1
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Shah R, Aslam MA, Spanjaard A, de Groot D, Zürcher LM, Altelaar M, Hoekman L, Pritchard CEJ, Pilzecker B, van den Berk PCM, Jacobs H. Dual role of proliferating cell nuclear antigen monoubiquitination in facilitating Fanconi anemia-mediated interstrand crosslink repair. PNAS NEXUS 2024; 3:pgae242. [PMID: 38957451 PMCID: PMC11217772 DOI: 10.1093/pnasnexus/pgae242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 06/03/2024] [Indexed: 07/04/2024]
Abstract
The Fanconi anemia (FA) repair pathway governs repair of highly genotoxic DNA interstrand crosslinks (ICLs) and relies on translesion synthesis (TLS). TLS is facilitated by REV1 or site-specific monoubiquitination of proliferating cell nuclear antigen (PCNA) (PCNA-Ub) at lysine 164 (K164). A PcnaK164R/K164R but not Rev1-/- mutation renders mammals hypersensitive to ICLs. Besides the FA pathway, alternative pathways have been associated with ICL repair (1, 2), though the decision making between those remains elusive. To study the dependence and relevance of PCNA-Ub in FA repair, we intercrossed PcnaK164R/+; Fancg-/+ mice. A combined mutation (PcnaK164R/K164R; Fancg-/- ) was found embryonically lethal. RNA-seq of primary double-mutant (DM) mouse embryonic fibroblasts (MEFs) revealed elevated levels of replication stress-induced checkpoints. To exclude stress-induced confounders, we utilized a Trp53 knock-down to obtain a model to study ICL repair in depth. Regarding ICL-induced cell toxicity, cell cycle arrest, and replication fork progression, single-mutant and DM MEFs were found equally sensitive, establishing PCNA-Ub to be critical for FA-ICL repair. Immunoprecipitation and spectrometry-based analysis revealed an unknown role of PCNA-Ub in excluding mismatch recognition complex MSH2/MSH6 from being recruited to ICLs. In conclusion, our results uncovered a dual function of PCNA-Ub in ICL repair, i.e. exclude MSH2/MSH6 recruitment to channel the ICL toward canonical FA repair, in addition to its established role in coordinating TLS opposite the unhooked ICL.
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Affiliation(s)
- Ronak Shah
- Department of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Muhammad Assad Aslam
- Department of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Department/Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Bosan Road, 60800 Multan, Pakistan
| | - Aldo Spanjaard
- Department of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Daniel de Groot
- Department of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Lisa M Zürcher
- Department of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Maarten Altelaar
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University and Netherlands Proteomics Centre, Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Liesbeth Hoekman
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Colin E J Pritchard
- Mouse Clinic for Cancer and Aging Transgenic Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Bas Pilzecker
- Department of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Paul C M van den Berk
- Department of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Heinz Jacobs
- Department of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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2
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Dhawka L, Palfini V, Hambright E, Blanco I, Poon C, Kahl A, Resch U, Bhawal R, Benakis C, Balachandran V, Holder A, Zhang S, Iadecola C, Hochrainer K. Post-ischemic ubiquitination at the postsynaptic density reversibly influences the activity of ischemia-relevant kinases. Commun Biol 2024; 7:321. [PMID: 38480905 PMCID: PMC10937959 DOI: 10.1038/s42003-024-06009-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 03/04/2024] [Indexed: 03/17/2024] Open
Abstract
Ubiquitin modifications alter protein function and stability, thereby regulating cell homeostasis and viability, particularly under stress. Ischemic stroke induces protein ubiquitination at the ischemic periphery, wherein cells remain viable, however the identity of ubiquitinated proteins is unknown. Here, we employed a proteomics approach to identify these proteins in mice undergoing ischemic stroke. The data are available in a searchable web interface ( https://hochrainerlab.shinyapps.io/StrokeUbiOmics/ ). We detected increased ubiquitination of 198 proteins, many of which localize to the postsynaptic density (PSD) of glutamatergic neurons. Among these were proteins essential for maintaining PSD architecture, such as PSD95, as well as NMDA and AMPA receptor subunits. The largest enzymatic group at the PSD with elevated post-ischemic ubiquitination were kinases, such as CaMKII, PKC, Cdk5, and Pyk2, whose aberrant activities are well-known to contribute to post-ischemic neuronal death. Concurrent phospho-proteomics revealed altered PSD-associated phosphorylation patterns, indicative of modified kinase activities following stroke. PSD-located CaMKII, PKC, and Cdk5 activities were decreased while Pyk2 activity was increased after stroke. Removal of ubiquitin restored kinase activities to pre-stroke levels, identifying ubiquitination as the responsible molecular mechanism for post-ischemic kinase regulation. These findings unveil a previously unrecognized role of ubiquitination in the regulation of essential kinases involved in ischemic injury.
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Affiliation(s)
- Luvna Dhawka
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Victoria Palfini
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Emma Hambright
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Ismary Blanco
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Carrie Poon
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Anja Kahl
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Ulrike Resch
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Ruchika Bhawal
- Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Corinne Benakis
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Institute for Stroke and Dementia Research, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Vaishali Balachandran
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Alana Holder
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Sheng Zhang
- Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Costantino Iadecola
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Karin Hochrainer
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
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3
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Li D, Jing J, Dong X, Zhang C, Wang J, Wan X. Activating transcription factor 3: A potential therapeutic target for inflammatory pulmonary diseases. Immun Inflamm Dis 2023; 11:e1028. [PMID: 37773692 PMCID: PMC10515505 DOI: 10.1002/iid3.1028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 09/05/2023] [Accepted: 09/09/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Activating transcription factor 3 (ATF3) is a nuclear protein that is widely expressed in a variety of cells. It is a stress-inducible transcription gene and a member of the activating transcription factor/cAMP responsive element-binding protein (ATF/CREB) family. METHODS The comprehensive literature review was conducted by searching PubMed and Google Scholar. Search terms used were "ATF3", "ATF3 and (ALI or ARDS)", "ATF3 and COPD", "ATF3 and PF", and "ATF3 and Posttranslational modifications". RESULTS Recent studies have shown that ATF3 plays a critical role in many inflammatory pulmonary diseases, including acute lung injury (ALI)/acute respiratory distress syndrome (ARDS), chronic obstructive pulmonary disease (COPD), and pulmonary fibrosis (PF). ATF3 participates in many signaling pathways and complex pathophysiological processes, such as inflammation, immunity, endoplasmic reticulum stress, and cell proliferation. However, the role of ATF3 in current studies is controversial, and there are reports showing that ATF3 plays different roles in different pulmonary diseases. CONCLUSIONS In this review, we first summarized the structure, function, and mechanism of ATF3 in various inflammatory pulmonary diseases. The impact of ATF3 on disease pathogenesis and the clinical implications was particularly focused on, with an overall aim to identify new targets for treating inflammatory pulmonary diseases.
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Affiliation(s)
- Dandan Li
- Department of Critical Care MedicineThe First Affiliated Hospital of Dalian Medical UniversityDalianChina
| | - Juanjuan Jing
- Department of Critical Care MedicineThe First Affiliated Hospital of Dalian Medical UniversityDalianChina
| | - Xue Dong
- Department of Critical Care MedicineThe First Affiliated Hospital of Dalian Medical UniversityDalianChina
| | - Chenyang Zhang
- Department of Critical Care MedicineThe First Affiliated Hospital of Dalian Medical UniversityDalianChina
| | - Jia Wang
- Department of Critical Care MedicineThe First Affiliated Hospital of Dalian Medical UniversityDalianChina
| | - Xianyao Wan
- Department of Critical Care MedicineThe First Affiliated Hospital of Dalian Medical UniversityDalianChina
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4
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Dhawka L, Palfini V, Hambright E, Blanco I, Poon C, Kahl A, Resch U, Bhawal R, Benakis C, Balachandran V, Zhang S, Iadecola C, Hochrainer K. Post-ischemic ubiquitination at the postsynaptic density reversibly influences the activity of ischemia-relevant kinases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.552860. [PMID: 37662420 PMCID: PMC10473581 DOI: 10.1101/2023.08.21.552860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Ubiquitin modifications alter protein function and stability, thereby regulating cell homeostasis and viability, particularly under stress. Ischemic stroke induces protein ubiquitination at the ischemic periphery, wherein cells remain viable, however the identity of ubiquitinated proteins is unknown. Here, we employed a proteomics approach to identify these proteins in mice undergoing ischemic stroke. The data are available in a searchable web interface ( https://hochrainerlab.shinyapps.io/StrokeUbiOmics/ ). We detected increased ubiquitination of 198 proteins, many of which localize to the postsynaptic density (PSD) of glutamatergic neurons. Among these were proteins essential for maintaining PSD architecture, such as PSD95, as well as NMDA and AMPA receptor subunits. The largest enzymatic group at the PSD with elevated post-ischemic ubiquitination were kinases, such as CaMKII, PKC, Cdk5, and Pyk2, whose aberrant activities are well-known to contribute to post-ischemic neuronal death. Concurrent phospho-proteomics revealed altered PSD-associated phosphorylation patterns, indicative of modified kinase activities following stroke. PSD-located CaMKII, PKC, and Cdk5 activities were decreased while Pyk2 activity was increased after stroke. Removal of ubiquitin restored kinase activities to pre-stroke levels, identifying ubiquitination as the responsible molecular mechanism for post-ischemic kinase regulation. These findings unveil a previously unrecognized role of ubiquitination in the regulation of essential kinases involved in ischemic injury.
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5
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Benton D, Chernoff J. TRIMming away colon cancer: TRIM21-mediated ubiquitination as an activator of the Hippo tumor suppressor pathway. Cell Chem Biol 2023; 30:699-701. [PMID: 37478825 DOI: 10.1016/j.chembiol.2023.06.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/23/2023]
Abstract
In this issue of Cell Chemical Biology, Liu et al.1 identify TRIM21-mediated ubiquitination of the Hippo pathway kinase MST2, promoting its dimerization and activation. The antidepressant Vilazodone was found to bind to TRIM21, enhancing its activity toward MST2, increasing Hippo activation, and reducing colorectal cancer metastasis.
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Affiliation(s)
- Dorothy Benton
- Cancer Signaling and Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Jonathan Chernoff
- Cancer Signaling and Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.
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6
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The ubiquitination landscape of the influenza A virus polymerase. Nat Commun 2023; 14:787. [PMID: 36774438 PMCID: PMC9922279 DOI: 10.1038/s41467-023-36389-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 01/30/2023] [Indexed: 02/13/2023] Open
Abstract
During influenza A virus (IAV) infections, viral proteins are targeted by cellular E3 ligases for modification with ubiquitin. Here, we decipher and functionally explore the ubiquitination landscape of the IAV polymerase proteins during infection of human alveolar epithelial cells by applying mass spectrometry analysis of immuno-purified K-ε-GG (di-glycyl)-remnant-bearing peptides. We have identified 59 modified lysines across the three subunits, PB2, PB1 and PA of the viral polymerase of which 17 distinctively affect mRNA transcription, vRNA replication and the generation of recombinant viruses via non-proteolytic mechanisms. Moreover, further functional and in silico analysis indicate that ubiquitination at K578 in the PB1 thumb domain is mechanistically linked to dynamic structural transitions of the viral polymerase that are required for vRNA replication. Mutations K578A and K578R differentially affect the generation of recombinant viruses by impeding cRNA and vRNA synthesis, NP binding as well as polymerase dimerization. Collectively, our results demonstrate that the ubiquitin-mediated charge neutralization at PB1-K578 disrupts the interaction to an unstructured loop in the PB2 N-terminus that is required to coordinate polymerase dimerization and facilitate vRNA replication. This provides evidence that IAV exploits the cellular ubiquitin system to modulate the activity of the viral polymerase for viral replication.
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7
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Jin Q, Gutierrez Diaz B, Pieters T, Zhou Y, Narang S, Fijalkwoski I, Borin C, Van Laere J, Payton M, Cho BK, Han C, Sun L, Serafin V, Yacu G, Von Loocke W, Basso G, Veltri G, Dreveny I, Ben-Sahra I, Goo YA, Safgren SL, Tsai YC, Bornhauser B, Suraneni PK, Gaspar-Maia A, Kandela I, Van Vlierberghe P, Crispino JD, Tsirigos A, Ntziachristos P. Oncogenic deubiquitination controls tyrosine kinase signaling and therapy response in acute lymphoblastic leukemia. SCIENCE ADVANCES 2022; 8:eabq8437. [PMID: 36490346 PMCID: PMC9733937 DOI: 10.1126/sciadv.abq8437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
Dysregulation of kinase signaling pathways favors tumor cell survival and therapy resistance in cancer. Here, we reveal a posttranslational regulation of kinase signaling and nuclear receptor activity via deubiquitination in T cell acute lymphoblastic leukemia (T-ALL). We observed that the ubiquitin-specific protease 11 (USP11) is highly expressed and associates with poor prognosis in T-ALL. USP11 ablation inhibits leukemia progression in vivo, sparing normal hematopoiesis. USP11 forms a complex with USP7 to deubiquitinate the oncogenic lymphocyte cell-specific protein-tyrosine kinase (LCK) and enhance its activity. Impairment of LCK activity leads to increased glucocorticoid receptor (GR) expression and glucocorticoids sensitivity. Genetic knockout of USP7 improved the antileukemic efficacy of glucocorticoids in vivo. The transcriptional activation of GR target genes is orchestrated by the deubiquitinase activity and mediated via an increase in enhancer-promoter interaction intensity. Our data unveil how dysregulated deubiquitination controls leukemia survival and drug resistance, suggesting previously unidentified therapeutic combinations toward targeting leukemia.
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Affiliation(s)
- Qi Jin
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Blanca Gutierrez Diaz
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Tim Pieters
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Yalu Zhou
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Sonali Narang
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, Office of Science and Research, New York University School of Medicine, New York, NY, USA
| | - Igor Fijalkwoski
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Cristina Borin
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Jolien Van Laere
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium
| | - Monique Payton
- Division of Experimental Hematology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Byoung-Kyu Cho
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Cuijuan Han
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Limin Sun
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Valentina Serafin
- Oncohematology Laboratory, Department of Women’s and Children’s Health, University of Padova, Padova, Italy
- Department of Surgery Oncology and Gastroenterology, Oncology and Immunology Section, University of Padova, Padova, Italy
| | - George Yacu
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
| | - Wouter Von Loocke
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Giuseppe Basso
- Oncohematology Laboratory, Department of Women’s and Children’s Health, University of Padova, Padova, Italy
- Department of Surgery Oncology and Gastroenterology, Oncology and Immunology Section, University of Padova, Padova, Italy
| | - Giulia Veltri
- Oncohematology Laboratory, Department of Women’s and Children’s Health, University of Padova, Padova, Italy
| | - Ingrid Dreveny
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Issam Ben-Sahra
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Young Ah Goo
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Stephanie L. Safgren
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Yi-Chien Tsai
- University Children’s Hospital, Division of Pediatric Oncology, University of Zurich, Zurich, Switzerland
| | - Beat Bornhauser
- University Children’s Hospital, Division of Pediatric Oncology, University of Zurich, Zurich, Switzerland
| | | | - Alexandre Gaspar-Maia
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Irawati Kandela
- Center for Developmental Therapeutics, Northwestern University, Evanston, IL, USA
| | - Pieter Van Vlierberghe
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - John D. Crispino
- Division of Experimental Hematology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, Office of Science and Research, New York University School of Medicine, New York, NY, USA
| | - Panagiotis Ntziachristos
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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8
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Weigle AT, Feng J, Shukla D. Thirty years of molecular dynamics simulations on posttranslational modifications of proteins. Phys Chem Chem Phys 2022; 24:26371-26397. [PMID: 36285789 PMCID: PMC9704509 DOI: 10.1039/d2cp02883b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Posttranslational modifications (PTMs) are an integral component to how cells respond to perturbation. While experimental advances have enabled improved PTM identification capabilities, the same throughput for characterizing how structural changes caused by PTMs equate to altered physiological function has not been maintained. In this Perspective, we cover the history of computational modeling and molecular dynamics simulations which have characterized the structural implications of PTMs. We distinguish results from different molecular dynamics studies based upon the timescales simulated and analysis approaches used for PTM characterization. Lastly, we offer insights into how opportunities for modern research efforts on in silico PTM characterization may proceed given current state-of-the-art computing capabilities and methodological advancements.
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Affiliation(s)
- Austin T Weigle
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jiangyan Feng
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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9
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Trulsson F, Akimov V, Robu M, van Overbeek N, Berrocal DAP, Shah RG, Cox J, Shah GM, Blagoev B, Vertegaal ACO. Deubiquitinating enzymes and the proteasome regulate preferential sets of ubiquitin substrates. Nat Commun 2022; 13:2736. [PMID: 35585066 PMCID: PMC9117253 DOI: 10.1038/s41467-022-30376-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 04/27/2022] [Indexed: 12/24/2022] Open
Abstract
The ubiquitin-proteasome axis has been extensively explored at a system-wide level, but the impact of deubiquitinating enzymes (DUBs) on the ubiquitinome remains largely unknown. Here, we compare the contributions of the proteasome and DUBs on the global ubiquitinome, using UbiSite technology, inhibitors and mass spectrometry. We uncover large dynamic ubiquitin signalling networks with substrates and sites preferentially regulated by DUBs or by the proteasome, highlighting the role of DUBs in degradation-independent ubiquitination. DUBs regulate substrates via at least 40,000 unique sites. Regulated networks of ubiquitin substrates are involved in autophagy, apoptosis, genome integrity, telomere integrity, cell cycle progression, mitochondrial function, vesicle transport, signal transduction, transcription, pre-mRNA splicing and many other cellular processes. Moreover, we show that ubiquitin conjugated to SUMO2/3 forms a strong proteasomal degradation signal. Interestingly, PARP1 is hyper-ubiquitinated in response to DUB inhibition, which increases its enzymatic activity. Our study uncovers key regulatory roles of DUBs and provides a resource of endogenous ubiquitination sites to aid the analysis of substrate specific ubiquitin signalling.
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Affiliation(s)
- Fredrik Trulsson
- Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Vyacheslav Akimov
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Mihaela Robu
- Laboratory for Skin Cancer Research, CHU de Québec Laval University Hospital Research Centre, Québec, QC, Canada
| | - Nila van Overbeek
- Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | | | - Rashmi G Shah
- Laboratory for Skin Cancer Research, CHU de Québec Laval University Hospital Research Centre, Québec, QC, Canada
| | - Jürgen Cox
- Computational Systems Biochemistry Research Group, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Girish M Shah
- Laboratory for Skin Cancer Research, CHU de Québec Laval University Hospital Research Centre, Québec, QC, Canada
| | - Blagoy Blagoev
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
| | - Alfred C O Vertegaal
- Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands.
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10
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Johnson JR, Crosby DC, Hultquist JF, Kurland AP, Adhikary P, Li D, Marlett J, Swann J, Hüttenhain R, Verschueren E, Johnson TL, Newton BW, Shales M, Simon VA, Beltrao P, Frankel AD, Marson A, Cox JS, Fregoso OI, Young JAT, Krogan NJ. Global post-translational modification profiling of HIV-1-infected cells reveals mechanisms of host cellular pathway remodeling. Cell Rep 2022; 39:110690. [PMID: 35417684 PMCID: PMC9429972 DOI: 10.1016/j.celrep.2022.110690] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 03/07/2022] [Accepted: 03/24/2022] [Indexed: 01/03/2023] Open
Abstract
Viruses must effectively remodel host cellular pathways to replicate and evade immune defenses, and they must do so with limited genomic coding capacity. Targeting post-translational modification (PTM) pathways provides a mechanism by which viruses can broadly and rapidly transform a hostile host environment into a hospitable one. We use mass spectrometry-based proteomics to quantify changes in protein abundance and two PTM types-phosphorylation and ubiquitination-in response to HIV-1 infection with viruses harboring targeted deletions of a subset of HIV-1 genes. PTM analysis reveals a requirement for Aurora kinase activity in HIV-1 infection and identified putative substrates of a phosphatase that is degraded during infection. Finally, we demonstrate that the HIV-1 Vpr protein inhibits histone H1 ubiquitination, leading to defects in DNA repair.
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Affiliation(s)
- Jeffrey R Johnson
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA; Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA.
| | - David C Crosby
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Judd F Hultquist
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA; Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Andrew P Kurland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Prithy Adhikary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Donna Li
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - John Marlett
- Viral Vector Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Justine Swann
- Viral Vector Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Ruth Hüttenhain
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA; Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Erik Verschueren
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA; Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Tasha L Johnson
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA; Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Billy W Newton
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA; Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Michael Shales
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA; Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Viviana A Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CD10 1SD, UK
| | - Alan D Frankel
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94720, USA; Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Jeffery S Cox
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Oliver I Fregoso
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - John A T Young
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA; Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA.
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11
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Carroll EC, Marqusee S. Site-specific ubiquitination: Deconstructing the degradation tag. Curr Opin Struct Biol 2022; 73:102345. [PMID: 35247748 DOI: 10.1016/j.sbi.2022.102345] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/28/2021] [Accepted: 01/17/2022] [Indexed: 02/04/2023]
Abstract
Ubiquitin is a small eukaryotic protein so named for its cellular abundance and originally recognized for its role as the posttranslational modification (PTM) "tag" condemning substrates to degradation by the 26S proteasome. Since its discovery in the 1970s, protein ubiquitination has also been identified as a key regulatory feature in dozens of non-degradative cellular processes. This myriad of roles illustrates the versatility of ubiquitin as a PTM; however, understanding the cellular and molecular factors that enable discrimination between degradative versus non-degradative ubiquitination events has been a persistent challenge. Here, we discuss recent advances in uncovering how site-specificity - the exact residue that gets modified - modulates distinct protein fates and cellular outcomes with an emphasis on how ubiquitination site specificity regulates proteasomal degradation. We explore recent advances in structural biology, biophysics, and cell biology that have enabled a broader understanding of the role of ubiquitination in altering the dynamics of the target protein, including implications for the design of targeted protein degradation therapeutics.
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Affiliation(s)
- Emma C Carroll
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, 94038, USA.
| | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, 94720, USA; QB3 Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA, 94720, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, 94720, USA.
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12
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Chang SC, Zhang BX, Ding JL. E2-E3 ubiquitin enzyme pairing - partnership in provoking or mitigating cancers. Biochim Biophys Acta Rev Cancer 2022; 1877:188679. [DOI: 10.1016/j.bbcan.2022.188679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/31/2021] [Accepted: 01/11/2022] [Indexed: 02/08/2023]
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13
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Affinity capture in bottom-up protein analysis - Overview of current status of proteolytic peptide capture using antibodies and molecularly imprinted polymers. Anal Chim Acta 2021; 1182:338714. [PMID: 34602193 DOI: 10.1016/j.aca.2021.338714] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/17/2022]
Abstract
Antibody-based affinity capture has become the gold standard in sample preparation for determination of low-abundance protein biomarkers in biological matrices prior to liquid chromatography-mass spectrometry (LC-MS) determination. This comprises both capture of intact proteins prior to the digestion step and capture of proteolytic peptides after digestion of the sample. The latter can be performed both using antibodies specifically developed to capture target proteolytic peptides, as well as by the less explored use of anti-protein antibodies to capture the proteolytic epitope peptide. Molecularly imprinted polymers (MIPs), also called plastic antibodies are another affinity-based approach emerging as sample preparation technique in LC-MS based protein biomarker analysis. The current review gives a critical and comprehensive overview of proteolytic peptide capture using antibodies and MIPs in LC-MS based protein biomarker determination during the last five years. The main emphasis is on capture of non-modified peptides, while a brief overview of affinity capture of peptides containing post-translational modifications (PTMs) is provided.
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14
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Garcia LR, Tenev T, Newman R, Haich RO, Liccardi G, John SW, Annibaldi A, Yu L, Pardo M, Young SN, Fitzgibbon C, Fernando W, Guppy N, Kim H, Liang LY, Lucet IS, Kueh A, Roxanis I, Gazinska P, Sims M, Smyth T, Ward G, Bertin J, Beal AM, Geddes B, Choudhary JS, Murphy JM, Aurelia Ball K, Upton JW, Meier P. Ubiquitylation of MLKL at lysine 219 positively regulates necroptosis-induced tissue injury and pathogen clearance. Nat Commun 2021; 12:3364. [PMID: 34099649 PMCID: PMC8184782 DOI: 10.1038/s41467-021-23474-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 04/29/2021] [Indexed: 12/19/2022] Open
Abstract
Necroptosis is a lytic, inflammatory form of cell death that not only contributes to pathogen clearance but can also lead to disease pathogenesis. Necroptosis is triggered by RIPK3-mediated phosphorylation of MLKL, which is thought to initiate MLKL oligomerisation, membrane translocation and membrane rupture, although the precise mechanism is incompletely understood. Here, we show that K63-linked ubiquitin chains are attached to MLKL during necroptosis and that ubiquitylation of MLKL at K219 significantly contributes to the cytotoxic potential of phosphorylated MLKL. The K219R MLKL mutation protects animals from necroptosis-induced skin damage and renders cells resistant to pathogen-induced necroptosis. Mechanistically, we show that ubiquitylation of MLKL at K219 is required for higher-order assembly of MLKL at membranes, facilitating its rupture and necroptosis. We demonstrate that K219 ubiquitylation licenses MLKL activity to induce lytic cell death, suggesting that necroptotic clearance of pathogens as well as MLKL-dependent pathologies are influenced by the ubiquitin-signalling system.
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Affiliation(s)
- Laura Ramos Garcia
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - Tencho Tenev
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Richard Newman
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Rachel O Haich
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Gianmaria Liccardi
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Institute of Biochemistry I, Medical Faculty, Joseph-Stelzmann-Str. 44, University of Cologne, Cologne, Germany
| | - Sidonie Wicky John
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Alessandro Annibaldi
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Lu Yu
- Functional Proteomics Group, The Institute of Cancer Research, London, UK
| | - Mercedes Pardo
- Functional Proteomics Group, The Institute of Cancer Research, London, UK
| | - Samuel N Young
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Cheree Fitzgibbon
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Winnie Fernando
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Naomi Guppy
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Hyojin Kim
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Lung-Yu Liang
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Isabelle S Lucet
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Andrew Kueh
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Ioannis Roxanis
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Patrycja Gazinska
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | | | | | - John Bertin
- Innate Immunity Research Unit, GlaxoSmithKline, Collegeville, PA, USA
- Immunology and Inflammation Research Therapeutic Area at Sanofi, Cambridge, MA, USA
| | - Allison M Beal
- Innate Immunity Research Unit, GlaxoSmithKline, Collegeville, PA, USA
| | - Brad Geddes
- Innate Immunity Research Unit, GlaxoSmithKline, Collegeville, PA, USA
| | - Jyoti S Choudhary
- Functional Proteomics Group, The Institute of Cancer Research, London, UK
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - K Aurelia Ball
- Department of Chemistry, Skidmore College, Saratoga Springs, NY, USA
| | - Jason W Upton
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Pascal Meier
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
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15
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Ubiquitination and Deubiquitination in Oral Disease. Int J Mol Sci 2021; 22:ijms22115488. [PMID: 34070986 PMCID: PMC8197098 DOI: 10.3390/ijms22115488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/15/2021] [Accepted: 05/18/2021] [Indexed: 01/07/2023] Open
Abstract
Oral health is an integral part of the general health and well-being of individuals. The presence of oral disease is potentially indicative of a number of systemic diseases and may contribute to their early diagnosis and treatment. The ubiquitin (Ub) system has been shown to play a role in cellular immune response, cellular development, and programmed cell death. Ubiquitination is a post-translational modification that occurs in eukaryotes. Its mechanism involves a number of factors, including Ub-activating enzymes, Ub-conjugating enzymes, and Ub protein ligases. Deubiquitinating enzymes, which are proteases that reversely modify proteins by removing Ub or Ub-like molecules or remodeling Ub chains on target proteins, have recently been regarded as crucial regulators of ubiquitination-mediated degradation and are known to significantly affect cellular pathways, a number of biological processes, DNA damage response, and DNA repair pathways. Research has increasingly shown evidence of the relationship between ubiquitination, deubiquitination, and oral disease. This review investigates recent progress in discoveries in diseased oral sites and discusses the roles of ubiquitination and deubiquitination in oral disease.
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16
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González-Rubio G, Sellers-Moya Á, Martín H, Molina M. A walk-through MAPK structure and functionality with the 30-year-old yeast MAPK Slt2. Int Microbiol 2021; 24:531-543. [PMID: 33993419 DOI: 10.1007/s10123-021-00183-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/29/2021] [Accepted: 05/05/2021] [Indexed: 01/10/2023]
Abstract
Mitogen-activated protein kinases (MAPKs) are evolutionarily conserved signaling proteins involved in the regulation of most eukaryotic cellular processes. They are downstream components of essential signal transduction pathways activated by the external stimuli, in which the signal is conveyed through phosphorylation cascades. The excellent genetic and biochemical tractability of simple eukaryotes such as Saccharomyces cerevisiae has significantly contributed to gain fundamental information into the physiology of these key proteins. The budding yeast MAPK Slt2 was identified 30 years ago and was later revealed as a fundamental element of the cell wall integrity (CWI) pathway, one of the five MAPK routes of S. cerevisiae. As occurs with other MAPKs, whereas Slt2 displays the core typical structural traits of eukaryotic protein kinases, it also features conserved domains among MAPKs that allow an exquisite spatio-temporal regulation of their activity and binding to activating kinases, downregulatory phosphatases, or nuclear transcription factors. Additionally, Slt2 bears a regulatory extra C-terminal tail unique among S. cerevisiae MAPKs. Here, we review the structural and functional basis for the signaling role of Slt2 in the context of the molecular architecture of this important family of protein kinases.
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Affiliation(s)
- Gema González-Rubio
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Universidad Complutense de Madrid, Pza. Ramón y Cajal s/n, 28040, Madrid, Spain
| | - Ángela Sellers-Moya
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Universidad Complutense de Madrid, Pza. Ramón y Cajal s/n, 28040, Madrid, Spain
| | - Humberto Martín
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Universidad Complutense de Madrid, Pza. Ramón y Cajal s/n, 28040, Madrid, Spain.
| | - María Molina
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Universidad Complutense de Madrid, Pza. Ramón y Cajal s/n, 28040, Madrid, Spain.
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17
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Mechanistic basis for ubiquitin modulation of a protein energy landscape. Proc Natl Acad Sci U S A 2021; 118:2025126118. [PMID: 33723075 DOI: 10.1073/pnas.2025126118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ubiquitin is a common posttranslational modification canonically associated with targeting proteins to the 26S proteasome for degradation and also plays a role in numerous other nondegradative cellular processes. Ubiquitination at certain sites destabilizes the substrate protein, with consequences for proteasomal processing, while ubiquitination at other sites has little energetic effect. How this site specificity-and, by extension, the myriad effects of ubiquitination on substrate proteins-arises remains unknown. Here, we systematically characterize the atomic-level effects of ubiquitination at various sites on a model protein, barstar, using a combination of NMR, hydrogen-deuterium exchange mass spectrometry, and molecular dynamics simulation. We find that, regardless of the site of modification, ubiquitination does not induce large structural rearrangements in the substrate. Destabilizing modifications, however, increase fluctuations from the native state resulting in exposure of the substrate's C terminus. Both of the sites occur in regions of barstar with relatively high conformational flexibility. Nevertheless, destabilization appears to occur through different thermodynamic mechanisms, involving a reduction in entropy in one case and a loss in enthalpy in another. By contrast, ubiquitination at a nondestabilizing site protects the substrate C terminus through intermittent formation of a structural motif with the last three residues of ubiquitin. Thus, the biophysical effects of ubiquitination at a given site depend greatly on local context. Taken together, our results reveal how a single posttranslational modification can generate a broad array of distinct effects, providing a framework to guide the design of proteins and therapeutics with desired degradation and quality control properties.
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18
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Perez-Jimenez E, Viana R, Muñoz-Ballester C, Vendrell-Tornero C, Moll-Diaz R, Garcia-Gimeno MA, Sanz P. Endocytosis of the glutamate transporter 1 is regulated by laforin and malin: Implications in Lafora disease. Glia 2020; 69:1170-1183. [PMID: 33368637 DOI: 10.1002/glia.23956] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/10/2020] [Accepted: 12/10/2020] [Indexed: 01/13/2023]
Abstract
Lafora disease (LD) is a fatal rare type of progressive myoclonus epilepsy that appears during early adolescence. The disease is caused by mutations in EPM2A or EPM2B genes, which encode laforin, a glucan phosphatase, and malin, an E3-ubiquitin ligase, respectively. Although the exact roles of laforin and malin are still not well understood, it is known that they work as a complex in which laforin recruits targets that will be ubiquitinated by malin. Recently, we suggested that the type of epilepsy that accompanies LD could be due to deficiencies in the function of the astrocytic glutamate transporter GLT-1. We described that astrocytes from LD mouse models presented decreased levels of GLT-1 at the plasma membrane, leading to increased levels of glutamate in the brain parenchyma. In this work, we present evidence indicating that in the absence of a functional laforin/malin complex (as in LD cellular models) there is an alteration in the ubiquitination of GLT-1, which could be the cause of the reduction in the levels of GLT-1 at the plasma membrane. On the contrary, overexpression of the laforin/malin complex promotes the retention of GLT-1 at the plasma membrane. This retention may be due to the direct ubiquitination of GLT-1 and/or to an opposite effect of this complex on the dynamics of the Nedd4.2-mediated endocytosis of the transporter. This work, therefore, presents new pieces of evidence on the regulation of GLT-1 by the laforin/malin complex, highlighting its value as a therapeutic target for the amelioration of the type of epilepsy that accompanies LD.
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Affiliation(s)
- Eva Perez-Jimenez
- Consejo Superior de Investigaciones Científicas, Instituto de Biomedicina de Valencia, Valencia, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Biomedicina de Valencia, Valencia, Spain
| | - Rosa Viana
- Consejo Superior de Investigaciones Científicas, Instituto de Biomedicina de Valencia, Valencia, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Biomedicina de Valencia, Valencia, Spain
| | - Carmen Muñoz-Ballester
- Consejo Superior de Investigaciones Científicas, Instituto de Biomedicina de Valencia, Valencia, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Biomedicina de Valencia, Valencia, Spain
| | - Carlos Vendrell-Tornero
- Consejo Superior de Investigaciones Científicas, Instituto de Biomedicina de Valencia, Valencia, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Biomedicina de Valencia, Valencia, Spain
| | - Raquel Moll-Diaz
- Consejo Superior de Investigaciones Científicas, Instituto de Biomedicina de Valencia, Valencia, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Biomedicina de Valencia, Valencia, Spain
| | | | - Pascual Sanz
- Consejo Superior de Investigaciones Científicas, Instituto de Biomedicina de Valencia, Valencia, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Biomedicina de Valencia, Valencia, Spain
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19
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Heim VJ, Dagley LF, Stafford CA, Hansen FM, Clayer E, Bankovacki A, Webb AI, Lucet IS, Silke J, Nachbur U. A regulatory region on RIPK2 is required for XIAP binding and NOD signaling activity. EMBO Rep 2020; 21:e50400. [PMID: 32954645 DOI: 10.15252/embr.202050400] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/30/2020] [Accepted: 08/13/2020] [Indexed: 01/01/2023] Open
Abstract
Signaling via the intracellular pathogen receptors nucleotide-binding oligomerization domain-containing proteins NOD1 and NOD2 requires receptor interacting kinase 2 (RIPK2), an adaptor kinase that can be targeted for the treatment of various inflammatory diseases. However, the molecular mechanisms of how RIPK2 contributes to NOD signaling are not completely understood. We generated FLAG-tagged RIPK2 knock-in mice using CRISPR/Cas9 technology to study NOD signaling mechanisms at the endogenous level. Using cells from these mice, we were able to generate a detailed map of post-translational modifications on RIPK2. Similar to other reports, we did not detect ubiquitination of RIPK2 lysine 209 during NOD2 signaling. However, using site-directed mutagenesis we identified a new regulatory region on RIPK2, which dictates the crucial interaction with the E3 ligase XIAP and downstream signaling outcomes.
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Affiliation(s)
- Valentin J Heim
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Vic., Australia
| | - Laura F Dagley
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Vic., Australia
| | - Che A Stafford
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fynn M Hansen
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Elise Clayer
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Vic., Australia
| | - Aleksandra Bankovacki
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Vic., Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Vic., Australia
| | - Isabelle S Lucet
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Vic., Australia
| | - John Silke
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Vic., Australia
| | - Ueli Nachbur
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Vic., Australia
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20
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Yin G, Zhang J, Nair V, Truong V, Chaia A, Petela J, Harrison J, Gorfe AA, Campbell SL. KRAS Ubiquitination at Lysine 104 Retains Exchange Factor Regulation by Dynamically Modulating the Conformation of the Interface. iScience 2020; 23:101448. [PMID: 32882514 PMCID: PMC7479270 DOI: 10.1016/j.isci.2020.101448] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/13/2020] [Accepted: 08/06/2020] [Indexed: 12/13/2022] Open
Abstract
RAS proteins function as highly regulated molecular switches that control cellular growth. In addition to regulatory proteins, RAS undergoes a number of posttranslational modifications (PTMs) that regulate its activity. Lysine 104, a hot spot for multiple PTMs, is a highly conserved residue that forms key interactions that stabilize the RAS helix-2(H2)/helix-3(H3) interface. Mutation at 104 attenuates interaction with guanine nucleotide exchange factors (GEFs), whereas ubiquitination at lysine 104 retains GEF regulation. To elucidate how ubiquitination modulates RAS function, we generated monoubiquitinated KRAS at 104 using chemical biology approaches and conducted biochemical, NMR, and computational analyses. We find that ubiquitination promotes a new dynamic interaction network and alters RAS conformational dynamics to retain GEF function. These findings reveal a mechanism by which ubiquitination can regulate protein function.
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Affiliation(s)
- Guowei Yin
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Jerry Zhang
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vinay Nair
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Vinh Truong
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Angelo Chaia
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Johnny Petela
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joseph Harrison
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Alemayehu A. Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Sharon L. Campbell
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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21
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Groppe JC. Induced degradation of protein kinases by bifunctional small molecules: a next-generation strategy. Expert Opin Drug Discov 2019; 14:1237-1253. [DOI: 10.1080/17460441.2019.1660641] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jay C. Groppe
- Department of Biomedical Sciences, Texas A&M University College of Dentistry, Dallas, TX, USA
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22
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Choi YM, An S, Bae S, Jung JH. Mdm2 is required for HDAC3 monoubiquitination and stability. Biochem Biophys Res Commun 2019; 517:353-358. [PMID: 31358320 DOI: 10.1016/j.bbrc.2019.07.052] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 07/17/2019] [Indexed: 01/01/2023]
Abstract
HDAC3, one of the class I histone deacetylase modulates epigenetic landscape through histone modification. HDAC3 also interacts with non-histone proteins including p53 for deacetylation. Moreover, HDAC3 serves as a transcriptional repressor, interacting with NCor1/SMRT complex. Although HDAC3 plays a critical role for cellular homeostasis, regulatory mechanism of HDAC3 have been poorly understood. Here we report a novel regulatory mechanism of HDAC3 about its monoubiquitination and stabilization by Mdm2. HDAC3 levels were increased by ectopic expression of Mdm2 and decreased by Mdm2 ablation in various cell lines. We found that Mdm2 directly interacts with HDAC3 and induces HDAC3 protein levels without alteration of mRNA levels. Ectopic expression of wild type but not RING mutant of Mdm2 increased HDAC3 monoubiquitination. In addition, MdmX is beneficial for mdm2-mediated HDAC3 regulation. Ablation of Mdm2 and Mdm2/MdmX decreased cell migration along with the decrease of HDAC3 levels. These data provide an evidence that Mdm2 positively regulates HDAC3 monoubiquitination and stability.
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Affiliation(s)
- Yeong Min Choi
- GeneCellPharm Corporation, 375 Munjeong 2(i)-dong, Songpa-gu Seoul, 05836, Republic of Korea
| | - Sungkwan An
- Research Institute for Molecular-Targeted Drugs, Department of Cosmetics Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Seunghee Bae
- Research Institute for Molecular-Targeted Drugs, Department of Cosmetics Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jin Hyuk Jung
- GeneCellPharm Corporation, 375 Munjeong 2(i)-dong, Songpa-gu Seoul, 05836, Republic of Korea.
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23
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Rinaldi L, Delle Donne R, Catalanotti B, Torres-Quesada O, Enzler F, Moraca F, Nisticò R, Chiuso F, Piccinin S, Bachmann V, Lindner HH, Garbi C, Scorziello A, Russo NA, Synofzik M, Stelzl U, Annunziato L, Stefan E, Feliciello A. Feedback inhibition of cAMP effector signaling by a chaperone-assisted ubiquitin system. Nat Commun 2019; 10:2572. [PMID: 31189917 PMCID: PMC6561907 DOI: 10.1038/s41467-019-10037-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 04/12/2019] [Indexed: 02/07/2023] Open
Abstract
Activation of G-protein coupled receptors elevates cAMP levels promoting dissociation of protein kinase A (PKA) holoenzymes and release of catalytic subunits (PKAc). This results in PKAc-mediated phosphorylation of compartmentalized substrates that control central aspects of cell physiology. The mechanism of PKAc activation and signaling have been largely characterized. However, the modes of PKAc inactivation by regulated proteolysis were unknown. Here, we identify a regulatory mechanism that precisely tunes PKAc stability and downstream signaling. Following agonist stimulation, the recruitment of the chaperone-bound E3 ligase CHIP promotes ubiquitylation and proteolysis of PKAc, thus attenuating cAMP signaling. Genetic inactivation of CHIP or pharmacological inhibition of HSP70 enhances PKAc signaling and sustains hippocampal long-term potentiation. Interestingly, primary fibroblasts from autosomal recessive spinocerebellar ataxia 16 (SCAR16) patients carrying germline inactivating mutations of CHIP show a dramatic dysregulation of PKA signaling. This suggests the existence of a negative feedback mechanism for restricting hormonally controlled PKA activities.
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Affiliation(s)
- Laura Rinaldi
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II, 80131, Naples, Italy
| | - Rossella Delle Donne
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II, 80131, Naples, Italy
| | - Bruno Catalanotti
- Department of Pharmacy, University Federico II, 80131, Naples, Italy
| | - Omar Torres-Quesada
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, A-6020, Innsbruck, Austria
| | - Florian Enzler
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, A-6020, Innsbruck, Austria
| | - Federica Moraca
- Department of Chemical Sciences, University Federico II, 80131, Naples, Italy
| | - Robert Nisticò
- European Brain Research Institute, Rita Levi-Montalcini Foundation and Department of Biology, University Tor Vergata, 00143, Rome, Italy
| | - Francesco Chiuso
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II, 80131, Naples, Italy
| | - Sonia Piccinin
- European Brain Research Institute, Rita Levi-Montalcini Foundation and Department of Biology, University Tor Vergata, 00143, Rome, Italy
| | - Verena Bachmann
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, A-6020, Innsbruck, Austria
| | - Herbert H Lindner
- Division of Clinical Biochemistry, Biocenter Medical University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Corrado Garbi
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II, 80131, Naples, Italy
| | - Antonella Scorziello
- Department of Neuroscience, Reproductive and Odontostomatological Sciences, University Federico II, 80131, Naples, Italy
| | | | - Matthis Synofzik
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research (HIH), University of Tübingen and German Center for Neurodegenerative Diseases (DZNE), 72076, Tübingen, Germany
| | - Ulrich Stelzl
- Institute of Pharmaceutical Sciences, University of Graz and BioTechMed-Graz, 8010, Graz, Austria
| | | | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, A-6020, Innsbruck, Austria
| | - Antonio Feliciello
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II, 80131, Naples, Italy.
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24
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Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II. PLoS Comput Biol 2019; 15:e1006796. [PMID: 31150387 PMCID: PMC6576796 DOI: 10.1371/journal.pcbi.1006796] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 06/17/2019] [Accepted: 03/28/2019] [Indexed: 12/16/2022] Open
Abstract
The calcium calmodulin-dependent protein kinase II (CaMKII) is a dodecameric holoenzyme important for encoding memory. Its activation, triggered by binding of calcium-calmodulin, persists autonomously after calmodulin dissociation. One (receiver) kinase captures and subsequently phosphorylates the regulatory domain peptide of a donor kinase forming a chained dimer as the first stage of autonomous activation. Protein dynamics simulations examined the conformational changes triggered by dimer formation and phosphorylation, aimed to provide a molecular rationale for human mutations that result in learning disabilities. Ensembles generated from X-ray crystal structures were characterized by network centrality and community analysis. Mutual information related collective motions to local fragment dynamics encoded with a structural alphabet. Implicit solvent tCONCOORD conformational ensembles revealed the dynamic architecture of inactive kinase domains was co-opted in the activated dimer but the network hub shifted from the nucleotide binding cleft to the captured peptide. Explicit solvent molecular dynamics (MD) showed nucleotide and substrate binding determinants formed coupled nodes in long-range signal relays between regulatory peptides in the dimer. Strain in the extended captured peptide was balanced by reduced flexibility of the receiver kinase C-lobe core. The relays were organized around a hydrophobic patch between the captured peptide and a key binding helix. The human mutations aligned along the relays. Thus, these mutations could disrupt the allosteric network alternatively, or in addition, to altered binding affinities. Non-binding protein sectors distant from the binding sites mediated the allosteric signalling; providing possible targets for inhibitor design. Phosphorylation of the peptide modulated the dielectric of its binding pocket to strengthen the patch, non-binding sectors, domain interface and temporal correlations between parallel relays. These results provide the molecular details underlying the reported positive kinase cooperativity to enrich the discussion on how autonomous activation by phosphorylation leads to long-term behavioural effects. Protein kinases play central roles in intracellular signalling. Auto-phosphorylation by bound nucleotide typically precedes phosphate transfer to multiple substrates. Protein conformational changes are central to kinase function, altering binding affinities to change cellular location and shunt from one signal pathway to another. In the brain, the multi-subunit kinase, CaMKII is activated by calcium-calmodulin upon calcium jumps produced by synaptic stimulation. Auto-transphosphorylation of a regulatory peptide enables the kinase to remain activated and mediate long-term behavioural effects after return to basal calcium levels. A database of mutated residues responsible for these effects is difficult to reconcile solely with impaired nucleotide or substrate binding. Therefore, we have computationally generated interaction networks to map the conformational plasticity of the kinase domains where most mutations localize. The network generated from the atomic structure of a phosphorylated dimer resolves protein sectors based on their collective motions. The sectors link nucleotide and substrate binding sites in self-reinforcing relays between regulatory peptides. The self-reinforcement is strengthened by phosphorylation consistent with the reported positive cooperativity of kinase activity with calcium-calmodulin concentration. The network gives a better match with the mutations and, in addition, reveals target sites for drug development.
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25
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Roewenstrunk J, Di Vona C, Chen J, Borras E, Dong C, Arató K, Sabidó E, Huen MSY, de la Luna S. A comprehensive proteomics-based interaction screen that links DYRK1A to RNF169 and to the DNA damage response. Sci Rep 2019; 9:6014. [PMID: 30979931 PMCID: PMC6461666 DOI: 10.1038/s41598-019-42445-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 03/29/2019] [Indexed: 12/15/2022] Open
Abstract
Dysregulation of the DYRK1A protein kinase has been associated with human disease. On the one hand, its overexpression in trisomy 21 has been linked to certain pathological traits of Down syndrome, while on the other, inactivating mutations in just one allele are responsible for a distinct yet rare clinical syndrome, DYRK1A haploinsufficiency. Moreover, altered expression of this kinase may also provoke other human pathologies, including cancer and diabetes. Although a few DYRK1A substrates have been described, its upstream regulators and downstream targets are still poorly understood, an information that could shed light on the functions of DYRK1A in the cell. Here, we carried out a proteomic screen using antibody-based affinity purification coupled to mass spectrometry to identify proteins that directly or indirectly bind to endogenous DYRK1A. We show that the use of a cell line not expressing DYRK1A, generated by CRISPR/Cas9 technology, was needed in order to discriminate between true positives and non-specific interactions. Most of the proteins identified in the screen are novel candidate DYRK1A interactors linked to a variety of activities in the cell. The in-depth characterization of DYRK1A's functional interaction with one of them, the E3 ubiquitin ligase RNF169, revealed a role for this kinase in the DNA damage response. We found that RNF169 is a DYRK1A substrate and we identified several of its phosphorylation sites. In particular, one of these sites appears to modify the ability of RNF169 to displace 53BP1 from sites of DNA damage. Indeed, DYRK1A depletion increases cell sensitivity to ionizing irradiation. Therefore, our unbiased proteomic screen has revealed a novel activity of DYRK1A, expanding the complex role of this kinase in controlling cell homeostasis.
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Affiliation(s)
- Julia Roewenstrunk
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Chiara Di Vona
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Jie Chen
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, S.A.R., Hong Kong, China
| | - Eva Borras
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Chao Dong
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, S.A.R., Hong Kong, China
| | - Krisztina Arató
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Michael S Y Huen
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, S.A.R., Hong Kong, China
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, S.A.R., Hong Kong, China
| | - Susana de la Luna
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain.
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain.
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26
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Veggiani G, Sidhu SS. Peptides meet ubiquitin: Simple interactions regulating complex cell signaling. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Gianluca Veggiani
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research; University of Toronto; Toronto Ontario Canada
- Department of Molecular Genetics; University of Toronto; Toronto Ontario Canada
| | - Sachdev S. Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research; University of Toronto; Toronto Ontario Canada
- Department of Molecular Genetics; University of Toronto; Toronto Ontario Canada
- Department of Biochemistry; University of Toronto; Toronto Ontario Canada
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27
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Wade BE, Zhao J, Ma J, Hart CM, Sutliff RL. Hypoxia-induced alterations in the lung ubiquitin proteasome system during pulmonary hypertension pathogenesis. Pulm Circ 2018; 8:2045894018788267. [PMID: 29927354 PMCID: PMC6146334 DOI: 10.1177/2045894018788267] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Pulmonary hypertension (PH) is a clinical disorder characterized by sustained
increases in pulmonary vascular resistance and pressure that can lead to right
ventricular (RV) hypertrophy and ultimately RV failure and death. The molecular
pathogenesis of PH remains incompletely defined, and existing treatments are
associated with suboptimal outcomes and persistent morbidity and mortality.
Reports have suggested a role for the ubiquitin proteasome system (UPS) in PH,
but the extent of UPS-mediated non-proteolytic protein alterations during PH
pathogenesis has not been previously defined. To further examine UPS
alterations, the current study employed C57BL/6J mice exposed to normoxia or
hypoxia for 3 weeks. Lung protein ubiquitination was evaluated by mass
spectrometry to identify differentially ubiquitinated proteins relative to
normoxic controls. Hypoxia stimulated differential ubiquitination of 198
peptides within 131 proteins (p < 0.05). These proteins were
screened to identify candidates within pathways involved in PH pathogenesis.
Some 51.9% of the differentially ubiquitinated proteins were implicated in at
least one known pathway contributing to PH pathogenesis, and 13% were involved
in three or more PH pathways. Anxa2, App, Jak1, Lmna, Pdcd6ip, Prkch1, and Ywhah
were identified as mediators in PH pathways that undergo differential
ubiquitination during PH pathogenesis. To our knowledge, this is the first study
to report global changes in protein ubiquitination in the lung during PH
pathogenesis. These findings suggest signaling nodes that are dynamically
regulated by the UPS during PH pathogenesis. Further exploration of these
differentially ubiquitinated proteins and related pathways can provide new
insights into the role of the UPS in PH pathogenesis.
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Affiliation(s)
- Brandy E Wade
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Atlanta Veterans' Affairs and Emory University Medical Centers, Decatur, Georgia, USA
| | - Jingru Zhao
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Atlanta Veterans' Affairs and Emory University Medical Centers, Decatur, Georgia, USA
| | - Jing Ma
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Atlanta Veterans' Affairs and Emory University Medical Centers, Decatur, Georgia, USA
| | - C Michael Hart
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Atlanta Veterans' Affairs and Emory University Medical Centers, Decatur, Georgia, USA
| | - Roy L Sutliff
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Atlanta Veterans' Affairs and Emory University Medical Centers, Decatur, Georgia, USA
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28
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Levy Y. Protein Assembly and Building Blocks: Beyond the Limits of the LEGO Brick Metaphor. Biochemistry 2017; 56:5040-5048. [PMID: 28809494 DOI: 10.1021/acs.biochem.7b00666] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Proteins, like other biomolecules, have a modular and hierarchical structure. Various building blocks are used to construct proteins of high structural complexity and diverse functionality. In multidomain proteins, for example, domains are fused to each other in different combinations to achieve different functions. Although the LEGO brick metaphor is justified as a means of simplifying the complexity of three-dimensional protein structures, several fundamental properties (such as allostery or the induced-fit mechanism) make deviation from it necessary to respect the plasticity, softness, and cross-talk that are essential to protein function. In this work, we illustrate recently reported protein behavior in multidomain proteins that deviates from the LEGO brick analogy. While earlier studies showed that a protein domain is often unaffected by being fused to another domain or becomes more stable following the formation of a new interface between the tethered domains, destabilization due to tethering has been reported for several systems. We illustrate that tethering may sometimes result in a multidomain protein behaving as "less than the sum of its parts". We survey these cases for which structure additivity does not guarantee thermodynamic additivity. Protein destabilization due to fusion to other domains may be linked in some cases to biological function and should be taken into account when designing large assemblies.
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Affiliation(s)
- Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science , Rehovot 76100, Israel
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29
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Filipčík P, Curry JR, Mace PD. When Worlds Collide-Mechanisms at the Interface between Phosphorylation and Ubiquitination. J Mol Biol 2017; 429:1097-1113. [PMID: 28235544 DOI: 10.1016/j.jmb.2017.02.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/13/2017] [Accepted: 02/14/2017] [Indexed: 02/08/2023]
Abstract
Phosphorylation and ubiquitination are pervasive post-translational modifications that impact all processes inside eukaryotic cells. The role of each modification has been studied for decades, and functional interplay between the two has long been demonstrated and even more widely postulated. However, our understanding of the molecular features that allow phosphorylation to control protein ubiquitination and ubiquitin to control phosphorylation has only recently begun to build. Here, we review examples of regulation between ubiquitination and phosphorylation, aiming to describe mechanisms at the molecular level. In general, these examples illustrate phosphorylation as a versatile switch throughout ubiquitination pathways, and ubiquitination primarily impacting kinase signalling in a more emphatic manner through scaffolding or degradation. Examples of regulation between these two processes are likely to grow even further as advances in molecular biology, proteomics, and computation allow a system-level understanding of signalling. Many new cases could involve similar principles to those described here, but the extensive co-regulation of these two systems leaves no doubt that they still have many surprises in store.
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Affiliation(s)
- Pavel Filipčík
- Biochemistry Department, School of Biomedical Sciences, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin 9054, New Zealand
| | - Jack R Curry
- Biochemistry Department, School of Biomedical Sciences, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin 9054, New Zealand
| | - Peter D Mace
- Biochemistry Department, School of Biomedical Sciences, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin 9054, New Zealand.
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