1
|
Bradley D, Hogrebe A, Dandage R, Dubé AK, Leutert M, Dionne U, Chang A, Villén J, Landry CR. The fitness cost of spurious phosphorylation. EMBO J 2024:10.1038/s44318-024-00200-7. [PMID: 39256561 DOI: 10.1038/s44318-024-00200-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 07/23/2024] [Accepted: 07/24/2024] [Indexed: 09/12/2024] Open
Abstract
The fidelity of signal transduction requires the binding of regulatory molecules to their cognate targets. However, the crowded cell interior risks off-target interactions between proteins that are functionally unrelated. How such off-target interactions impact fitness is not generally known. Here, we use Saccharomyces cerevisiae to inducibly express tyrosine kinases. Because yeast lacks bona fide tyrosine kinases, the resulting tyrosine phosphorylation is biologically spurious. We engineered 44 yeast strains each expressing a tyrosine kinase, and quantitatively analysed their phosphoproteomes. This analysis resulted in ~30,000 phosphosites mapping to ~3500 proteins. The number of spurious pY sites generated correlates strongly with decreased growth, and we predict over 1000 pY events to be deleterious. However, we also find that many of the spurious pY sites have a negligible effect on fitness, possibly because of their low stoichiometry. This result is consistent with our evolutionary analyses demonstrating a lack of phosphotyrosine counter-selection in species with tyrosine kinases. Our results suggest that, alongside the risk for toxicity, the cell can tolerate a large degree of non-functional crosstalk as interaction networks evolve.
Collapse
Affiliation(s)
- David Bradley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexander Hogrebe
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Rohan Dandage
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Mario Leutert
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Ugo Dionne
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexis Chang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada.
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada.
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada.
- Department of Biology, Université Laval, Québec, QC, Canada.
| |
Collapse
|
2
|
Her J, Zheng H, Bunting SF. RNF4 sustains Myc-driven tumorigenesis by facilitating DNA replication. J Clin Invest 2024; 134:e167419. [PMID: 38530355 PMCID: PMC11093604 DOI: 10.1172/jci167419] [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: 11/22/2022] [Accepted: 03/20/2024] [Indexed: 03/27/2024] Open
Abstract
The mammalian SUMO-targeted E3 ubiquitin ligase Rnf4 has been reported to act as a regulator of DNA repair, but the importance of RNF4 as a tumor suppressor has not been tested. Using a conditional-knockout mouse model, we deleted Rnf4 in the B cell lineage to test the importance of RNF4 for growth of somatic cells. Although Rnf4-conditional-knockout B cells exhibited substantial genomic instability, Rnf4 deletion caused no increase in tumor susceptibility. In contrast, Rnf4 deletion extended the healthy lifespan of mice expressing an oncogenic c-myc transgene. Rnf4 activity is essential for normal DNA replication, and in its absence, there was a failure in ATR-CHK1 signaling of replication stress. Factors that normally mediate replication fork stability, including members of the Fanconi anemia gene family and the helicases PIF1 and RECQL5, showed reduced accumulation at replication forks in the absence of RNF4. RNF4 deficiency also resulted in an accumulation of hyper-SUMOylated proteins in chromatin, including members of the SMC5/6 complex, which contributes to replication failure by a mechanism dependent on RAD51. These findings indicate that RNF4, which shows increased expression in multiple human tumor types, is a potential target for anticancer therapy, especially in tumors expressing c-myc.
Collapse
Affiliation(s)
- Joonyoung Her
- Department of Molecular Biology and Biochemistry and
| | - Haiyan Zheng
- Biological Mass Spectrometry Facility, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | | |
Collapse
|
3
|
Szulc NA, Piechota M, Biriczová L, Thapa P, Pokrzywa W. Lysine deserts and cullin-RING ligase receptors: Navigating untrodden paths in proteostasis. iScience 2023; 26:108344. [PMID: 38026164 PMCID: PMC10665810 DOI: 10.1016/j.isci.2023.108344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 09/15/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
The ubiquitin-proteasome system (UPS) governs the degradation of proteins by ubiquitinating their lysine residues. Our study focuses on lysine deserts - regions in proteins conspicuously low in lysine residues - in averting ubiquitin-dependent proteolysis. We spotlight the prevalence of lysine deserts among bacteria leveraging the pupylation-dependent proteasomal degradation, and in the UPS of eukaryotes. To further scrutinize this phenomenon, we focused on human receptors VHL and SOCS1 to ascertain if lysine deserts could limit their ubiquitination within the cullin-RING ligase (CRL) complex. Our data indicate that the wild-type and lysine-free variants of VHL and SOCS1 maintain consistent turnover rates, unaltered by CRL-mediated ubiquitination, hinting at a protective mechanism facilitated by lysine deserts. Nonetheless, we noted their ubiquitination at non-lysine sites, alluding to alternative regulation by the UPS. Our research underscores the role of lysine deserts in limiting CRL-mediated ubiquitin tagging while promoting non-lysine ubiquitination, thereby advancing our understanding of proteostasis.
Collapse
Affiliation(s)
- Natalia A. Szulc
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Małgorzata Piechota
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Lilla Biriczová
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Pankaj Thapa
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Wojciech Pokrzywa
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| |
Collapse
|
4
|
Bradley D, Hogrebe A, Dandage R, Dubé AK, Leutert M, Dionne U, Chang A, Villén J, Landry CR. The fitness cost of spurious phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.08.561337. [PMID: 37873463 PMCID: PMC10592693 DOI: 10.1101/2023.10.08.561337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The fidelity of signal transduction requires the binding of regulatory molecules to their cognate targets. However, the crowded cell interior risks off-target interactions between proteins that are functionally unrelated. How such off-target interactions impact fitness is not generally known, but quantifying this is required to understand the constraints faced by cell systems as they evolve. Here, we use the model organism S. cerevisiae to inducibly express tyrosine kinases. Because yeast lacks bona fide tyrosine kinases, most of the resulting tyrosine phosphorylation is spurious. This provides a suitable system to measure the impact of artificial protein interactions on fitness. We engineered 44 yeast strains each expressing a tyrosine kinase, and quantitatively analysed their phosphoproteomes. This analysis resulted in ~30,000 phosphosites mapping to ~3,500 proteins. Examination of the fitness costs in each strain revealed a strong correlation between the number of spurious pY sites and decreased growth. Moreover, the analysis of pY effects on protein structure and on protein function revealed over 1000 pY events that we predict to be deleterious. However, we also find that a large number of the spurious pY sites have a negligible effect on fitness, possibly because of their low stoichiometry. This result is consistent with our evolutionary analyses demonstrating a lack of phosphotyrosine counter-selection in species with bona fide tyrosine kinases. Taken together, our results suggest that, alongside the risk for toxicity, the cell can tolerate a large degree of non-functional crosstalk as interaction networks evolve.
Collapse
Affiliation(s)
- David Bradley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexander Hogrebe
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Rohan Dandage
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Mario Leutert
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Ugo Dionne
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexis Chang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| |
Collapse
|
5
|
Kampmeyer C, Grønbæk-Thygesen M, Oelerich N, Tatham MH, Cagiada M, Lindorff-Larsen K, Boomsma W, Hofmann K, Hartmann-Petersen R. Lysine deserts prevent adventitious ubiquitylation of ubiquitin-proteasome components. Cell Mol Life Sci 2023; 80:143. [PMID: 37160462 PMCID: PMC10169902 DOI: 10.1007/s00018-023-04782-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/15/2023] [Accepted: 04/17/2023] [Indexed: 05/11/2023]
Abstract
In terms of its relative frequency, lysine is a common amino acid in the human proteome. However, by bioinformatics we find hundreds of proteins that contain long and evolutionarily conserved stretches completely devoid of lysine residues. These so-called lysine deserts show a high prevalence in intrinsically disordered proteins with known or predicted functions within the ubiquitin-proteasome system (UPS), including many E3 ubiquitin-protein ligases and UBL domain proteasome substrate shuttles, such as BAG6, RAD23A, UBQLN1 and UBQLN2. We show that introduction of lysine residues into the deserts leads to a striking increase in ubiquitylation of some of these proteins. In case of BAG6, we show that ubiquitylation is catalyzed by the E3 RNF126, while RAD23A is ubiquitylated by E6AP. Despite the elevated ubiquitylation, mutant RAD23A appears stable, but displays a partial loss of function phenotype in fission yeast. In case of UBQLN1 and BAG6, introducing lysine leads to a reduced abundance due to proteasomal degradation of the proteins. For UBQLN1 we show that arginine residues within the lysine depleted region are critical for its ability to form cytosolic speckles/inclusions. We propose that selective pressure to avoid lysine residues may be a common evolutionary mechanism to prevent unwarranted ubiquitylation and/or perhaps other lysine post-translational modifications. This may be particularly relevant for UPS components as they closely and frequently encounter the ubiquitylation machinery and are thus more susceptible to nonspecific ubiquitylation.
Collapse
Affiliation(s)
- Caroline Kampmeyer
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Martin Grønbæk-Thygesen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Nicole Oelerich
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Michael H Tatham
- Centre for Gene Regulation and Expression, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, UK
| | - Matteo Cagiada
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Wouter Boomsma
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark.
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Cologne, Germany.
| | - Rasmus Hartmann-Petersen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
6
|
SUMO orchestrates multiple alternative DNA-protein crosslink repair pathways. Cell Rep 2021; 37:110034. [PMID: 34818558 PMCID: PMC10042627 DOI: 10.1016/j.celrep.2021.110034] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/27/2020] [Accepted: 11/01/2021] [Indexed: 02/05/2023] Open
Abstract
Endogenous metabolites, environmental agents, and therapeutic drugs promote formation of covalent DNA-protein crosslinks (DPCs). Persistent DPCs compromise genome integrity and are eliminated by multiple repair pathways. Aberrant Top1-DNA crosslinks, or Top1ccs, are processed by Tdp1 and Wss1 functioning in parallel pathways in Saccharomyces cerevisiae. It remains obscure how cells choose between diverse mechanisms of DPC repair. Here, we show that several SUMO biogenesis factors (Ulp1, Siz2, Slx5, and Slx8) control repair of Top1cc or an analogous DPC lesion. Genetic analysis reveals that SUMO promotes Top1cc processing in the absence of Tdp1 but has an inhibitory role if cells additionally lack Wss1. In the tdp1Δ wss1Δ mutant, the E3 SUMO ligase Siz2 stimulates sumoylation in the vicinity of the DPC, but not SUMO conjugation to Top1. This Siz2-dependent sumoylation inhibits alternative DPC repair mechanisms, including Ddi1. Our findings suggest that SUMO tunes available repair pathways to facilitate faithful DPC repair.
Collapse
|
7
|
Liu JCY, Kühbacher U, Larsen NB, Borgermann N, Garvanska DH, Hendriks IA, Ackermann L, Haahr P, Gallina I, Guérillon C, Branigan E, Hay RT, Azuma Y, Nielsen ML, Duxin JP, Mailand N. Mechanism and function of DNA replication-independent DNA-protein crosslink repair via the SUMO-RNF4 pathway. EMBO J 2021; 40:e107413. [PMID: 34346517 PMCID: PMC8441304 DOI: 10.15252/embj.2020107413] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 07/03/2021] [Accepted: 07/12/2021] [Indexed: 11/09/2022] Open
Abstract
DNA-protein crosslinks (DPCs) obstruct essential DNA transactions, posing a serious threat to genome stability and functionality. DPCs are proteolytically processed in a ubiquitin- and DNA replication-dependent manner by SPRTN and the proteasome but can also be resolved via targeted SUMOylation. However, the mechanistic basis of SUMO-mediated DPC resolution and its interplay with replication-coupled DPC repair remain unclear. Here, we show that the SUMO-targeted ubiquitin ligase RNF4 defines a major pathway for ubiquitylation and proteasomal clearance of SUMOylated DPCs in the absence of DNA replication. Importantly, SUMO modifications of DPCs neither stimulate nor inhibit their rapid DNA replication-coupled proteolysis. Instead, DPC SUMOylation provides a critical salvage mechanism to remove DPCs formed after DNA replication, as DPCs on duplex DNA do not activate interphase DNA damage checkpoints. Consequently, in the absence of the SUMO-RNF4 pathway cells are able to enter mitosis with a high load of unresolved DPCs, leading to defective chromosome segregation and cell death. Collectively, these findings provide mechanistic insights into SUMO-driven pathways underlying replication-independent DPC resolution and highlight their critical importance in maintaining chromosome stability and cellular fitness.
Collapse
Affiliation(s)
- Julio C Y Liu
- Protein Signaling ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Ulrike Kühbacher
- Protein Signaling ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Nicolai B Larsen
- Protein Signaling ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Nikoline Borgermann
- Protein Signaling ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Dimitriya H Garvanska
- Protein Signaling ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Ivo A Hendriks
- Protein Signaling ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Leena Ackermann
- Protein Signaling ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Peter Haahr
- Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Irene Gallina
- Protein Signaling ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Claire Guérillon
- Protein Signaling ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Emma Branigan
- Centre for Gene Regulation and ExpressionSchool of Life SciencesUniversity of DundeeDundeeUK
| | - Ronald T Hay
- Centre for Gene Regulation and ExpressionSchool of Life SciencesUniversity of DundeeDundeeUK
| | - Yoshiaki Azuma
- Department of Molecular BiosciencesUniversity of KansasLawrenceKSUSA
| | - Michael Lund Nielsen
- Protein Signaling ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Julien P Duxin
- Protein Signaling ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Niels Mailand
- Protein Signaling ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
- Center for Chromosome StabilityDepartment of Cellular and Molecular MedicineUniversity of CopenhagenCopenhagenDenmark
| |
Collapse
|
8
|
Maddi K, Sam DK, Bonn F, Prgomet S, Tulowetzke E, Akutsu M, Lopez-Mosqueda J, Dikic I. Wss1 Promotes Replication Stress Tolerance by Degrading Histones. Cell Rep 2021; 30:3117-3126.e4. [PMID: 32130911 DOI: 10.1016/j.celrep.2020.02.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 11/29/2019] [Accepted: 02/04/2020] [Indexed: 12/23/2022] Open
Abstract
Timely completion of DNA replication is central to accurate cell division and to the maintenance of genomic stability. However, certain DNA-protein interactions can physically impede DNA replication fork progression. Cells remove or bypass these physical impediments by different mechanisms to preserve DNA macromolecule integrity and genome stability. In Saccharomyces cerevisiae, Wss1, the DNA-protein crosslink repair protease, allows cells to tolerate hydroxyurea-induced replication stress, but the underlying mechanism by which Wss1 promotes this function has remained unknown. Here, we report that Wss1 provides cells tolerance to replication stress by directly degrading core histone subunits that non-specifically and non-covalently bind to single-stranded DNA. Unlike Wss1-dependent proteolysis of covalent DNA-protein crosslinks, proteolysis of histones does not require Cdc48 nor SUMO-binding activities. Wss1 thus acts as a multi-functional protease capable of targeting a broad range of covalent and non-covalent DNA-binding proteins to preserve genome stability during adverse conditions.
Collapse
Affiliation(s)
- Karthik Maddi
- Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Daniel Kwesi Sam
- South Dakota State University, Department of Biology and Microbiology, Brookings, SD 57007, USA
| | - Florian Bonn
- Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Stefan Prgomet
- Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Eric Tulowetzke
- South Dakota State University, Department of Biology and Microbiology, Brookings, SD 57007, USA
| | - Masato Akutsu
- Buchmann Institute for Molecular Life Sciences, Goethe University, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Jaime Lopez-Mosqueda
- South Dakota State University, Department of Biology and Microbiology, Brookings, SD 57007, USA.
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.
| |
Collapse
|
9
|
Han B. A suite of mathematical solutions to describe ternary complex formation and their application to targeted protein degradation by heterobifunctional ligands. J Biol Chem 2020; 295:15280-15291. [PMID: 32859748 PMCID: PMC7650257 DOI: 10.1074/jbc.ra120.014715] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 08/25/2020] [Indexed: 01/30/2023] Open
Abstract
Small molecule–induced targeted protein degradation by heterobifunctional ligands or molecular glues represents a new modality in drug development, allowing development of therapeutic agents for targets previously considered undruggable. Successful target engagement requires the formation of a ternary complex (TC) when the ligand brings its target protein in contact with an E3 ubiquitin ligase. Unlike traditional drugs, where target engagement can be described by a simple bimolecular equilibrium equation, similar mathematical tools are currently not available to describe TC formation in a universal manner. This current limitation substantially increases the challenges of developing drugs with targeted protein degradation mechanism. In this article, I provide a full, exact, and universal mathematical description of the TC system at equilibrium for the first time. I have also constructed a comprehensive suite of mathematical tools for quantitative measurement of target engagement and equilibrium constants from experimental data. Mechanistic explanations are provided for many common challenges associated with developing this type of therapeutic agent. Insights from these analyses provide testable hypotheses and grant direction to drug development efforts in this promising area. The mathematical and analytical tools described in this article may also have broader applications in other areas of biology and chemistry in which ternary complexes are observed.
Collapse
Affiliation(s)
- Bomie Han
- Department of Molecular Pharmacology, Discovery Chemistry Research and Technologies, Lilly Research Laboratories, Eli Lilly and Co., Indianapolis, Indiana, USA.
| |
Collapse
|
10
|
Gaillard H, Santos-Pereira JM, Aguilera A. The Nup84 complex coordinates the DNA damage response to warrant genome integrity. Nucleic Acids Res 2019; 47:4054-4067. [PMID: 30715474 PMCID: PMC6486642 DOI: 10.1093/nar/gkz066] [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: 06/21/2018] [Revised: 01/24/2019] [Accepted: 01/25/2019] [Indexed: 02/07/2023] Open
Abstract
DNA lesions interfere with cellular processes such as transcription and replication and need to be adequately resolved to warrant genome integrity. Beyond their primary role in molecule transport, nuclear pore complexes (NPCs) function in other processes such as transcription, nuclear organization and DNA double strand break (DSB) repair. Here we found that the removal of UV-induced DNA lesions by nucleotide excision repair (NER) is compromised in the absence of the Nup84 nuclear pore component. Importantly, nup84Δ cells show an exacerbated sensitivity to UV in early S phase and delayed replication fork progression, suggesting that unrepaired spontaneous DNA lesions persist during S phase. In addition, nup84Δ cells are defective in the repair of replication-born DSBs by sister chromatid recombination (SCR) and rely on post-replicative repair functions for normal proliferation, indicating dysfunctions in the cellular pathways that enable replication on damaged DNA templates. Altogether, our data reveal a central role of the NPC in the DNA damage response to facilitate replication progression through damaged DNA templates by promoting efficient NER and SCR and preventing chromosomal rearrangements.
Collapse
Affiliation(s)
- Hélène Gaillard
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - José M Santos-Pereira
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| |
Collapse
|
11
|
Höpfler M, Kern MJ, Straub T, Prytuliak R, Habermann BH, Pfander B, Jentsch S. Slx5/Slx8-dependent ubiquitin hotspots on chromatin contribute to stress tolerance. EMBO J 2019; 38:embj.2018100368. [PMID: 31015336 PMCID: PMC6545562 DOI: 10.15252/embj.2018100368] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 03/29/2019] [Accepted: 04/03/2019] [Indexed: 12/27/2022] Open
Abstract
Chromatin is a highly regulated environment, and protein association with chromatin is often controlled by post‐translational modifications and the corresponding enzymatic machinery. Specifically, SUMO‐targeted ubiquitin ligases (STUbLs) have emerged as key players in nuclear quality control, genome maintenance, and transcription. However, how STUbLs select specific substrates among myriads of SUMOylated proteins on chromatin remains unclear. Here, we reveal a remarkable co‐localization of the budding yeast STUbL Slx5/Slx8 and ubiquitin at seven genomic loci that we term “ubiquitin hotspots”. Ubiquitylation at these sites depends on Slx5/Slx8 and protein turnover on the Cdc48 segregase. We identify the transcription factor‐like Ymr111c/Euc1 to associate with these sites and to be a critical determinant of ubiquitylation. Euc1 specifically targets Slx5/Slx8 to ubiquitin hotspots via bipartite binding of Slx5 that involves the Slx5 SUMO‐interacting motifs and an additional, novel substrate recognition domain. Interestingly, the Euc1‐ubiquitin hotspot pathway acts redundantly with chromatin modifiers of the H2A.Z and Rpd3L pathways in specific stress responses. Thus, our data suggest that STUbL‐dependent ubiquitin hotspots shape chromatin during stress adaptation.
Collapse
Affiliation(s)
- Markus Höpfler
- Max Planck Institute of Biochemistry, Molecular Cell Biology, Martinsried, Germany
| | - Maximilian J Kern
- Max Planck Institute of Biochemistry, Molecular Cell Biology, Martinsried, Germany
| | - Tobias Straub
- Biomedizinisches Centrum, Core Facility Bioinformatics, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Roman Prytuliak
- Max Planck Institute of Biochemistry, Computational Biology Group, Martinsried, Germany
| | - Bianca H Habermann
- Max Planck Institute of Biochemistry, Computational Biology Group, Martinsried, Germany.,Aix-Marseille Univ, CNRS, IBDM UMR 7288, Marseille Cedex 9, France
| | - Boris Pfander
- Max Planck Institute of Biochemistry, DNA Replication and Genome Integrity, Martinsried, Germany
| | - Stefan Jentsch
- Max Planck Institute of Biochemistry, Molecular Cell Biology, Martinsried, Germany
| |
Collapse
|