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Shein M, Hitzenberger M, Cheng TC, Rout SR, Leitl KD, Sato Y, Zacharias M, Sakata E, Schütz AK. Characterizing ATP processing by the AAA+ protein p97 at the atomic level. Nat Chem 2024; 16:363-372. [PMID: 38326645 PMCID: PMC10914628 DOI: 10.1038/s41557-024-01440-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 01/04/2024] [Indexed: 02/09/2024]
Abstract
The human enzyme p97 regulates various cellular pathways by unfolding hundreds of protein substrates in an ATP-dependent manner, making it an essential component of protein homeostasis and an impactful pharmacological target. The hexameric complex undergoes substantial conformational changes throughout its catalytic cycle. Here we elucidate the molecular motions that occur at the active site in the temporal window immediately before and after ATP hydrolysis by merging cryo-EM, NMR spectroscopy and molecular dynamics simulations. p97 populates a metastable reaction intermediate, the ADP·Pi state, which is poised between hydrolysis and product release. Detailed snapshots reveal that the active site is finely tuned to trap and eventually discharge the cleaved phosphate. Signalling pathways originating at the active site coordinate the action of the hexamer subunits and couple hydrolysis with allosteric conformational changes. Our multidisciplinary approach enables a glimpse into the sophisticated spatial and temporal orchestration of ATP handling by a prototype AAA+ protein.
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Affiliation(s)
- Mikhail Shein
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, München, Germany
- Bavarian NMR Center, Technical University of Munich, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Manuel Hitzenberger
- Physics Department and Center of Protein Assemblies, Technical University of Munich, Garching, Germany.
| | - Tat Cheung Cheng
- Institute for Neuropathology, University Medical Center Göttingen, Göttingen, Germany
- Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (MBExC), University of Göttingen, Göttingen, Germany
| | - Smruti R Rout
- Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (MBExC), University of Göttingen, Göttingen, Germany
- Institute for Auditory Neuroscience, University Medical Center Göttingen, Göttingen, Germany
| | - Kira D Leitl
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, München, Germany
- Bavarian NMR Center, Technical University of Munich, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Yusuke Sato
- Center for Research on Green Sustainable Chemistry, Graduate School of Engineering, Tottori University, Tottori, Japan
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Martin Zacharias
- Physics Department and Center of Protein Assemblies, Technical University of Munich, Garching, Germany.
| | - Eri Sakata
- Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (MBExC), University of Göttingen, Göttingen, Germany.
- Institute for Auditory Neuroscience, University Medical Center Göttingen, Göttingen, Germany.
| | - Anne K Schütz
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, München, Germany.
- Bavarian NMR Center, Technical University of Munich, Garching, Germany.
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.
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2
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Scalia F, Lo Bosco G, Paladino L, Vitale AM, Noori L, Conway de Macario E, Macario AJL, Bucchieri F, Cappello F, Lo Celso F. Structural and Dynamic Disturbances Revealed by Molecular Dynamics Simulations Predict the Impact on Function of CCT5 Chaperonin Mutations Associated with Rare Severe Distal Neuropathies. Int J Mol Sci 2023; 24:ijms24032018. [PMID: 36768350 PMCID: PMC9917133 DOI: 10.3390/ijms24032018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
Mutations in genes encoding molecular chaperones, for instance the genes encoding the subunits of the chaperonin CCT (chaperonin containing TCP-1, also known as TRiC), are associated with rare neurodegenerative disorders. Using a classical molecular dynamics approach, we investigated the occurrence of conformational changes and differences in physicochemical properties of the CCT5 mutations His147Arg and Leu224Val associated with a sensory and a motor distal neuropathy, respectively. The apical domain of both variants was substantially but differently affected by the mutations, although these were in other domains. The distribution of hydrogen bonds and electrostatic potentials on the surface of the mutant subunits differed from the wild-type molecule. Structural and dynamic analyses, together with our previous experimental data, suggest that genetic mutations may cause different changes in the protein-binding capacity of CCT5 variants, presumably within both hetero- and/or homo-oligomeric complexes. Further investigations are necessary to elucidate the molecular pathogenic pathways of the two variants that produce the two distinct phenotypes. The data and clinical observations by us and others indicate that CCT chaperonopathies are more frequent than currently believed and should be investigated in patients with neuropathies.
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Affiliation(s)
- Federica Scalia
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BiND), University of Palermo, 90127 Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
- Correspondence: (F.S.); (F.C.)
| | - Giosuè Lo Bosco
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
- Department of Mathematics and Computer Science, University of Palermo, 90123 Palermo, Italy
| | - Letizia Paladino
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BiND), University of Palermo, 90127 Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
| | - Alessandra Maria Vitale
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BiND), University of Palermo, 90127 Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
| | - Leila Noori
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BiND), University of Palermo, 90127 Palermo, Italy
- Department of Anatomy, School of Medicine, Tehran University of Medical Science, Tehran 1417653911, Iran
| | - Everly Conway de Macario
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore—Institute of Marine and Environmental Technology (IMET), Baltimore, MD 21202, USA
| | - Alberto J. L. Macario
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore—Institute of Marine and Environmental Technology (IMET), Baltimore, MD 21202, USA
| | - Fabio Bucchieri
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BiND), University of Palermo, 90127 Palermo, Italy
| | - Francesco Cappello
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BiND), University of Palermo, 90127 Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
- Correspondence: (F.S.); (F.C.)
| | - Fabrizio Lo Celso
- Department of Physics and Chemistry—Emilio Segrè, University of Palermo, 90128 Palermo, Italy
- Ionic Liquids Laboratory, Institute of Structure of Matter, Italian National Research Council (ISM-CNR), 00133 Rome, Italy
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3
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Hong Z, Gong W, Yang J, Li S, Liu Z, Perrett S, Zhang H. Exploration of the cysteine reactivity of human inducible Hsp70 and cognate Hsc70. J Biol Chem 2022; 299:102723. [PMID: 36410435 PMCID: PMC9800336 DOI: 10.1016/j.jbc.2022.102723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 11/20/2022] Open
Abstract
Hsp70s are multifunctional proteins and serve as the central hub of the protein quality control network. Hsp70s are also related to a number of diseases and have been established as drug targets. Human HspA1A (hHsp70) and HspA8 (hHsc70) are the major cytosolic Hsp70s, and they have both overlapping and distinct functions. hHsp70 contains five cysteine residues, and hHsc70 contains four cysteine residues. Previous studies have shown these cysteine residues can undergo different cysteine modifications such as oxidation or reaction with electrophiles to regulate their function, and hHsp70 and hHsc70 have different cysteine reactivity. To address the mechanism of the differences in cysteine reactivity between hHsp70 and hHsc70, we studied the factors that determine this reactivity by Ellman assay for the quantification of accessible free thiols and NMR analysis for the assessment of structural dynamics. We found the lower cysteine reactivity of hHsc70 is probably due to its lower structural dynamics and the stronger inhibition effect of interaction between the α-helical lid subdomain of the substrate-binding domain (SBDα) and the β-sheet substrate-binding subdomain (SBDβ) on cysteine reactivity of hHsc70. We determined that Gly557 in hHsp70 contributes significantly to the higher structural dynamics and cysteine reactivity of hHsp70 SBDα. Exploring the cysteine reactivity of hHsp70 and hHsc70 facilitates an understanding of the effects of redox reactions and electrophiles on their chaperone activity and regulation mechanisms, and how these differences allow them to undertake distinct cellular roles.
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Affiliation(s)
- Zhouping Hong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Weibin Gong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jie Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China,University of the Chinese Academy of Sciences, Beijing, China
| | - Sainan Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China,University of the Chinese Academy of Sciences, Beijing, China
| | - Zhenyan Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Sarah Perrett
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China,University of the Chinese Academy of Sciences, Beijing, China,For correspondence: Hong Zhang; Sarah Perrett
| | - Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China,University of the Chinese Academy of Sciences, Beijing, China,For correspondence: Hong Zhang; Sarah Perrett
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Santiago A, Morano KA. Oxidation of two cysteines within yeast Hsp70 impairs proteostasis while directly triggering an Hsf1-dependent cytoprotective response. J Biol Chem 2022; 298:102424. [PMID: 36030825 PMCID: PMC9508553 DOI: 10.1016/j.jbc.2022.102424] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/17/2022] Open
Abstract
Neurodegenerative diseases such as Alzheimer’s, Parkinson’s, and Huntington’s diseases affect millions of Americans every year. One factor linked to the formation of aggregates associated with these diseases is damage sustained to proteins by oxidative stress. Management of protein misfolding by the ubiquitous Hsp70 chaperone family can be modulated by modification of two key cysteines in the ATPase domain by oxidizing or thiol-modifying compounds. To investigate the biological consequences of cysteine modification on the Hsp70 Ssa1 in budding yeast, we generated cysteine null (cysteine to serine) and oxidomimetic (cysteine to aspartic acid) mutant variants of both C264 and C303 and demonstrate reduced ATP binding, hydrolysis, and protein folding properties in both the oxidomimetic and hydrogen peroxide–treated Ssa1. In contrast, cysteine nullification rendered Ssa1 insensitive to oxidative inhibition. Additionally, we determined the oxidomimetic ssa1-2CD (C264D, C303D) allele was unable to function as the sole Ssa1 isoform in yeast cells and also exhibited dominant negative effects on cell growth and viability. Ssa1 binds to and represses Hsf1, the major transcription factor controlling the heat shock response, and we found the oxidomimetic Ssa1 failed to stably interact with Hsf1, resulting in constitutive activation of the heat shock response. Consistent with our in vitro findings, ssa1-2CD cells were compromised for de novo folding, post-stress protein refolding, and in regulated degradation of a model terminally misfolded protein. Together, these findings pinpoint Hsp70 as a key link between oxidative stress and proteostasis, information critical to understanding cytoprotective systems that prevent and manage cellular insults underlying complex disease states.
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Affiliation(s)
- Alec Santiago
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth Houston, Houston, Texas, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences at UTHealth Houston, Houston, Texas, USA
| | - Kevin A Morano
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth Houston, Houston, Texas, USA.
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Santiago AM, Gonçalves DL, Morano KA. Mechanisms of sensing and response to proteotoxic stress. Exp Cell Res 2020; 395:112240. [PMID: 32827554 DOI: 10.1016/j.yexcr.2020.112240] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/13/2020] [Accepted: 08/18/2020] [Indexed: 12/25/2022]
Abstract
Cells are continuously subject to various stresses, battling both exogenous insults as well as toxic by-products of normal cellular metabolism and nutrient deprivation. Throughout the millennia, cells developed a core set of general stress responses that promote survival and reproduction under adverse circumstances. Past and current research efforts have been devoted to understanding how cells sense stressors and how that input is deciphered and transduced, resulting in stimulation of stress management pathways. A prime element of cellular stress responses is the increased transcription and translation of proteins specialized in managing and mitigating distinct types of stress. In this review, we focus on recent developments in our understanding of cellular sensing of proteotoxic stressors that impact protein synthesis, folding, and maturation provided by the model eukaryote the budding yeast, Saccharomyces cerevisiae, with reference to similarities and differences with other model organisms and humans.
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Affiliation(s)
- Alec M Santiago
- Department of Microbiology and Molecular Genetics, McGovern Medical School, UTHealth, Houston, TX, 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, UTHealth, Houston, TX, 77030, USA
| | - Davi L Gonçalves
- Department of Microbiology and Molecular Genetics, McGovern Medical School, UTHealth, Houston, TX, 77030, USA
| | - Kevin A Morano
- Department of Microbiology and Molecular Genetics, McGovern Medical School, UTHealth, Houston, TX, 77030, USA.
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Liu Y, Deng M, Wang Y, Wang H, Li C, Wu H. Identification of differentially expressed genes and biological pathways in para-carcinoma tissues of HCC with different metastatic potentials. Oncol Lett 2020; 19:3799-3814. [PMID: 32382332 PMCID: PMC7202278 DOI: 10.3892/ol.2020.11493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 01/30/2020] [Indexed: 12/02/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a malignant tumor with extensive metastasis. Changes in the tumor microenvironment provide favorable conditions for tumor metastasis. However, the role of changes to the tumor microenvironment in HCC metastasis is yet to be elucidated. The Gene Expression Omnibus expression profile GSE5093 consists of 20 noncancerous tissues surrounding HCC tissues, including 9 metastasis-inclined microenvironment samples with detectable metastases and 11 metastasis-averse microenvironment samples without detectable metastases. The present study assessed 35 HCC samples to verify the results of chip analysis. In total, 712 upregulated and 459 downregulated genes were identified, with 1,033 nodes, 7,589 edges and 10 hub genes. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that the differentially expressed genes were significantly enriched in ‘cell-cell adhesion’, ‘cell proliferation’ and ‘protein binding’. The top 10 hub genes were identified via a protein-protein interaction analysis. The 3 most significant modules were identified from the protein-protein network. Moreover, an association between hub genes and patient prognosis was identified. In conclusion, these candidate genes and pathways may help elucidate the mechanisms underlying HCC metastasis and identify more options for targeted therapy.
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Affiliation(s)
- Yan Liu
- Department of Gastroenterology, The Chengdu Fifth People's Hospital, Chengdu, Sichuan 611130, P.R. China
| | - Mingming Deng
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Yimeng Wang
- Department of Gastroenterology, The Chengdu Fifth People's Hospital, Chengdu, Sichuan 611130, P.R. China
| | - Huiqin Wang
- Department of Gastroenterology, The Chengdu Fifth People's Hospital, Chengdu, Sichuan 611130, P.R. China
| | - Changping Li
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Hao Wu
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
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Moseng MA, Nix JC, Page RC. Biophysical Consequences of EVEN-PLUS Syndrome Mutations for the Function of Mortalin. J Phys Chem B 2019; 123:3383-3396. [PMID: 30933555 DOI: 10.1021/acs.jpcb.9b00071] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
HSPA9, the gene coding for the mitochondrial chaperone mortalin, is involved in various cellular roles such as mitochondrial protein import, folding, degradation, Fe-S cluster biogenesis, mitochondrial homeostasis, and regulation of the antiapoptotic protein p53. Mutations in the HSPA9 gene, particularly within the region coding for the nucleotide-binding domain (NBD), cause the autosomal disorder known as EVEN-PLUS syndrome. The resulting mutants R126W and Y128C are located on the surface of the mortalin-NBD near the binding interface with the interdomain linker (IDL). We used differential scanning fluorimetry (DSF), biolayer interferometry, X-ray crystallography, ATP hydrolysis assays, and Rosetta docking simulations to study the structural and functional consequences of the EVEN-PLUS syndrome-associated R126W and Y128C mutations within the mortalin-NBD. These results indicate that the surface mutations R126W and Y128C have far-reaching effects that disrupt ATP hydrolysis, interdomain linker binding, and thermostability and increase the propensity for aggregation. The structural differences observed provide insight into how the conformations of mortalin differ from other heat shock protein 70 (Hsp70) homologues. Combined, our biophysical and structural studies contribute to the understanding of the molecular basis for how disease-associated mortalin mutations affect mortalin functionality and the pathogenesis of EVEN-PLUS syndrome.
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Affiliation(s)
- Mitchell A Moseng
- Department of Chemistry and Biochemistry , Miami University , Oxford , Ohio 45056 , United States
| | - Jay C Nix
- Molecular Biology Consortium, Beamline 4.2.2, Advanced Light Source , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Richard C Page
- Department of Chemistry and Biochemistry , Miami University , Oxford , Ohio 45056 , United States
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Oliverio R, Nguyen P, Kdeiss B, Ord S, Daniels AJ, Nikolaidis N. Functional characterization of natural variants found on the major stress inducible 70-kDa heat shock gene, HSPA1A, in humans. Biochem Biophys Res Commun 2018; 506:799-804. [PMID: 30384997 DOI: 10.1016/j.bbrc.2018.10.148] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 10/23/2018] [Indexed: 10/28/2022]
Abstract
In this report, we investigated the effects of natural single nucleotide polymorphisms on the function of HSPA1A, the major stress-inducible Hsp70 gene in humans. We first established that all mutant proteins retain their ability to hydrolyze ATP, but three of them had a significantly lower rate of ATP hydrolysis as compared to the wild-type (WT) protein. We also used Isothermal Titration Calorimetry and found that although all mutants bind to protein substrate with dissociation constants similar to the WT protein, four of them had increased reaction entropies. We also tested whether these mutations affect the ability of HSPA1A to refold heat-denatured luciferase. These assays revealed that one mutation resulted in significantly lower levels while a second one resulted in higher levels of the refolded enzyme. We then determined whether the mutations affected the ability of HSPA1A to prevent apoptosis caused by poly-glutamine carrying huntingtin proteins. This assay determined that three of the mutations caused increased cell apoptosis as compared to the WT. Our results reveal that although none of these naturally occurring mutations exists on positions of known function, some alter the molecular chaperone activities of HSPA1A most probably by affecting the allosteric communication between its two major domains.
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Affiliation(s)
- Ryan Oliverio
- Department of Biological Science, Center for Applied Biotechnology Studies, and Center for Computational and Applied Mathematics, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, 92834-6850, USA
| | - Peter Nguyen
- Department of Biological Science, Center for Applied Biotechnology Studies, and Center for Computational and Applied Mathematics, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, 92834-6850, USA
| | - Brianna Kdeiss
- Department of Biological Science, Center for Applied Biotechnology Studies, and Center for Computational and Applied Mathematics, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, 92834-6850, USA
| | - Sara Ord
- Department of Biological Science, Center for Applied Biotechnology Studies, and Center for Computational and Applied Mathematics, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, 92834-6850, USA
| | - Amanda J Daniels
- Department of Biological Science, Center for Applied Biotechnology Studies, and Center for Computational and Applied Mathematics, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, 92834-6850, USA
| | - Nikolas Nikolaidis
- Department of Biological Science, Center for Applied Biotechnology Studies, and Center for Computational and Applied Mathematics, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, 92834-6850, USA.
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Wang J, Choi H, Chung NC, Cao Q, Ng DCM, Mirza B, Scruggs SB, Wang D, Garlid AO, Ping P. Integrated Dissection of Cysteine Oxidative Post-translational Modification Proteome During Cardiac Hypertrophy. J Proteome Res 2018; 17:4243-4257. [PMID: 30141336 DOI: 10.1021/acs.jproteome.8b00372] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cysteine oxidative modification of cellular proteins is crucial for many aspects of cardiac hypertrophy development. However, integrated dissection of multiple types of cysteine oxidative post-translational modifications (O-PTM) of proteomes in cardiac hypertrophy is currently missing. Here we developed a novel discovery platform that encompasses a customized biotin switch-based quantitative proteomics pipeline and an advanced analytic workflow to comprehensively profile the landscape of cysteine O-PTM in an ISO-induced cardiac hypertrophy mouse model. Specifically, we identified a total of 1655 proteins containing 3324 oxidized cysteine sites by at least one of the following three modifications: reversible cysteine O-PTM, cysteine sulfinylation (CysSO2H), and cysteine sulfonylation (CysSO3H). Analyzing the hypertrophy signatures that are reproducibly discovered from this computational workflow unveiled four biological processes with increased cysteine O-PTM. Among them, protein phosphorylation, creatine metabolism, and response to elevated Ca2+ pathways exhibited an elevation of cysteine O-PTM in early stages, whereas glucose metabolism enzymes were increasingly modified in later stages, illustrating a temporal regulatory map in cardiac hypertrophy. Our cysteine O-PTM platform depicts a dynamic and integrated landscape of the cysteine oxidative proteome, through the extracted molecular signatures, and provides critical mechanistic insights in cardiac hypertrophy. Data are available via ProteomeXchange with identifier PXD010336.
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