1
|
Falco JA, Wynia-Smith SL, McCoy J, Smith BC, Weerapana E. Identification of Protein Targets of S-Nitroso-Coenzyme A-Mediated S-Nitrosation Using Chemoproteomics. ACS Chem Biol 2024; 19:193-207. [PMID: 38159293 PMCID: PMC11154738 DOI: 10.1021/acschembio.3c00654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
S-Nitrosation is a cysteine post-translational modification fundamental to cellular signaling. This modification regulates protein function in numerous biological processes in the nervous, cardiovascular, and immune systems. Small molecule or protein nitrosothiols act as mediators of NO signaling by transferring the NO group (formally NO+) to a free thiol on a target protein through a transnitrosation reaction. The protein targets of specific transnitrosating agents and the extent and functional effects of S-nitrosation on these target proteins have been poorly characterized. S-nitroso-coenzyme A (CoA-SNO) was recently identified as a mediator of endogenous S-nitrosation. Here, we identified direct protein targets of CoA-SNO-mediated transnitrosation using a competitive chemical-proteomic approach that quantified the extent of modification on 789 cysteine residues in response to CoA-SNO. A subset of cysteines displayed high susceptibility to modification by CoA-SNO, including previously uncharacterized sites of S-nitrosation. We further validated and functionally characterized the functional effects of S-nitrosation on the protein targets phosphofructokinase (platelet type), ATP citrate synthase, and ornithine aminotransferase.
Collapse
Affiliation(s)
- Julia A. Falco
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | - Sarah L. Wynia-Smith
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - James McCoy
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | - Brian C. Smith
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | |
Collapse
|
2
|
Vokač D, Stangler Herodež Š, Krgović D, Kokalj Vokač N. The Role of Next-Generation Sequencing in the Management of Patients with Suspected Non-Ischemic Cardiomyopathy after Syncope or Termination of Sudden Arrhythmic Death. Genes (Basel) 2024; 15:72. [PMID: 38254962 PMCID: PMC10815304 DOI: 10.3390/genes15010072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Cardiac arrhythmias and sudden death are frequent in patients with non-ischemic cardiomyopathy and can precede heart failure or additional symptoms where malignant cardiac arrhythmias are mostly the consequence of advanced cardiomyopathy and heart failure. Finding these subgroups and making an early diagnosis could be lifesaving. In our retrospective study, we are presenting arrhythmic types of frequent cardiomyopathies where an arrhythmogenic substrate is less well defined, as in ischemic or structural heart disease. In the period of 2 years, next-generation sequencing (NGS) tests along with standard clinical tests were performed in 208 patients (67 women and 141 men; mean age, 51.2 ± 19.4 years) without ischemic or an overt structural heart disease after syncope or aborted sudden cardiac death. Genetic variants were detected in 34.4% of the study population, with a significant proportion of pathogenic variants (P) (14.4%) and variants of unknown significance (VUS) (20%). Regardless of genotype, all patients were stratified according to clinical guidelines for aggressive treatment of sudden cardiac death with an implantable cardioverter defibrillator (ICD). The P variant identified by NGS serves for an accurate diagnosis and, thus, better prevention and specific treatment of patients and their relatives. Results in our study suggest that targeted sequencing of genes associated with cardiovascular disease is an important addendum for final diagnosis, allowing the identification of a molecular genetic cause in a vast proportion of patients for a definitive diagnosis and a more specific way of treatment. VUS in this target population poses a high risk and should be considered possibly pathogenic in reanalysis.
Collapse
Affiliation(s)
- Damijan Vokač
- Department of Cardiology and Angiology, Division of Internal Medicine, University Medical Centre Maribor, 2000 Maribor, Slovenia;
| | - Špela Stangler Herodež
- Clinical Institute for Genetic Diagnostics, University Medical Centre Maribor, 2000 Maribor, Slovenia; (Š.S.H.); (D.K.)
- Medical Faculty, University of Maribor, 2000 Maribor, Slovenia
| | - Danijela Krgović
- Clinical Institute for Genetic Diagnostics, University Medical Centre Maribor, 2000 Maribor, Slovenia; (Š.S.H.); (D.K.)
- Medical Faculty, University of Maribor, 2000 Maribor, Slovenia
| | - Nadja Kokalj Vokač
- Clinical Institute for Genetic Diagnostics, University Medical Centre Maribor, 2000 Maribor, Slovenia; (Š.S.H.); (D.K.)
- Medical Faculty, University of Maribor, 2000 Maribor, Slovenia
| |
Collapse
|
3
|
Zhou HL, Grimmett ZW, Venetos NM, Stomberski CT, Qian Z, McLaughlin PJ, Bansal PK, Zhang R, Reynolds JD, Premont RT, Stamler JS. An enzyme that selectively S-nitrosylates proteins to regulate insulin signaling. Cell 2023; 186:5812-5825.e21. [PMID: 38056462 PMCID: PMC10794992 DOI: 10.1016/j.cell.2023.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 09/01/2023] [Accepted: 11/03/2023] [Indexed: 12/08/2023]
Abstract
Acyl-coenzyme A (acyl-CoA) species are cofactors for numerous enzymes that acylate thousands of proteins. Here, we describe an enzyme that uses S-nitroso-CoA (SNO-CoA) as its cofactor to S-nitrosylate multiple proteins (SNO-CoA-assisted nitrosylase, SCAN). Separate domains in SCAN mediate SNO-CoA and substrate binding, allowing SCAN to selectively catalyze SNO transfer from SNO-CoA to SCAN to multiple protein targets, including the insulin receptor (INSR) and insulin receptor substrate 1 (IRS1). Insulin-stimulated S-nitrosylation of INSR/IRS1 by SCAN reduces insulin signaling physiologically, whereas increased SCAN activity in obesity causes INSR/IRS1 hypernitrosylation and insulin resistance. SCAN-deficient mice are thus protected from diabetes. In human skeletal muscle and adipose tissue, SCAN expression increases with body mass index and correlates with INSR S-nitrosylation. S-nitrosylation by SCAN/SNO-CoA thus defines a new enzyme class, a unique mode of receptor tyrosine kinase regulation, and a revised paradigm for NO function in physiology and disease.
Collapse
Affiliation(s)
- Hua-Lin Zhou
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Zachary W Grimmett
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Nicholas M Venetos
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Colin T Stomberski
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Zhaoxia Qian
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Precious J McLaughlin
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Puneet K Bansal
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Rongli Zhang
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - James D Reynolds
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Anesthesiology and Perioperative Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Richard T Premont
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Jonathan S Stamler
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA.
| |
Collapse
|
4
|
Seth P, Hausladen A, Premont RT, Stamler JS. Protocol for preparing Thiopropyl Sepharose resin used for capturing S-nitrosylated proteins. STAR Protoc 2023; 4:102430. [PMID: 37925633 PMCID: PMC10652206 DOI: 10.1016/j.xpro.2023.102430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/26/2023] [Accepted: 06/12/2023] [Indexed: 11/07/2023] Open
Abstract
S-nitrosothiol (SNO)-Resin Assisted Capture (SNO-RAC) relies on a Thiopropyl Sepharose resin to identify S-nitrosylated proteins (SNO-proteins) and sites of S-nitrosylation. Here, we present a protocol for preparing Thiopropyl Sepharose resin with efficiency of SNO-protein capture comparable to the discontinued commercial version. We describe steps for amine coupling, disulfide reduction, and generation of thiol reactive resin. We then detail quality control procedures. This resin is also suitable for Acyl-RAC assays to capture palmitoylated proteins. For complete details on the use and execution of the SNO-RAC protocol, please refer to Forrester et al.,1 Fonseca et al.,2 and Seth et al.3.
Collapse
Affiliation(s)
- Puneet Seth
- Institute for Transformative Molecular Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; University Hospitals, Cleveland, OH 44106, USA
| | - Alfred Hausladen
- Institute for Transformative Molecular Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Richard T Premont
- Institute for Transformative Molecular Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; University Hospitals, Cleveland, OH 44106, USA; Harrington Discovery Institute, University Hospitals, Cleveland, OH 44106, USA
| | - Jonathan S Stamler
- Institute for Transformative Molecular Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; University Hospitals, Cleveland, OH 44106, USA; Harrington Discovery Institute, University Hospitals, Cleveland, OH 44106, USA.
| |
Collapse
|
5
|
Stomberski CT, Venetos NM, Zhou HL, Qian Z, Collison BR, Field SJ, Premont RT, Stamler JS. A multienzyme S-nitrosylation cascade regulates cholesterol homeostasis. Cell Rep 2022; 41:111538. [PMID: 36288700 PMCID: PMC9667709 DOI: 10.1016/j.celrep.2022.111538] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/03/2022] [Accepted: 09/30/2022] [Indexed: 11/03/2022] Open
Abstract
Accumulating evidence suggests that protein S-nitrosylation is enzymatically regulated and that specificity in S-nitrosylation derives from dedicated S-nitrosylases and denitrosylases that conjugate and remove S-nitrosothiols, respectively. Here, we report that mice deficient in the protein denitrosylase SCoR2 (S-nitroso-Coenzyme A Reductase 2; AKR1A1) exhibit marked reductions in serum cholesterol due to reduced secretion of the cholesterol-regulating protein PCSK9. SCoR2 associates with endoplasmic reticulum (ER) secretory machinery to control an S-nitrosylation cascade involving ER cargo-selection proteins SAR1 and SURF4, which moonlight as S-nitrosylases. SAR1 acts as a SURF4 nitrosylase and SURF4 as a PCSK9 nitrosylase to inhibit PCSK9 secretion, while SCoR2 counteracts nitrosylase activity by promoting PCSK9 denitrosylation. Inhibition of PCSK9 by an NO-based drug requires nitrosylase activity, and small-molecule inhibition of SCoR2 phenocopies the PCSK9-mediated reductions in cholesterol observed in SCoR2-deficient mice. Our results reveal enzymatic machinery controlling cholesterol levels through S-nitrosylation and suggest a distinct treatment paradigm for cardiovascular disease.
Collapse
Affiliation(s)
- Colin T Stomberski
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44016, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Nicholas M Venetos
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44016, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Hua-Lin Zhou
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44016, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44016, USA
| | - Zhaoxia Qian
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44016, USA
| | - Bryce R Collison
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Seth J Field
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44016, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44016, USA
| | - Richard T Premont
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44016, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44016, USA
| | - Jonathan S Stamler
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44016, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44016, USA.
| |
Collapse
|
6
|
Zhou HL, Premont RT, Stamler JS. The manifold roles of protein S-nitrosylation in the life of insulin. Nat Rev Endocrinol 2022; 18:111-128. [PMID: 34789923 PMCID: PMC8889587 DOI: 10.1038/s41574-021-00583-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/08/2021] [Indexed: 02/04/2023]
Abstract
Insulin, which is released by pancreatic islet β-cells in response to elevated levels of glucose in the blood, is a critical regulator of metabolism. Insulin triggers the uptake of glucose and fatty acids into the liver, adipose tissue and muscle, and promotes the storage of these nutrients in the form of glycogen and lipids. Dysregulation of insulin synthesis, secretion, transport, degradation or signal transduction all cause failure to take up and store nutrients, resulting in type 1 diabetes mellitus, type 2 diabetes mellitus and metabolic dysfunction. In this Review, we make the case that insulin signalling is intimately coupled to protein S-nitrosylation, in which nitric oxide groups are conjugated to cysteine thiols to form S-nitrosothiols, within effectors of insulin action. We discuss the role of S-nitrosylation in the life cycle of insulin, from its synthesis and secretion in pancreatic β-cells, to its signalling and degradation in target tissues. Finally, we consider how aberrant S-nitrosylation contributes to metabolic diseases, including the roles of human genetic mutations and cellular events that alter S-nitrosylation of insulin-regulating proteins. Given the growing influence of S-nitrosylation in cellular metabolism, the field of metabolic signalling could benefit from renewed focus on S-nitrosylation in type 2 diabetes mellitus and insulin-related disorders.
Collapse
Affiliation(s)
- Hua-Lin Zhou
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Richard T Premont
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Jonathan S Stamler
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
- Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA.
| |
Collapse
|
7
|
Proteome-wide modulation of S-nitrosylation in Trypanosoma cruzi trypomastigotes upon interaction with the host extracellular matrix. J Proteomics 2020; 231:104020. [PMID: 33096306 DOI: 10.1016/j.jprot.2020.104020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 09/20/2020] [Accepted: 10/15/2020] [Indexed: 12/16/2022]
Abstract
Trypanosoma cruzi trypomastigotes adhere to extracellular matrix (ECM) to invade mammalian host cells regulating intracellular signaling pathways. Herein, resin-assisted enrichment of thiols combined with mass spectrometry were employed to map site-specific S-nitrosylated (SNO) proteins from T. cruzi trypomastigotes incubated (MTy) or not (Ty) with ECM. We confirmed the reduction of S-nitrosylation upon incubation with ECM, associated with a rewiring of the subcellular distribution and intracellular signaling pathways. Forty, 248 and 85 SNO-peptides were identified only in MTy, Ty or in both conditions, respectively. SNO proteins were enriched in ribosome, transport, carbohydrate and lipid metabolisms. Nitrosylation of histones H2B and H3 on Cys64 and Cys126, respectively, is described. Protein-protein interaction networks revealed ribosomal proteins, proteins involved in carbon and fatty acid metabolism to be among the enriched protein complexes. Kinases, phosphatases and enzymes involved in the metabolism of carbohydrates, lipids and amino acids were identified as nitrosylated and phosphorylated, suggesting a post-translational modifications crosstalk. In silico mapping of nitric oxide synthase (NOS) genes, previously uncharacterized, matched to four putative T. cruzi proteins expressing C-terminal NOS domain. Our results provide the first site-specific characterization of S-nitrosylated proteins in T. cruzi and their modulation upon ECM incubation before infection of the mammalian hosts. SIGNIFICANCE: Protein S-nitrosylation represents a major molecular mechanism for signal transduction by nitric oxide. We present for the first time a proteomic profile of S-nitrosylated proteins from infective forms of T. cruzi, showing a decrease in SNO proteins after incubation of the parasite with the extracellular matrix, a necessary step for the parasite invasion of the host mammalian cells. We also show for the first time nitrosylation of H2B (Cys64) and H3 (Cys126) histones, sites not conserved in higher eukaryotic cells, and suggest that some specific histone isoforms are sensitive to NO signaling. S-nitrosylation in H2B and H3 histones are more abundant in MTy. Moreover, proteins involved in translation, glycolytic pathway and fatty acid metabolism are enriched in the present dataset. Comparison of the SNO proteome and the phosphoproteome, obtained previously under the same experimental conditions, show that most of the proteins sharing both modifications are involved in metabolic pathways, transport and ribosome function. The data suggest that both PTMs are involved in reprogramming the metabolism of T. cruzi in response to environmental changes. Although NO synthesis was detected in T. cruzi, the identification of NOS remains elusive. Analysis in silico showed two genes similar in domains to NADPH-dependent cytochrome-P450 reductase and two putative oxidoreductases, but no oxygenase domain of NOS was mapped in the T. cruzi genome. It is tempting to speculate that NO synthase-like from T. cruzi and its early NO-mediated pathways triggered in response to host interaction constitute potential diagnostic and therapeutic targets.
Collapse
|
8
|
Stomberski CT, Hess DT, Stamler JS. Protein S-Nitrosylation: Determinants of Specificity and Enzymatic Regulation of S-Nitrosothiol-Based Signaling. Antioxid Redox Signal 2019; 30:1331-1351. [PMID: 29130312 PMCID: PMC6391618 DOI: 10.1089/ars.2017.7403] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SIGNIFICANCE Protein S-nitrosylation, the oxidative modification of cysteine by nitric oxide (NO) to form protein S-nitrosothiols (SNOs), mediates redox-based signaling that conveys, in large part, the ubiquitous influence of NO on cellular function. S-nitrosylation regulates protein activity, stability, localization, and protein-protein interactions across myriad physiological processes, and aberrant S-nitrosylation is associated with diverse pathophysiologies. Recent Advances: It is recently recognized that S-nitrosylation endows S-nitroso-protein (SNO-proteins) with S-nitrosylase activity, that is, the potential to trans-S-nitrosylate additional proteins, thereby propagating SNO-based signals, analogous to kinase-mediated signaling cascades. In addition, it is increasingly appreciated that cellular S-nitrosylation is governed by dynamically coupled equilibria between SNO-proteins and low-molecular-weight SNOs, which are controlled by a growing set of enzymatic denitrosylases comprising two main classes (high and low molecular weight). S-nitrosylases and denitrosylases, which together control steady-state SNO levels, may be identified with distinct physiology and pathophysiology ranging from cardiovascular and respiratory disorders to neurodegeneration and cancer. CRITICAL ISSUES The target specificity of protein S-nitrosylation and the stability and reactivity of protein SNOs are determined substantially by enzymatic machinery comprising highly conserved transnitrosylases and denitrosylases. Understanding the differential functionality of SNO-regulatory enzymes is essential, and is amenable to genetic and pharmacological analyses, read out as perturbation of specific equilibria within the SNO circuitry. FUTURE DIRECTIONS The emerging picture of NO biology entails equilibria among potentially thousands of different SNOs, governed by denitrosylases and nitrosylases. Thus, to elucidate the operation and consequences of S-nitrosylation in cellular contexts, studies should consider the roles of SNO-proteins as both targets and transducers of S-nitrosylation, functioning according to enzymatically governed equilibria.
Collapse
Affiliation(s)
- Colin T Stomberski
- 1 Institute for Transformative Molecular Medicine, Case Western Reserve University, Cleveland, Ohio.,2 Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio
| | - Douglas T Hess
- 1 Institute for Transformative Molecular Medicine, Case Western Reserve University, Cleveland, Ohio.,3 Department of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Jonathan S Stamler
- 2 Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio.,3 Department of Medicine, Case Western Reserve University, Cleveland, Ohio.,4 Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio
| |
Collapse
|
9
|
Seth P, Hsieh PN, Jamal S, Wang L, Gygi SP, Jain MK, Coller J, Stamler JS. Regulation of MicroRNA Machinery and Development by Interspecies S-Nitrosylation. Cell 2019; 176:1014-1025.e12. [PMID: 30794773 PMCID: PMC6559381 DOI: 10.1016/j.cell.2019.01.037] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/20/2018] [Accepted: 01/23/2019] [Indexed: 02/04/2023]
Abstract
Bioactive molecules can pass between microbiota and host to influence host cellular functions. However, general principles of interspecies communication have not been discovered. We show here in C. elegans that nitric oxide derived from resident bacteria promotes widespread S-nitrosylation of the host proteome. We further show that microbiota-dependent S-nitrosylation of C. elegans Argonaute protein (ALG-1)-at a site conserved and S-nitrosylated in mammalian Argonaute 2 (AGO2)-alters its function in controlling gene expression via microRNAs. By selectively eliminating nitric oxide generation by the microbiota or S-nitrosylation in ALG-1, we reveal unforeseen effects on host development. Thus, the microbiota can shape the post-translational landscape of the host proteome to regulate microRNA activity, gene expression, and host development. Our findings suggest a general mechanism by which the microbiota may control host cellular functions, as well as a new role for gasotransmitters.
Collapse
Affiliation(s)
- Puneet Seth
- Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Paishiun N Hsieh
- Department of Medicine, Case Cardiovascular Research Institute, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Harrington Heart and Vascular Institute, University Hospitals Cleveland Medical Center, 2103 Cornell Road, Cleveland, OH 44106, USA; Department of Pathology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Suhib Jamal
- Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Liwen Wang
- Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mukesh K Jain
- Department of Medicine, Case Cardiovascular Research Institute, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Harrington Heart and Vascular Institute, University Hospitals Cleveland Medical Center, 2103 Cornell Road, Cleveland, OH 44106, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Jeff Coller
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jonathan S Stamler
- Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA.
| |
Collapse
|
10
|
Stomberski CT, Zhou HL, Wang L, van den Akker F, Stamler JS. Molecular recognition of S-nitrosothiol substrate by its cognate protein denitrosylase. J Biol Chem 2018; 294:1568-1578. [PMID: 30538128 DOI: 10.1074/jbc.ra118.004947] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 12/05/2018] [Indexed: 11/06/2022] Open
Abstract
Protein S-nitrosylation mediates a large part of nitric oxide's influence on cellular function by providing a fundamental mechanism to control protein function across different species and cell types. At steady state, cellular S-nitrosylation reflects dynamic equilibria between S-nitrosothiols (SNOs) in proteins and small molecules (low-molecular-weight SNOs) whose levels are regulated by dedicated S-nitrosylases and denitrosylases. S-Nitroso-CoA (SNO-CoA) and its cognate denitrosylases, SNO-CoA reductases (SCoRs), are newly identified determinants of protein S-nitrosylation in both yeast and mammals. Because SNO-CoA is a minority species among potentially thousands of cellular SNOs, SCoRs must preferentially recognize this SNO substrate. However, little is known about the molecular mechanism by which cellular SNOs are recognized by their cognate enzymes. Using mammalian cells, molecular modeling, substrate-capture assays, and mutagenic analyses, we identified a single conserved surface Lys (Lys-127) residue as well as active-site interactions of the SNO group that mediate recognition of SNO-CoA by SCoR. Comparing SCoRK127A versus SCoRWT HEK293 cells, we identified a SNO-CoA-dependent nitrosoproteome, including numerous metabolic protein substrates. Finally, we discovered that the SNO-CoA/SCoR system has a role in mitochondrial metabolism. Collectively, our findings provide molecular insights into the basis of specificity in SNO-CoA-mediated metabolic signaling and suggest a role for SCoR-regulated S-nitrosylation in multiple metabolic processes.
Collapse
Affiliation(s)
- Colin T Stomberski
- Institute for Transformative Molecular Medicine, Case Western Reserve University, Cleveland, Ohio 44106; Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106
| | - Hua-Lin Zhou
- Institute for Transformative Molecular Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Liwen Wang
- Center for Proteomics and Bioinformatics, Department of Nutrition, Case Western Reserve University, Cleveland, Ohio 44106
| | - Focco van den Akker
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106
| | - Jonathan S Stamler
- Institute for Transformative Molecular Medicine, Case Western Reserve University, Cleveland, Ohio 44106; Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio 44106.
| |
Collapse
|
11
|
Affiliation(s)
- Divya Seth
- From the Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University (D.S., J.S.S.) and Harrington Discovery Institute (J.S.S.), University Hospitals Case Medical Center, Cleveland, OH
| | - Jonathan S Stamler
- From the Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University (D.S., J.S.S.) and Harrington Discovery Institute (J.S.S.), University Hospitals Case Medical Center, Cleveland, OH.
| |
Collapse
|
12
|
Simonyan V, Mazumder R. High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis. Genes (Basel) 2014; 5:957-81. [PMID: 25271953 PMCID: PMC4276921 DOI: 10.3390/genes5040957] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 09/22/2014] [Accepted: 09/22/2014] [Indexed: 12/30/2022] Open
Abstract
The High-performance Integrated Virtual Environment (HIVE) is a high-throughput cloud-based infrastructure developed for the storage and analysis of genomic and associated biological data. HIVE consists of a web-accessible interface for authorized users to deposit, retrieve, share, annotate, compute and visualize Next-generation Sequencing (NGS) data in a scalable and highly efficient fashion. The platform contains a distributed storage library and a distributed computational powerhouse linked seamlessly. Resources available through the interface include algorithms, tools and applications developed exclusively for the HIVE platform, as well as commonly used external tools adapted to operate within the parallel architecture of the system. HIVE is composed of a flexible infrastructure, which allows for simple implementation of new algorithms and tools. Currently, available HIVE tools include sequence alignment and nucleotide variation profiling tools, metagenomic analyzers, phylogenetic tree-building tools using NGS data, clone discovery algorithms, and recombination analysis algorithms. In addition to tools, HIVE also provides knowledgebases that can be used in conjunction with the tools for NGS sequence and metadata analysis.
Collapse
Affiliation(s)
- Vahan Simonyan
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.
| | - Raja Mazumder
- Department of Biochemistry and Molecular Medicine, George Washington University, Washington, DC 20037, USA.
| |
Collapse
|
13
|
Pan Y, Karagiannis K, Zhang H, Dingerdissen H, Shamsaddini A, Wan Q, Simonyan V, Mazumder R. Human germline and pan-cancer variomes and their distinct functional profiles. Nucleic Acids Res 2014; 42:11570-88. [PMID: 25232094 PMCID: PMC4191387 DOI: 10.1093/nar/gku772] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Identification of non-synonymous single nucleotide variations (nsSNVs) has exponentially increased due to advances in Next-Generation Sequencing technologies. The functional impacts of these variations have been difficult to ascertain because the corresponding knowledge about sequence functional sites is quite fragmented. It is clear that mapping of variations to sequence functional features can help us better understand the pathophysiological role of variations. In this study, we investigated the effect of nsSNVs on more than 17 common types of post-translational modification (PTM) sites, active sites and binding sites. Out of 1 705 285 distinct nsSNVs on 259 216 functional sites we identified 38 549 variations that significantly affect 10 major functional sites. Furthermore, we found distinct patterns of site disruptions due to germline and somatic nsSNVs. Pan-cancer analysis across 12 different cancer types led to the identification of 51 genes with 106 nsSNV affected functional sites found in 3 or more cancer types. 13 of the 51 genes overlap with previously identified Significantly Mutated Genes (Nature. 2013 Oct 17;502(7471)). 62 mutations in these 13 genes affecting functional sites such as DNA, ATP binding and various PTM sites occur across several cancers and can be prioritized for additional validation and investigations.
Collapse
Affiliation(s)
- Yang Pan
- The Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA
| | - Konstantinos Karagiannis
- The Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA
| | - Haichen Zhang
- The Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA
| | - Hayley Dingerdissen
- The Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA
| | - Amirhossein Shamsaddini
- The Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA
| | - Quan Wan
- The Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA
| | - Vahan Simonyan
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Raja Mazumder
- The Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA McCormick Genomic and Proteomic Center, George Washington University, Washington, DC 20037, USA
| |
Collapse
|