMP synthesis inhibitors, function in cancer treatment in light of emerging evidence that dTMP synthesis occurs in the nucleus. Nuclear localization of the de novo dTMP synthesis pathway requires modification of the pathway enzymes by the small ubiquitin-like modifier (SUMO) protein. SUMOylation is required for nuclear localization of the de novo dTMP biosynthesis pathway, and disruption in the SUMO pathway inhibits cell proliferation in several cancer models. We summarize evidence that the nuclear localization of the dTMP biosynthesis pathway is a critical factor in the efficacy of antifolate-based therapies that target dTMP synthesis.
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29
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Oulhen N, Wessel GM. Differential Nanos 2 protein stability results in selective germ cell accumulation in the sea urchin. Dev Biol 2016; 418:146-156. [PMID: 27424271 DOI: 10.1016/j.ydbio.2016.07.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Revised: 06/21/2016] [Accepted: 07/12/2016] [Indexed: 01/18/2023]
Abstract
Nanos is a translational regulator required for the survival and maintenance of primordial germ cells. In the sea urchin, Strongylocentrotus purpuratus (Sp), Nanos 2 mRNA is broadly transcribed but accumulates specifically in the small micromere (sMic) lineage, in part because of the 3'UTR element GNARLE leads to turnover in somatic cells but retention in the sMics. Here we found that the Nanos 2 protein is also selectively stabilized; it is initially translated throughout the embryo but turned over in the future somatic cells and retained only in the sMics, the future germ line in this animal. This differential stability of Nanos protein is dependent on the open reading frame (ORF), and is independent of the sumoylation and ubiquitylation pathways. Manipulation of the ORF indicates that 68 amino acids in the N terminus of the Nanos protein are essential for its stability in the sMics whereas a 45 amino acid element adjacent to the zinc fingers targets its degradation. Further, this regulation of Nanos protein is cell autonomous, following formation of the germ line. These results are paradigmatic for the unique presence of Nanos in the germ line by a combination of selective RNA retention, distinctive translational control mechanisms (Oulhen et al., 2013), and now also by defined Nanos protein stability.
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Affiliation(s)
- Nathalie Oulhen
- Department of Molecular and Cell Biology and Biochemistry, Brown University, 185 Meeting St., Providence, RI 02912, USA
| | - Gary M Wessel
- Department of Molecular and Cell Biology and Biochemistry, Brown University, 185 Meeting St., Providence, RI 02912, USA.
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30
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Functional Crosstalk between the PP2A and SUMO Pathways Revealed by Analysis of STUbL Suppressor, razor 1-1. PLoS Genet 2016; 12:e1006165. [PMID: 27398807 PMCID: PMC4939958 DOI: 10.1371/journal.pgen.1006165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/11/2016] [Indexed: 12/04/2022] Open
Abstract
Posttranslational modifications (PTMs) provide dynamic regulation of the cellular proteome, which is critical for both normal cell growth and for orchestrating rapid responses to environmental stresses, e.g. genotoxins. Key PTMs include ubiquitin, the Small Ubiquitin-like MOdifier SUMO, and phosphorylation. Recently, SUMO-targeted ubiquitin ligases (STUbLs) were found to integrate signaling through the SUMO and ubiquitin pathways. In general, STUbLs are recruited to target proteins decorated with poly-SUMO chains to ubiquitinate them and drive either their extraction from protein complexes, and/or their degradation at the proteasome. In fission yeast, reducing or preventing the formation of SUMO chains can circumvent the essential and DNA damage response functions of STUbL. This result indicates that whilst some STUbL "targets" have been identified, the crucial function of STUbL is to antagonize SUMO chain formation. Herein, by screening for additional STUbL suppressors, we reveal crosstalk between the serine/threonine phosphatase PP2A-Pab1B55 and the SUMO pathway. A hypomorphic Pab1B55 mutant not only suppresses STUbL dysfunction, but also mitigates the phenotypes associated with deletion of the SUMO protease Ulp2, or mutation of the STUbL cofactor Rad60. Together, our results reveal a novel role for PP2A-Pab1B55 in modulating SUMO pathway output, acting in parallel to known critical regulators of SUMOylation homeostasis. Given the broad evolutionary functional conservation of the PP2A and SUMO pathways, our results could be relevant to the ongoing attempts to therapeutically target these factors. Posttranslational modifiers (PTMs) orchestrate the proteins and processes that control genome stability and cell growth. Accordingly, deregulation of PTMs causes disease, but can also be harnessed therapeutically. Crosstalk between PTMs is widespread, and acts to increase specificity and selectivity in signal transduction. Such crosstalk exists between two major PTMs, SUMO and ubiquitin, wherein a SUMO-targeted ubiquitin ligase (STUbL) can additionally mark SUMO-modified proteins with ubiquitin. Thereby, STUbL generates a hybrid SUMO-ubiquitin signal that is recognized by selective effectors, which can extract proteins from complexes and/or direct their degradation at the proteasome. STUbL function is critical to maintain genome stability, and it also mediates the therapeutic effects of arsenic trioxide in leukemia treatment. Therefore, a full appreciation of STUbL regulation and integration with other PTMs is warranted. Unexpectedly, we find that reduced activity of PP2A, a major cellular phosphatase, compensates for STUbL inactivation. Our results indicate that PP2A-regulated phosphorylation reduces the SUMO chain output of the SUMO pathway, thus reducing cellular dependency on STUbL and the functionally related factors Ulp2 and Rad60. Our data not only reveal a striking level of plasticity in signaling through certain PTMs, but also highlight potential "escape" mechanisms for SUMO pathway-based therapies.
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31
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Bustard DE, Ball LG, Cobb JA. Non-Smc element 5 (Nse5) of the Smc5/6 complex interacts with SUMO pathway components. Biol Open 2016; 5:777-85. [PMID: 27215325 PMCID: PMC4920195 DOI: 10.1242/bio.018440] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The Smc5/6 complex in Saccharomyces cerevisiae contains six essential non-Smc elements, Nse1-6. With the exception of Nse2 (also known as Mms21), which is an E3 small ubiquitin-like modifier (SUMO) ligase, very little is understood about the role of these components or their contribution to Smc5/6 functionality. Our characterization of Nse5 establishes a previously unidentified relationship between the Smc5/6 complex and factors of the SUMO pathway. Nse5 physically associates with the E2 conjugating enzyme, Ubc9, where contacts are stabilized by non-covalent interactions with SUMO. SUMO also mediates the interactions between Nse5 and the two PIAS family E3 SUMO ligases, Siz1 and Siz2. Cells carrying the nse5-ts1 allele or lacking either SIZ1 or SIZ2 exhibit a reduction in Smc5 sumoylation upon MMS treatment and demonstrate functional redundancy for SUMO mediated events in the presence of DNA damage. Overall, given the extensive connection between Nse5 and components of the SUMO pathway, we speculate that one function of the Smc5/6 complex might be as a scaffold center to enable sumoylation events in budding yeast.
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Affiliation(s)
- Denise E Bustard
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N.W., Calgary, Alberta, Canada T2N 4N1
| | - Lindsay G Ball
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N.W., Calgary, Alberta, Canada T2N 4N1
| | - Jennifer A Cobb
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N.W., Calgary, Alberta, Canada T2N 4N1
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32
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Silva S, Altmannova V, Luke-Glaser S, Henriksen P, Gallina I, Yang X, Choudhary C, Luke B, Krejci L, Lisby M. Mte1 interacts with Mph1 and promotes crossover recombination and telomere maintenance. Genes Dev 2016; 30:700-17. [PMID: 26966248 PMCID: PMC4803055 DOI: 10.1101/gad.276204.115] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/17/2016] [Indexed: 11/25/2022]
Abstract
Mph1 is a member of the conserved FANCM family of DNA motor proteins that play key roles in genome maintenance processes underlying Fanconi anemia, a cancer predisposition syndrome in humans. Here, we identify Mte1 as a novel interactor of the Mph1 helicase in Saccharomyces cerevisiae. In vitro, Mte1 (Mph1-associated telomere maintenance protein 1) binds directly to DNA with a preference for branched molecules such as D loops and fork structures. In addition, Mte1 stimulates the helicase and fork regression activities of Mph1 while inhibiting the ability of Mph1 to dissociate recombination intermediates. Deletion of MTE1 reduces crossover recombination and suppresses the sensitivity of mph1Δ mutant cells to replication stress. Mph1 and Mte1 interdependently colocalize at DNA damage-induced foci and dysfunctional telomeres, and MTE1 deletion results in elongated telomeres. Taken together, our data indicate that Mte1 plays a role in regulation of crossover recombination, response to replication stress, and telomere maintenance.
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Affiliation(s)
- Sonia Silva
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | | | | | - Peter Henriksen
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Irene Gallina
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Xuejiao Yang
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Chunaram Choudhary
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Brian Luke
- Institute of Molecular Biology gGmbH (IMB), 55128 Mainz, Germany
| | - Lumir Krejci
- Department of Biology, Masaryk University, CZ-62500 Brno, Czech Republic; National Centre for Biomolecular Research, Masaryk University, CZ-62500 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, CZ-656 91 Brno, Czech Republic; Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, CZ-656 91 Brno, Czech Republic
| | - Michael Lisby
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark; Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen N, Denmark
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33
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Li S, Besson S, Blackburn C, Carroll M, Ferguson RK, Flynn H, Gillen K, Leigh R, Lindner D, Linkert M, Moore WJ, Ramalingam B, Rozbicki E, Rustici G, Tarkowska A, Walczysko P, Williams E, Allan C, Burel JM, Moore J, Swedlow JR. Metadata management for high content screening in OMERO. Methods 2016; 96:27-32. [PMID: 26476368 PMCID: PMC4773399 DOI: 10.1016/j.ymeth.2015.10.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/13/2015] [Indexed: 01/18/2023] Open
Abstract
High content screening (HCS) experiments create a classic data management challenge-multiple, large sets of heterogeneous structured and unstructured data, that must be integrated and linked to produce a set of "final" results. These different data include images, reagents, protocols, analytic output, and phenotypes, all of which must be stored, linked and made accessible for users, scientists, collaborators and where appropriate the wider community. The OME Consortium has built several open source tools for managing, linking and sharing these different types of data. The OME Data Model is a metadata specification that supports the image data and metadata recorded in HCS experiments. Bio-Formats is a Java library that reads recorded image data and metadata and includes support for several HCS screening systems. OMERO is an enterprise data management application that integrates image data, experimental and analytic metadata and makes them accessible for visualization, mining, sharing and downstream analysis. We discuss how Bio-Formats and OMERO handle these different data types, and how they can be used to integrate, link and share HCS experiments in facilities and public data repositories. OME specifications and software are open source and are available at https://www.openmicroscopy.org.
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Affiliation(s)
- Simon Li
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Sébastien Besson
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Colin Blackburn
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Mark Carroll
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Richard K Ferguson
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Helen Flynn
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Kenneth Gillen
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Roger Leigh
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Dominik Lindner
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | | | - William J Moore
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Balaji Ramalingam
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | | | - Gabriella Rustici
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Aleksandra Tarkowska
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Petr Walczysko
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Eleanor Williams
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | | | - Jean-Marie Burel
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Josh Moore
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK; Glencoe Software, Inc., Seattle, WA, USA
| | - Jason R Swedlow
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK; Glencoe Software, Inc., Seattle, WA, USA.
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34
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SUMO Pathway Modulation of Regulatory Protein Binding at the Ribosomal DNA Locus in Saccharomyces cerevisiae. Genetics 2016; 202:1377-94. [PMID: 26837752 DOI: 10.1534/genetics.116.187252] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 01/20/2016] [Indexed: 11/18/2022] Open
Abstract
In this report, we identify cellular targets of Ulp2, one of two Saccharomyces cerevisiae small ubiquitin-related modifier (SUMO) proteases, and investigate the function of SUMO modification of these proteins. PolySUMO conjugates from ulp2Δ and ulp2Δ slx5Δ cells were isolated using an engineered affinity reagent containing the four SUMO-interacting motifs (SIMs) of Slx5, a component of the Slx5/Slx8 SUMO-targeted ubiquitin ligase (STUbL). Two proteins identified, Net1 and Tof2, regulate ribosomal DNA (rDNA) silencing and were found to be hypersumoylated in ulp2Δ,slx5Δ, and ulp2Δ slx5Δ cells. The increase in sumoylation of Net1 and Tof2 in ulp2Δ, but not ulp1ts cells, indicates that these nucleolar proteins are specific substrates of Ulp2 Based on quantitative chromatin-immunoprecipitation assays, both Net1 and Tof2 lose binding to their rDNA sites in ulp2Δ cells and both factors largely regain this association in ulp2Δ slx5Δ A parsimonious interpretation of these results is that hypersumoylation of these proteins causes them to be ubiquitylated by Slx5/Slx8, impairing their association with rDNA. Fob1, a protein that anchors both Net1 and Tof2 to the replication-fork barrier (RFB) in the rDNA repeats, is sumoylated in wild-type cells, and its modification levels increase specifically in ulp2Δ cells. Fob1 experiences a 50% reduction in rDNA binding in ulp2Δ cells, which is also rescued by elimination of Slx5 Additionally, overexpression of Sir2, another RFB-associated factor, suppresses the growth defect of ulp2Δ cells. Our data suggest that regulation of rDNA regulatory proteins by Ulp2 and the Slx5/Slx8 STUbL may be the cause of multiple ulp2Δ cellular defects.
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35
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Chen YJ, Chuang YC, Chuang CN, Cheng YH, Chang CR, Leng CH, Wang TF. S. cerevisiae Mre11 recruits conjugated SUMO moieties to facilitate the assembly and function of the Mre11-Rad50-Xrs2 complex. Nucleic Acids Res 2016; 44:2199-213. [PMID: 26743002 PMCID: PMC4797280 DOI: 10.1093/nar/gkv1523] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 12/19/2015] [Indexed: 01/04/2023] Open
Abstract
Double-strand breaks (DSBs) in chromosomes are the most challenging type of DNA damage. The yeast and mammalian Mre11-Rad50-Xrs2/Nbs1 (MRX/N)-Sae2/Ctp1 complex catalyzes the resection of DSBs induced by secondary structures, chemical adducts or covalently-attached proteins. MRX/N also initiates two parallel DNA damage responses-checkpoint phosphorylation and global SUMOylation-to boost a cell's ability to repair DSBs. However, the molecular mechanism of this SUMO-mediated response is not completely known. In this study, we report that Saccharomyces cerevisiae Mre11 can non-covalently recruit the conjugated SUMO moieties, particularly the poly-SUMO chain. Mre11 has two evolutionarily-conserved SUMO-interacting motifs, Mre11(SIM1) and Mre11(SIM2), which reside on the outermost surface of Mre11. Mre11(SIM1) is indispensable for MRX assembly. Mre11(SIM2) non-covalently links MRX with the SUMO enzymes (E2/Ubc9 and E3/Siz2) to promote global SUMOylation of DNA repair proteins. Mre11(SIM2) acts independently of checkpoint phosphorylation. During meiosis, the mre11(SIM2) mutant, as for mre11S, rad50S and sae2Δ, allows initiation but not processing of Spo11-induced DSBs. Using MRX and DSB repair as a model, our work reveals a general principle in which the conjugated SUMO moieties non-covalently facilitate the assembly and functions of multi-subunit protein complexes.
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Affiliation(s)
- Yu-Jie Chen
- Graduate Program of Biotechnology in Medicine, National Tsing Hua University and National Health Research Institutes, Taiwan Institute of Biotechnology, National Tsing Hua University, Hsinchu 300, Taiwan National Institute of Infectious Diseases and Vaccinology, National Health Research Institute, Miaoli 350, Taiwan Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Chien Chuang
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Chi-Ning Chuang
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Yun-Hsin Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Chuang-Rung Chang
- Graduate Program of Biotechnology in Medicine, National Tsing Hua University and National Health Research Institutes, Taiwan Institute of Biotechnology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Chih-Hsiang Leng
- Graduate Program of Biotechnology in Medicine, National Tsing Hua University and National Health Research Institutes, Taiwan National Institute of Infectious Diseases and Vaccinology, National Health Research Institute, Miaoli 350, Taiwan
| | - Ting-Fang Wang
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
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Køhler JB, Tammsalu T, Jørgensen MM, Steen N, Hay RT, Thon G. Targeting of SUMO substrates to a Cdc48-Ufd1-Npl4 segregase and STUbL pathway in fission yeast. Nat Commun 2015; 6:8827. [PMID: 26537787 PMCID: PMC4667616 DOI: 10.1038/ncomms9827] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 10/08/2015] [Indexed: 12/26/2022] Open
Abstract
In eukaryotes, the conjugation of proteins to the small ubiquitin-like modifier (SUMO) regulates numerous cellular functions. A proportion of SUMO conjugates are targeted for degradation by SUMO-targeted ubiquitin ligases (STUbLs) and it has been proposed that the ubiquitin-selective chaperone Cdc48/p97-Ufd1-Npl4 facilitates this process. However, the extent to which the two pathways overlap, and how substrates are selected, remains unknown. Here we address these questions in fission yeast through proteome-wide analyses of SUMO modification sites. We identify over a thousand sumoylated lysines in a total of 468 proteins and quantify changes occurring in the SUMO modification status when the STUbL or Ufd1 pathways are compromised by mutations. The data suggest the coordinated processing of several classes of SUMO conjugates, many dynamically associated with centromeres or telomeres. They provide new insights into subnuclear organization and chromosome biology, and, altogether, constitute an extensive resource for the molecular characterization of SUMO function and dynamics.
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Affiliation(s)
- Julie Bonne Køhler
- Department of Biology, University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Triin Tammsalu
- Centre for Gene Regulation and Expression, Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Maria Mønster Jørgensen
- Department of Biology, University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Nana Steen
- Department of Biology, University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Ronald Thomas Hay
- Centre for Gene Regulation and Expression, Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Geneviève Thon
- Department of Biology, University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
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Abstract
The small ubiquitin-like modifier SUMO regulates many aspects of cellular physiology to maintain cell homeostasis, both under normal conditions and during cell stress. Components of the transcriptional apparatus and chromatin are among the most prominent SUMO substrates. The prevailing view is that SUMO serves to repress transcription. However, as we will discuss in this review, this model needs to be refined, because recent studies have revealed that SUMO can also have profound positive effects on transcription.
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Affiliation(s)
- Pierre Chymkowitch
- Department of Molecular Biology, Institute of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Aurélie Nguéa P
- Department of Molecular Biology, Institute of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Jorrit M Enserink
- Department of Molecular Biology, Institute of Microbiology, Oslo University Hospital, Oslo, Norway
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38
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Screen for multi-SUMO-binding proteins reveals a multi-SIM-binding mechanism for recruitment of the transcriptional regulator ZMYM2 to chromatin. Proc Natl Acad Sci U S A 2015; 112:E4854-63. [PMID: 26283374 DOI: 10.1073/pnas.1509716112] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein SUMOylation has emerged as an important regulatory event, particularly in nuclear processes such as transcriptional control and DNA repair. In this context, small ubiquitin-like modifier (SUMO) often provides a binding platform for the recruitment of proteins via their SUMO-interacting motifs (SIMs). Recent discoveries point to an important role for multivalent SUMO binding through multiple SIMs in the binding partner as exemplified by poly-SUMOylation acting as a binding platform for ubiquitin E3 ligases such as ring finger protein 4. Here, we have investigated whether other types of protein are recruited through multivalent SUMO interactions. We have identified dozens of proteins that bind to multi-SUMO platforms, thereby uncovering a complex potential regulatory network. Multi-SUMO binding is mediated through multi-SIM modules, and the functional importance of these interactions is demonstrated for the transcriptional corepressor ZMYM2/ZNF198 where its multi-SUMO-binding activity is required for its recruitment to chromatin.
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SUMOylation-disrupting WAS mutation converts WASp from a transcriptional activator to a repressor of NF-κB response genes in T cells. Blood 2015; 126:1670-82. [PMID: 26261240 DOI: 10.1182/blood-2015-05-646182] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 08/08/2015] [Indexed: 11/20/2022] Open
Abstract
In Wiskott-Aldrich syndrome (WAS), immunodeficiency and autoimmunity often comanifest, yet how WAS mutations misregulate chromatin-signaling in Thelper (TH) cells favoring development of auto-inflammation over protective immunity is unclear. Previously, we identified an essential promoter-specific, coactivator role of nuclear-WASp in TH1 gene transcription. Here we identify small ubiquitin-related modifier (SUMO)ylation as a novel posttranslational modification of WASp, impairment of which converts nuclear-WASp from a transcriptional coactivator to a corepressor of nuclear factor (NF)-κB response genes in human (TH)1-differentiating cells. V75M, one of many disease-causing mutations occurring in SUMO*motif (72-ψψψψKDxxxxSY-83) of WASp, compromises WASp-SUMOylation, associates with COMMD1 to attenuate NF-κB signaling, and recruits histone deacetylases-6 (HDAC6) to p300-marked promoters of NF-κB response genes that pattern immunity but not inflammation. Consequently, proteins mediating adaptive immunity (IFNG, STAT1, TLR1) are deficient, whereas those mediating auto-inflammation (GM-CSF, TNFAIP2, IL-1β) are paradoxically increased in TH1 cells expressing SUMOylation-deficient WASp. Moreover, SUMOylation-deficient WASp favors ectopic development of the TH17-like phenotype (↑IL17A, IL21, IL22, IL23R, RORC, and CSF2) under TH1-skewing conditions, suggesting a role for WASp in modulating TH1/TH17 plasticity. Notably, pan-histone deacetylase inhibitors lift promoter-specific repression imposed by SUMOylation-deficient WASp and restore misregulated gene expression. Our findings uncovering a SUMOylation-based mechanism controlling WASp's dichotomous roles in transcription may have implications for personalized therapy for patients carrying mutations that perturb WASp-SUMOylation.
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40
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Abstract
DNA damage response pathways are crucial for protecting genome stability in all eukaryotes. Saccharomyces cerevisiaeDna2 has both helicase and nuclease activities that are essential for Okazaki fragment maturation, and Dna2 is involved in long-range DNA end resection at double-strand breaks. Dna2 forms nuclear foci in response to DNA replication stress and to double-strand breaks. We find that Dna2-GFP focus formation occurs mainly during S phase in unperturbed cells. Dna2 colocalizes in nuclear foci with 25 DNA repair proteins that define recombination repair centers in response to phleomycin-induced DNA damage. To systematically identify genes that affect Dna2 focus formation, we crossed Dna2-GFP into 4293 nonessential gene deletion mutants and assessed Dna2-GFP nuclear focus formation after phleomycin treatment. We identified 37 gene deletions that affect Dna2-GFP focus formation, 12 with fewer foci and 25 with increased foci. Together these data comprise a useful resource for understanding Dna2 regulation in response to DNA damage.
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Abstract
The ubiquitin family member Sumo has important functions in many cellular processes including DNA repair, transcription and cell division. Numerous studies have shown that Sumo is essential for maintaining cell homeostasis when the cell encounters endogenous or environmental stress, such as osmotic stress, hypoxia, heat shock, genotoxic stress, and nutrient stress. Regulation of transcription is a key component of the Sumo stress response, and multiple mechanisms have been described by which Sumo can regulate transcription. Although many individual substrates have been described that are sumoylated during the Sumo stress response, an emerging concept is modification of entire complexes or pathways by Sumo. This review focuses on the function and regulation of Sumo during the stress response.
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Affiliation(s)
- Jorrit M Enserink
- Institute for Microbiology, Oslo University Hospital, Sognsvannsveien 20N-0027, Oslo, Norway
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42
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Eckhoff J, Dohmen RJ. In Vitro Studies Reveal a Sequential Mode of Chain Processing by the Yeast SUMO (Small Ubiquitin-related Modifier)-specific Protease Ulp2. J Biol Chem 2015; 290:12268-81. [PMID: 25833950 DOI: 10.1074/jbc.m114.622217] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Indexed: 11/06/2022] Open
Abstract
Sumoylation is a post-translational modification essential in most eukaryotes that regulates stability, localization, activity, or interaction of a multitude of proteins. It is a reversible process wherein counteracting ligases and proteases, respectively, mediate the conjugation and deconjugation of SUMO molecules to/from target proteins. Apart from attachment of single SUMO moieties to targets, formation of poly-SUMO chains occurs by the attachment of additional SUMO molecules to lysine residues in the N-terminal extensions of SUMO. In Saccharomyces cerevisiae there are apparently only two SUMO(Smt3)-specific proteases: Ulp1 and Ulp2. Ulp2 has been shown to be important for the control of poly-SUMO conjugates in cells and to dismantle SUMO chains in vitro, but the mechanism by which it acts remains to be elucidated. Applying an in vitro approach, we found that Ulp2 acts sequentially rather than stochastically, processing substrate-linked poly-SUMO chains from their distal ends down to two linked SUMO moieties. Furthermore, three linked SUMO units turned out to be the minimum length of a substrate-linked chain required for efficient binding to and processing by Ulp2. Our data suggest that Ulp2 disassembles SUMO chains by removing one SUMO moiety at a time from their ends (exo mechanism). Apparently, Ulp2 recognizes surfaces at or near the N terminus of the distal SUMO moiety, as attachments to this end significantly reduce cleavage efficiency. Our studies suggest that Ulp2 controls the dynamic range of SUMO chain lengths by trimming them from the distal ends.
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Affiliation(s)
- Julia Eckhoff
- From the Institute for Genetics, Biocenter, University of Cologne, D-50674 Cologne, Germany
| | - R Jürgen Dohmen
- From the Institute for Genetics, Biocenter, University of Cologne, D-50674 Cologne, Germany
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43
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Kalkat M, Chan PK, Wasylishen AR, Srikumar T, Kim SS, Ponzielli R, Bazett-Jones DP, Raught B, Penn LZ. Identification of c-MYC SUMOylation by mass spectrometry. PLoS One 2014; 9:e115337. [PMID: 25522242 PMCID: PMC4270761 DOI: 10.1371/journal.pone.0115337] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 11/21/2014] [Indexed: 01/10/2023] Open
Abstract
The c-MYC transcription factor is a master regulator of many cellular processes and deregulation of this oncogene has been linked to more than 50% of all cancers. This deregulation can take many forms, including altered post-translational regulation. Here, using immunoprecipitation combined with mass spectrometry, we identified a MYC SUMOylation site (K326). Abrogation of signaling through this residue by substitution with arginine (K326R) has no obvious effects on MYC half-life, intracellular localization, transcriptional targets, nor on the biological effects of MYC overexpression in two different cell systems assessed for soft agar colony formation, proliferation, and apoptosis. While we have definitively demonstrated that MYC SUMOylation can occur on K326, future work will be needed to elucidate the mechanisms and biological significance of MYC regulation by SUMOylation.
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Affiliation(s)
- Manpreet Kalkat
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Pak-Kei Chan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Amanda R. Wasylishen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Tharan Srikumar
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Sam S. Kim
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Romina Ponzielli
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - David P. Bazett-Jones
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Linda Z. Penn
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- * E-mail:
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44
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Lewicki MC, Srikumar T, Johnson E, Raught B. The S. cerevisiae SUMO stress response is a conjugation-deconjugation cycle that targets the transcription machinery. J Proteomics 2014; 118:39-48. [PMID: 25434491 DOI: 10.1016/j.jprot.2014.11.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 11/06/2014] [Accepted: 11/10/2014] [Indexed: 01/07/2023]
Abstract
UNLABELLED The small ubiquitin-related modifier (SUMO) "stress response" (SSR) is a poorly understood evolutionarily conserved phenomenon in which steady-state SUMO conjugate levels are dramatically increased in response to environmental stresses. Here we characterize Saccharomyces cerevisiae SSR kinetics in response to several different types of stress, demonstrate that SSR activation and inactivation do not require protein synthesis or proteasome-dependent degradation, and establish that the SSR is effected primarily by the Siz1 E3 ligase and inactivated by the SUMO-specific protease Ulp2. Affinity purification coupled with mass spectrometry identifies the primary hyperosmotic SSR targets as components of the TFIID and mediator complexes, Pol II-associated mRNA maturation factors, chromatin remodeling proteins, and the transcriptional co-repressor Tup1-Cyc8. Consistent with these findings, our data also suggest that ongoing transcription (but not translation) is required to activate the SSR. The SSR thus does not appear to be directly linked to the stress itself, but likely represents a synchronized wave of sumoylation that occurs as a consequence of the large-scale, coordinated changes in the transcriptional program in response to environmental stress. BIOLOGICAL SIGNIFICANCE SUMO is a ubiquitin-like protein with a number of important biological functions. Increased levels of sumoylation are associated with a number of human diseases, and previous reports have described an evolutionarily conserved "SUMO stress response" (SSR), in which SUMO conjugate levels are markedly increased in response to environmental stresses. However, the connection between cellular stress and sumoylation has remained poorly understood. Here we conduct the first in-depth characterization of the S. cerevisiae SSR. The SUMO system components required to effect it are identified, and SSR kinetics in response to different types of environmental stresses are established. Using mass spectrometry, we identify the principle osmotic shock-associated SSR targets as components of the basal transcription machinery, transcriptional regulators and chromatin remodeling complexes. Consistent with these data, we also observe that the sumoylation of SSR targets is dependent upon, and thus appears to be coupled with, transcription. Together, our data suggest that the SSR is not responsive to environmental stress per se, but more likely reflects a synchronized, transcription-coupled wave of sumoylation that accompanies the rapid, global re-programming of transcription in response to stress. This article is part of a Special Issue entitled: Protein dynamics in health and disease. Guest Editors: Pierre Thibault and Anne-Claude Gingras.
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Affiliation(s)
- Megan C Lewicki
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Tharan Srikumar
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Erica Johnson
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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Versteeg GA, Benke S, García-Sastre A, Rajsbaum R. InTRIMsic immunity: Positive and negative regulation of immune signaling by tripartite motif proteins. Cytokine Growth Factor Rev 2014; 25:563-76. [PMID: 25172371 PMCID: PMC7173094 DOI: 10.1016/j.cytogfr.2014.08.001] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 08/05/2014] [Indexed: 12/25/2022]
Abstract
During the immune response, striking the right balance between positive and negative regulation is critical to effectively mount an anti-microbial defense while preventing detrimental effects from exacerbated immune activation. Intra-cellular immune signaling is tightly regulated by various post-translational modifications, which allow for this dynamic response. One of the post-translational modifiers critical for immune control is ubiquitin, which can be covalently conjugated to lysines in target molecules, thereby altering their functional properties. This is achieved in a process involving E3 ligases which determine ubiquitination target specificity. One of the most prominent E3 ligase families is that of the tripartite motif (TRIM) proteins, which counts over 70 members in humans. Over the last years, various studies have contributed to the notion that many members of this protein family are important immune regulators. Recent studies into the mechanisms by which some of the TRIMs regulate the innate immune system have uncovered important immune regulatory roles of both covalently attached, as well as unanchored poly-ubiquitin chains. This review highlights TRIM evolution, recent findings in TRIM-mediated immune regulation, and provides an outlook to current research hurdles and future directions.
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Affiliation(s)
- Gijs A Versteeg
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria.
| | - Stefan Benke
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Ricardo Rajsbaum
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; University of Texas Medical Branch, Department of Microbiology and Immunology, 301 University Avenue, Galveston, TX 77555, USA
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46
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Abu Irqeba A, Li Y, Panahi M, Zhu M, Wang Y. Regulating global sumoylation by a MAP kinase Hog1 and its potential role in osmo-tolerance in yeast. PLoS One 2014; 9:e87306. [PMID: 24498309 PMCID: PMC3911979 DOI: 10.1371/journal.pone.0087306] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 12/23/2013] [Indexed: 12/01/2022] Open
Abstract
Sumoylation, a post-translational protein modification by small ubiquitin-like modifier (SUMO), has been implicated in many stress responses. Here we analyzed the potential role of sumoylation in osmo-response in yeast. We find that osmotic stress induces rapid accumulation of sumoylated species in normal yeast cells. Interestingly, disruption of MAP kinase Hog1 leads to a much higher level of accumulation of sumoylated conjugates that are independent of new protein synthesis. We also find that the accumulation of sumoylated species is dependent on a SUMO ligase Siz1. Notably, overexpression of SIZ1 in HOG1-disruption mutants (hog1Δ) but not in wild type cells leads to a markedly increased and prolonged accumulation of sumoylated species. Examination of osmo-tolerance of yeast mutants that display either an increase or a decrease in the global sumoylation level revealed an inverse relationship between accumulation of sumoylated conjugates and osmo-tolerance. Further investigation has shown that many of the sumoylated species induced by hyperosmotic stress are actually poly-sumoylated. Together, these findings indicate that abnormal accumulation of poly-sumoylated conjugates is harmful for osmo-tolerance in yeast, and suggest that Hog1 promotes adaptation to hyperosmotic stress partially via regulation of global sumoylation level.
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Affiliation(s)
- Ameair Abu Irqeba
- Department of Biology, Saint Louis University, St. Louis, Missouri, United States of America
| | - Yang Li
- Department of Biology, Saint Louis University, St. Louis, Missouri, United States of America
| | - Mahmoud Panahi
- Department of Biology, Saint Louis University, St. Louis, Missouri, United States of America
| | - Ming Zhu
- School of Medicine, Yunnan University, Kunming, Yunnan, China
| | - Yuqi Wang
- Department of Biology, Saint Louis University, St. Louis, Missouri, United States of America
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47
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D'Ambrosio LM, Lavoie BD. Pds5 prevents the PolySUMO-dependent separation of sister chromatids. Curr Biol 2014; 24:361-71. [PMID: 24485833 DOI: 10.1016/j.cub.2013.12.038] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 10/24/2013] [Accepted: 12/17/2013] [Indexed: 11/15/2022]
Abstract
BACKGROUND The establishment, maintenance, and dissolution of sister chromatid cohesion are sequentially coordinated during the cell cycle to ensure faithful chromosome transmission. This cell-cycle-dependent regulation of cohesion is mediated, in part, by distinct posttranslational modifications of cohesin, a protein complex consisting of the Smc1-Smc3 ATPase, the Mcd1/Scc1 α-kleisin, and Scc3. Although cohesion is established in S phase, cohesins are not sufficient to maintain cohesion as cells progress from G2 to the metaphase-to-anaphase transition. Rather, the cohesin-associated factor Pds5 is also required to keep sisters paired until anaphase onset. How Pds5 maintains cohesion at the molecular level and whether this maintenance involves the regulation of cohesin modifications remains to be defined. RESULTS In pds5 mutants, we find that Mcd1 is extensively SUMOylated and that premature sister separation requires Siz2-dependent polySUMOylation. Moreover, abrogation of Pds5 function promotes the proteasome-dependent degradation of Mcd1 and a significant loss of cohesin from chromatin independently of anaphase onset. We further demonstrate that inactivation of the Slx5-Slx8 SUMO-targeted ubiquitin ligase, required for targeting polySUMOylated factors for proteasome-mediated destruction, limits Mcd1 turnover and restores both cell growth and cohesion in metaphase cells defective for Pds5 function. CONCLUSIONS We propose that Pds5 maintains cohesion, at least in part, by antagonizing the polySUMO-dependent degradation of cohesin.
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Affiliation(s)
- Lisa M D'Ambrosio
- Department of Molecular Genetics, University of Toronto, Medical Sciences Building, Room 4278, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Brigitte D Lavoie
- Department of Molecular Genetics, University of Toronto, Medical Sciences Building, Room 4278, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
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48
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SUMO-targeted ubiquitin ligases. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:75-85. [PMID: 24018209 DOI: 10.1016/j.bbamcr.2013.08.022] [Citation(s) in RCA: 183] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 08/25/2013] [Accepted: 08/28/2013] [Indexed: 12/16/2022]
Abstract
Covalent posttranslational modification with SUMO (small ubiquitin-related modifier) modulates functions of a wide range of proteins in eukaryotic cells. Sumoylation affects the activity, interaction properties, subcellular localization and the stability of its substrate proteins. The recent discovery of a novel class of ubiquitin ligases (E3), termed ULS (E3-S) or STUbL, that recognize sumoylated proteins, links SUMO modification to the ubiquitin/proteasome system. Here we review recent insights into the properties and function of these ligases and their roles in regulating sumoylated proteins. This article is part of a Special Issue entitled: Ubiquitin-Proteasome System. Guest Editors: Thomas Sommer and Dieter H. Wolf.
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49
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Three distinct modes of Mec1/ATR and Tel1/ATM activation illustrate differential checkpoint targeting during budding yeast early meiosis. Mol Cell Biol 2013; 33:3365-76. [PMID: 23775120 DOI: 10.1128/mcb.00438-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recombination and synapsis of homologous chromosomes are hallmarks of meiosis in many organisms. Meiotic recombination is initiated by Spo11-induced DNA double-strand breaks (DSBs), whereas chromosome synapsis is mediated by a tripartite structure named the synaptonemal complex (SC). Previously, we proposed that budding yeast SC is assembled via noncovalent interactions between the axial SC protein Red1, SUMO chains or conjugates, and the central SC protein Zip1. Incomplete synapsis and unrepaired DNA are monitored by Mec1/Tel1-dependent checkpoint responses that prevent exit from the pachytene stage. Here, our results distinguished three distinct modes of Mec1/Tec1 activation during early meiosis that led to phosphorylation of three targets, histone H2A at S129 (γH2A), Hop1, and Zip1, which are involved, respectively, in DNA replication, the interhomolog recombination and chromosome synapsis checkpoint, and destabilization of homology-independent centromere pairing. γH2A phosphorylation is Red1 independent and occurs prior to Spo11-induced DSBs. DSB- and Red1-dependent Hop1 phosphorylation is activated via interaction of the Red1-SUMO chain/conjugate ensemble with the Ddc1-Rad17-Mec3 (9-1-1) checkpoint complex and the Mre11-Rad50-Xrs2 complex. During SC assembly, Zip1 outcompetes 9-1-1 from the Red1-SUMO chain ensemble to attenuate Hop1 phosphorylation. In contrast, chromosome synapsis cannot attenuate DSB-dependent and Red1-independent Zip1 phosphorylation. These results reveal how DNA replication, DSB repair, and chromosome synapsis are differentially monitored by the meiotic checkpoint network.
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Srikumar T, Lewicki MC, Raught B. A global S. cerevisiae small ubiquitin-related modifier (SUMO) system interactome. Mol Syst Biol 2013; 9:668. [PMID: 23712011 PMCID: PMC4039371 DOI: 10.1038/msb.2013.23] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 04/04/2013] [Indexed: 12/11/2022] Open
Abstract
A global physical interaction map of the SUMO system was generated to study its functional organization. This resource was used to validate several E3-specific substrates and uncover novel roles for Ubc9 and Ulp2 in ribosomal DNA maintenance. ![]()
Affinity purification coupled to mass spectrometry was used to construct the first global SUMO interactome in yeast. The analysis identified more than 450 proteins interacting physically with the SUMO E2 Ubc9, the E3 ligases Siz1 and Siz2, and the SUMO-specific proteases Ulp1 and Ulp2. Several Siz1- and Siz2-specific substrates were validated, such as Cdc12, Sum1, Tup1, Top2, Rpb3 and Spt16. Follow-up investigations revealed new important roles for Ubc9 and Ulp2 in ribosomal DNA maintenance.
The small ubiquitin-related modifier (SUMO) system has been implicated in a number of biological functions, yet the individual components of the SUMO machinery involved in each of these activities were largely unknown. Here we report the first global SUMO system interactome. Using affinity purification coupled with mass spectrometry, we identify >450 protein–protein interactions surrounding the SUMO E2, Siz type E3s and SUMO-specific proteases in budding yeast. Exploiting this information-rich resource, we validate several Siz1- and Siz2-specific substrates, identify a nucleoporin required for proper Ulp1 localization, and uncover important new roles for Ubc9 and Ulp2 in the maintenance of ribosomal DNA.
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Affiliation(s)
- Tharan Srikumar
- Ontario Cancer Institute, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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