1
|
Heissler SM, Chinthalapudi K. Structural and functional mechanisms of actin isoforms. FEBS J 2024. [PMID: 38779987 DOI: 10.1111/febs.17153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 04/01/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024]
Abstract
Actin is a highly conserved and fundamental protein in eukaryotes and participates in a broad spectrum of cellular functions. Cells maintain a conserved ratio of actin isoforms, with muscle and non-muscle actins representing the main actin isoforms in muscle and non-muscle cells, respectively. Actin isoforms have specific and redundant functional roles and display different biochemistries, cellular localization, and interactions with myosins and actin-binding proteins. Understanding the specific roles of actin isoforms from the structural and functional perspective is crucial for elucidating the intricacies of cytoskeletal dynamics and regulation and their implications in health and disease. Here, we review how the structure contributes to the functional mechanisms of actin isoforms with a special emphasis on the questions of how post-translational modifications and disease-linked mutations affect actin isoforms biochemistry, function, and interaction with actin-binding proteins and myosin motors.
Collapse
Affiliation(s)
- Sarah M Heissler
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart & Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Krishna Chinthalapudi
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart & Lung Research Institute, The Ohio State University, Columbus, OH, USA
| |
Collapse
|
2
|
Morales PN, Coons AN, Koopman AJ, Patel S, Chase PB, Parvatiyar MS, Pinto JR. Post-translational modifications of vertebrate striated muscle myosin heavy chains. Cytoskeleton (Hoboken) 2024. [PMID: 38587113 DOI: 10.1002/cm.21857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/06/2024] [Accepted: 03/25/2024] [Indexed: 04/09/2024]
Abstract
Post-translational modifications (PTMs) play a crucial role in regulating the function of many sarcomeric proteins, including myosin. Myosins comprise a family of motor proteins that play fundamental roles in cell motility in general and muscle contraction in particular. A myosin molecule consists of two myosin heavy chains (MyHCs) and two pairs of myosin light chains (MLCs); two MLCs are associated with the neck region of each MyHC's N-terminal head domain, while the two MyHC C-terminal tails form a coiled-coil that polymerizes with other MyHCs to form the thick filament backbone. Myosin undergoes extensive PTMs, and dysregulation of these PTMs may lead to abnormal muscle function and contribute to the development of myopathies and cardiovascular disorders. Recent studies have uncovered the significance of PTMs in regulating MyHC function and showed how these PTMs may provide additional modulation of contractile processes. Here, we discuss MyHC PTMs that have been biochemically and/or functionally studied in mammals' and rodents' striated muscle. We have identified hotspots or specific regions in three isoforms of myosin (MYH2, MYH6, and MYH7) where the prevalence of PTMs is more frequent and could potentially play a significant role in fine-tuning the activity of these proteins.
Collapse
Affiliation(s)
- Paula Nieto Morales
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida, USA
| | - Arianna N Coons
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Amelia J Koopman
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Sonu Patel
- Department of Health, Nutrition and Food Sciences, Florida State University, Tallahassee, Florida, USA
| | - P Bryant Chase
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Michelle S Parvatiyar
- Department of Health, Nutrition and Food Sciences, Florida State University, Tallahassee, Florida, USA
| | - Jose R Pinto
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida, USA
| |
Collapse
|
3
|
Huang Z, Zhou L, Duan J, Qin S, Jiang J, Chen H, Wang K, Liu R, Yuan M, Tang X, Nice EC, Wei Y, Zhang W, Huang C. Oxidative Stress Promotes Liver Cancer Metastasis via RNF25-Mediated E-Cadherin Protein Degradation. Adv Sci (Weinh) 2024; 11:e2306929. [PMID: 38286671 PMCID: PMC10987140 DOI: 10.1002/advs.202306929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/25/2023] [Indexed: 01/31/2024]
Abstract
Loss of E-cadherin (ECAD) is required in tumor metastasis. Protein degradation of ECAD in response to oxidative stress is found in metastasis of hepatocellular carcinoma (HCC) and is independent of transcriptional repression as usually known. Mechanistically, protein kinase A (PKA) senses oxidative stress by redox modification in its β catalytic subunit (PRKACB) at Cys200 and Cys344. The activation of PKA kinase activity subsequently induces RNF25 phosphorylation at Ser450 to initiate RNF25-catalyzed degradation of ECAD. Functionally, RNF25 repression induces ECAD protein expression and inhibits HCC metastasis in vitro and in vivo. Altogether, these results indicate that RNF25 is a critical regulator of ECAD protein turnover, and PKA is a necessary redox sensor to enable this process. This study provides some mechanistic insight into how oxidative stress-induced ECAD degradation promotes tumor metastasis of HCC.
Collapse
Affiliation(s)
- Zhao Huang
- Department of BiotherapyCancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
| | - Li Zhou
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Institute for Viral HepatitisDepartment of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400016China
| | - Jiufei Duan
- Department of BiotherapyCancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
| | - Siyuan Qin
- Department of BiotherapyCancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
| | - Jingwen Jiang
- West China School of Public Health and West China Fourth HospitalSichuan UniversityChengdu610041China
| | - Haining Chen
- Colorectal Cancer CenterDepartment of General SurgeryWest China HospitalSichuan UniversityChengdu610041China
| | - Kui Wang
- West China School of Basic Medical Sciences & Forensic MedicineState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
| | - Rui Liu
- State Key Laboratory of Oral DiseasesNational Clinical Research Center for Oral DiseasesResearch Unit of Oral Carcinogenesis and ManagementChinese Academy of Medical SciencesWest China Hospital of StomatologySichuan UniversityChengdu610041China
| | - Minlan Yuan
- Mental Health Center and Psychiatric LaboratoryThe State Key Laboratory of BiotherapyWest China Biomedical Big Data CenterWest China Hospital of Sichuan UniversityChengdu610041China
| | - Xiangdong Tang
- Sleep Medicine CenterDepartment of Respiratory and Critical Care MedicineMental Health CenterTranslational Neuroscience CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
| | - Edouard C. Nice
- Department of Biochemistry and Molecular BiologyMonash UniversityClaytonVIC3167Australia
| | - Yuquan Wei
- Department of BiotherapyCancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
| | - Wei Zhang
- Frontiers Medical CenterTianfu Jincheng LaboratoryChengdu610212China
- Medical Big Data CenterSichuan UniversityChengdu610041China
| | - Canhua Huang
- Department of BiotherapyCancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
- Frontiers Medical CenterTianfu Jincheng LaboratoryChengdu610212China
| |
Collapse
|
4
|
Bhardwaj S, Bulluss M, D'Aubeterre A, Derakhshani A, Penner R, Mahajan M, Mahajan VB, Dufour A. Integrating the analysis of human biopsies using post-translational modifications proteomics. Protein Sci 2024; 33:e4979. [PMID: 38533548 DOI: 10.1002/pro.4979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/07/2024] [Accepted: 03/16/2024] [Indexed: 03/28/2024]
Abstract
Proteome diversities and their biological functions are significantly amplified by post-translational modifications (PTMs) of proteins. Shotgun proteomics, which does not typically survey PTMs, provides an incomplete picture of the complexity of human biopsies in health and disease. Recent advances in mass spectrometry-based proteomic techniques that enrich and study PTMs are helping to uncover molecular detail from the cellular level to system-wide functions, including how the microbiome impacts human diseases. Protein heterogeneity and disease complexity are challenging factors that make it difficult to characterize and treat disease. The search for clinical biomarkers to characterize disease mechanisms and complexity related to patient diagnoses and treatment has proven challenging. Knowledge of PTMs is fundamentally lacking. Characterization of complex human samples that clarify the role of PTMs and the microbiome in human diseases will result in new discoveries. This review highlights the key role of proteomic techniques used to characterize unknown biological functions of PTMs derived from complex human biopsies. Through the integration of diverse methods used to profile PTMs, this review explores the genetic regulation of proteoforms, cells of origin expressing specific proteins, and several bioactive PTMs and their subsequent analyses by liquid chromatography and tandem mass spectrometry.
Collapse
Affiliation(s)
- Sonali Bhardwaj
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Mitchell Bulluss
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Ana D'Aubeterre
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Afshin Derakhshani
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Regan Penner
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - MaryAnn Mahajan
- Molecular Surgery Laboratory, Stanford University, Palo Alto, California, USA
| | - Vinit B Mahajan
- Molecular Surgery Laboratory, Stanford University, Palo Alto, California, USA
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California, USA
| | - Antoine Dufour
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
5
|
Gupta MN, Uversky VN. Protein structure-function continuum model: Emerging nexuses between specificity, evolution, and structure. Protein Sci 2024; 33:e4968. [PMID: 38532700 DOI: 10.1002/pro.4968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 02/18/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024]
Abstract
The rationale for replacing the old binary of structure-function with the trinity of structure, disorder, and function has gained considerable ground in recent years. A continuum model based on the expanded form of the existing paradigm can now subsume importance of both conformational flexibility and intrinsic disorder in protein function. The disorder is actually critical for understanding the protein-protein interactions in many regulatory processes, formation of membrane-less organelles, and our revised notions of specificity as amply illustrated by moonlighting proteins. While its importance in formation of amyloids and function of prions is often discussed, the roles of intrinsic disorder in infectious diseases and protein function under extreme conditions are also becoming clear. This review is an attempt to discuss how our current understanding of protein function, specificity, and evolution fit better with the continuum model. This integration of structure and disorder under a single model may bring greater clarity in our continuing quest for understanding proteins and molecular mechanisms of their functionality.
Collapse
Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| |
Collapse
|
6
|
Liu R, Wu J, Guo H, Yao W, Li S, Lu Y, Jia Y, Liang X, Tang J, Zhang H. Post-translational modifications of histones: Mechanisms, biological functions, and therapeutic targets. MedComm (Beijing) 2023; 4:e292. [PMID: 37220590 PMCID: PMC10200003 DOI: 10.1002/mco2.292] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/25/2023] Open
Abstract
Histones are DNA-binding basic proteins found in chromosomes. After the histone translation, its amino tail undergoes various modifications, such as methylation, acetylation, phosphorylation, ubiquitination, malonylation, propionylation, butyrylation, crotonylation, and lactylation, which together constitute the "histone code." The relationship between their combination and biological function can be used as an important epigenetic marker. Methylation and demethylation of the same histone residue, acetylation and deacetylation, phosphorylation and dephosphorylation, and even methylation and acetylation between different histone residues cooperate or antagonize with each other, forming a complex network. Histone-modifying enzymes, which cause numerous histone codes, have become a hot topic in the research on cancer therapeutic targets. Therefore, a thorough understanding of the role of histone post-translational modifications (PTMs) in cell life activities is very important for preventing and treating human diseases. In this review, several most thoroughly studied and newly discovered histone PTMs are introduced. Furthermore, we focus on the histone-modifying enzymes with carcinogenic potential, their abnormal modification sites in various tumors, and multiple essential molecular regulation mechanism. Finally, we summarize the missing areas of the current research and point out the direction of future research. We hope to provide a comprehensive understanding and promote further research in this field.
Collapse
Affiliation(s)
- Ruiqi Liu
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
| | - Jiajun Wu
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
- Otolaryngology & Head and Neck CenterCancer CenterDepartment of Head and Neck SurgeryZhejiang Provincial People's HospitalAffiliated People's Hospital, Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Haiwei Guo
- Otolaryngology & Head and Neck CenterCancer CenterDepartment of Head and Neck SurgeryZhejiang Provincial People's HospitalAffiliated People's Hospital, Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Weiping Yao
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
| | - Shuang Li
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentJinzhou Medical UniversityJinzhouLiaoningChina
| | - Yanwei Lu
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
| | - Yongshi Jia
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
| | - Xiaodong Liang
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
| | - Jianming Tang
- Department of Radiation OncologyThe First Hospital of Lanzhou UniversityLanzhou UniversityLanzhouGansuChina
| | - Haibo Zhang
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
| |
Collapse
|
7
|
Wilkins JT, Seckler HS, Rink J, Compton PD, Fornelli L, Thaxton CS, LeDuc R, Jacobs D, Doubleday PF, Sniderman A, Lloyd-Jones DM, Kelleher NL. Spectrum of Apolipoprotein AI and Apolipoprotein AII Proteoforms and Their Associations With Indices of Cardiometabolic Health: The CARDIA Study. J Am Heart Assoc 2021; 10:e019890. [PMID: 34472376 PMCID: PMC8649248 DOI: 10.1161/jaha.120.019890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Background ApoAI (apolipoproteins AI) and apoAII (apolipoprotein AII) are structural and functional proteins of high‐density lipoproteins (HDL) which undergo post‐translational modifications at specific residues, creating distinct proteoforms. While specific post‐translational modifications have been reported to alter apolipoprotein function, the full spectrum of apoAI and apoAII proteoforms and their associations with cardiometabolic phenotype remains unknown. Herein, we comprehensively characterize apoAI and apoAII proteoforms detectable in serum and their post‐translational modifications and quantify their associations with cardiometabolic health indices. Methods and Results Using top‐down proteomics (mass‐spectrometric analysis of intact proteins), we analyzed paired serum samples from 150 CARDIA (Coronary Artery Risk Development in Young Adults) study participants from year 20 and 25 exams. Measuring 15 apoAI and 9 apoAII proteoforms, 6 of which carried novel post‐translational modifications, we quantified associations between percent proteoform abundance and key cardiometabolic indices. Canonical (unmodified) apoAI had inverse associations with HDL cholesterol and HDL‐cholesterol efflux, and positive associations with obesity indices (body mass index, waist circumference), and triglycerides, whereas glycated apoAI showed positive associations with serum glucose and diabetes mellitus. Fatty‐acid‒modified ApoAI proteoforms had positive associations with HDL cholesterol and efflux, and inverse associations with obesity indices and triglycerides. Truncated and dimerized proteoforms of apoAII were associated with HDL cholesterol (positively) and obesity indices (inversely). Several proteoforms had no significant associations with phenotype. Conclusions Associations between apoAI and AII and cardiometabolic indices are proteoform‐specific. These results provide “proof‐of‐concept” that precise chemical characterization of human apolipoproteins will yield improved insights into the complex pathways through which proteins signify and mediate health and disease.
Collapse
Affiliation(s)
- John T Wilkins
- Department of Medicine (Cardiology) and Department of Preventive Medicine Northwestern University Chicago IL
| | - Henrique S Seckler
- Department of Chemistry Chemistry of Life Processes Institute and Proteomics Center of Excellence Northwestern University Evanston IL
| | - Jonathan Rink
- Department of Medicine (Urology) Northwestern University Chicago IL
| | - Philip D Compton
- Department of Chemistry Chemistry of Life Processes Institute and Proteomics Center of Excellence Northwestern University Evanston IL
| | - Luca Fornelli
- Department of Molecular Biology University of Oklahoma Norman OK
| | - C Shad Thaxton
- Department of Medicine (Urology) Northwestern University Chicago IL
| | - Rich LeDuc
- Department of Chemistry Chemistry of Life Processes Institute and Proteomics Center of Excellence Northwestern University Evanston IL
| | - David Jacobs
- Division of Epidemiology and Community Health School of Public Health University of Minnesota Minneapolis MN
| | - Peter F Doubleday
- Department of Chemistry Chemistry of Life Processes Institute and Proteomics Center of Excellence Northwestern University Evanston IL
| | - Allan Sniderman
- Mike and Valeria Rosenbloom Centre for Cardiovascular Prevention Department of Medicine McGill University Health Centre Montreal Quebec Canada
| | - Donald M Lloyd-Jones
- Department of Medicine (Cardiology) and Department of Preventive Medicine Northwestern University Chicago IL
| | - Neil L Kelleher
- Department of Chemistry Chemistry of Life Processes Institute and Proteomics Center of Excellence Northwestern University Evanston IL
| |
Collapse
|
8
|
Borgermann N, Ackermann L, Schwertman P, Hendriks IA, Thijssen K, Liu JC, Lans H, Nielsen ML, Mailand N. SUMOylation promotes protective responses to DNA-protein crosslinks. EMBO J 2019; 38:embj.2019101496. [PMID: 30914427 PMCID: PMC6463212 DOI: 10.15252/embj.2019101496] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/20/2019] [Accepted: 02/28/2019] [Indexed: 11/09/2022] Open
Abstract
DNA‐protein crosslinks (DPCs) are highly cytotoxic lesions that obstruct essential DNA transactions and whose resolution is critical for cell and organismal fitness. However, the mechanisms by which cells respond to and overcome DPCs remain incompletely understood. Recent studies unveiled a dedicated DPC repair pathway in higher eukaryotes involving the SprT‐type metalloprotease SPRTN/DVC1, which proteolytically processes DPCs during DNA replication in a ubiquitin‐regulated manner. Here, we show that chemically induced and defined enzymatic DPCs trigger potent chromatin SUMOylation responses targeting the crosslinked proteins and associated factors. Consequently, inhibiting SUMOylation compromises DPC clearance and cellular fitness. We demonstrate that ACRC/GCNA family SprT proteases interact with SUMO and establish important physiological roles of Caenorhabditis elegans GCNA‐1 and SUMOylation in promoting germ cell and embryonic survival upon DPC formation. Our findings provide first global insights into signaling responses to DPCs and reveal an evolutionarily conserved function of SUMOylation in facilitating responses to these lesions in metazoans that may complement replication‐coupled DPC resolution processes.
Collapse
Affiliation(s)
- Nikoline Borgermann
- Ubiquitin Signaling Group, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Leena Ackermann
- Ubiquitin Signaling Group, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Petra Schwertman
- Ubiquitin Signaling Group, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Ivo A Hendriks
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Karen Thijssen
- Department of Molecular Genetics, Oncode Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Julio Cy Liu
- Ubiquitin Signaling Group, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Hannes Lans
- Department of Molecular Genetics, Oncode Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Niels Mailand
- Ubiquitin Signaling Group, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark .,Center for Chromosome Stability, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
9
|
Lössl P, van de Waterbeemd M, Heck AJ. The diverse and expanding role of mass spectrometry in structural and molecular biology. EMBO J 2016; 35:2634-2657. [PMID: 27797822 PMCID: PMC5167345 DOI: 10.15252/embj.201694818] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/25/2016] [Accepted: 10/07/2016] [Indexed: 12/20/2022] Open
Abstract
The emergence of proteomics has led to major technological advances in mass spectrometry (MS). These advancements not only benefitted MS-based high-throughput proteomics but also increased the impact of mass spectrometry on the field of structural and molecular biology. Here, we review how state-of-the-art MS methods, including native MS, top-down protein sequencing, cross-linking-MS, and hydrogen-deuterium exchange-MS, nowadays enable the characterization of biomolecular structures, functions, and interactions. In particular, we focus on the role of mass spectrometry in integrated structural and molecular biology investigations of biological macromolecular complexes and cellular machineries, highlighting work on CRISPR-Cas systems and eukaryotic transcription complexes.
Collapse
Affiliation(s)
- Philip Lössl
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Michiel van de Waterbeemd
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Albert Jr Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
| |
Collapse
|
10
|
Decalf J, Tarbell KV, Casrouge A, Price JD, Linder G, Mottez E, Sultanik P, Mallet V, Pol S, Duffy D, Albert ML. Inhibition of DPP4 activity in humans establishes its in vivo role in CXCL10 post-translational modification: prospective placebo-controlled clinical studies. EMBO Mol Med 2016; 8:679-83. [PMID: 27137491 PMCID: PMC4888857 DOI: 10.15252/emmm.201506145] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Biochemical experiments, animal models, and observational studies in humans all support a role of dipeptidyl peptidase 4 (DPP4) in the N‐terminal truncation of CXCL10, which results in the generation of an antagonist form of the chemokine that limits T‐cell and NK cell migration. Motivated by the ability to regulate lymphocyte trafficking in vivo, we conducted two prospective clinical trials to test the effects of DPP4 inhibition on CXCL10 processing in healthy donors and in chronic hepatitis C patients, a disease in which DPP4 levels are found to be elevated. Participants were treated daily with 100 mg sitagliptin, a clinically approved DPP4 inhibitor. Plasma samples were analyzed using an ultrasensitive single‐molecule assay (Simoa) to distinguish the full‐length CXCL101–77 from the NH2‐truncated CXCL103–77, as compared to the total CXCL10 levels. Sitagliptin treatment resulted in a significant decrease in CXCL103–77 concentration, a reciprocal increase in CXCL101–77, with only minimal effects on total levels of the chemokine. These data provide the first direct evidence that in vivo DPP4 inhibition in humans can preserve the bioactive form of CXCL10, offering new therapeutic opportunities for DPP4 inhibitors.
Collapse
Affiliation(s)
- Jérémie Decalf
- The Laboratory of Dendritic Cell Immunobiology, Institut Pasteur, Paris, France INSERM U818, Paris, France
| | - Kristin V Tarbell
- Diabetes Endocrinology and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Armanda Casrouge
- The Laboratory of Dendritic Cell Immunobiology, Institut Pasteur, Paris, France INSERM U818, Paris, France
| | - Jeffrey D Price
- Diabetes Endocrinology and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Grace Linder
- Diabetes Endocrinology and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Estelle Mottez
- Center for Human Immunology, Institut Pasteur, Paris, France
| | - Philippe Sultanik
- Département d'Hépatologie, AP-HP, Hôpital Cochin, Université Paris Descartes, INSERM UMS20, Institut Pasteur, Paris, France
| | - Vincent Mallet
- Département d'Hépatologie, AP-HP, Hôpital Cochin, Université Paris Descartes, INSERM UMS20, Institut Pasteur, Paris, France
| | - Stanislas Pol
- Département d'Hépatologie, AP-HP, Hôpital Cochin, Université Paris Descartes, INSERM UMS20, Institut Pasteur, Paris, France
| | - Darragh Duffy
- The Laboratory of Dendritic Cell Immunobiology, Institut Pasteur, Paris, France INSERM U818, Paris, France Center for Human Immunology, Institut Pasteur, Paris, France
| | - Matthew L Albert
- The Laboratory of Dendritic Cell Immunobiology, Institut Pasteur, Paris, France INSERM U818, Paris, France Center for Human Immunology, Institut Pasteur, Paris, France Department of Cancer Immunotherapy, Genentech, South San Francisco, CA, USA
| |
Collapse
|
11
|
Beltrao P, Bork P, Krogan NJ, van Noort V. Evolution and functional cross-talk of protein post-translational modifications. Mol Syst Biol 2013; 9:714. [PMID: 24366814 PMCID: PMC4019982 DOI: 10.1002/msb.201304521] [Citation(s) in RCA: 247] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 11/18/2013] [Accepted: 11/22/2013] [Indexed: 12/19/2022] Open
Abstract
Protein post-translational modifications (PTMs) allow the cell to regulate protein activity and play a crucial role in the response to changes in external conditions or internal states. Advances in mass spectrometry now enable proteome wide characterization of PTMs and have revealed a broad functional role for a range of different types of modifications. Here we review advances in the study of the evolution and function of PTMs that were spurred by these technological improvements. We provide an overview of studies focusing on the origin and evolution of regulatory enzymes as well as the evolutionary dynamics of modification sites. Finally, we discuss different mechanisms of altering protein activity via post-translational regulation and progress made in the large-scale functional characterization of PTM function.
Collapse
Affiliation(s)
- Pedro Beltrao
- European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL‐EBI)CambridgeUK
| | - Peer Bork
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Max‐Delbruck‐Centre for Molecular MedicineBerlin‐BuchGermany
| | - Nevan J. Krogan
- Department of Cellular and Molecular PharmacologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
- California Institute for Quantitative BiosciencesSan FranciscoCaliforniaUSA
- J. David Gladstone InstitutesSan FranciscoCaliforniaUSA
| | - Vera van Noort
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| |
Collapse
|