Chemical proteomics reveals new targets of cysteine sulfinic acid reductase (original) (raw)
Paulsen, C. E. & Carroll, K. S. Cysteine-mediated redox signaling: chemistry, biology, and tools for discovery. Chem. Rev.113, 4633–4679 (2013). ArticleCASPubMedPubMed Central Google Scholar
Gupta, V. & Carroll, K. S. Sulfenic acid chemistry, detection and cellular lifetime. Biochim. Biophys. Acta.1840, 847–875 (2014). ArticleCASPubMed Google Scholar
Gupta, V., Yang, J., Liebler, D. C. & Carroll, K. S. Diverse redoxome reactivity profiles of carbon nucleophiles. J. Am. Chem. Soc.139, 5588–5595 (2017). ArticleCASPubMedPubMed Central Google Scholar
Yang, J., Gupta, V., Carroll, K. S. & Liebler, D. C. Site-specific mapping and quantification of protein _S_-sulphenylation in cells. Nat. Commun.5, 4776 (2014). ArticleCASPubMed Google Scholar
Gould, N. S. et al. Site-specific proteomic mapping identifies selectively modified regulatory cysteine residues in functionally distinct protein networks. Cell Chem. Biol.22, 965–975 (2015). CAS Google Scholar
Depuydt, M. et al. A periplasmic reducing system protects single cysteine residues from oxidation. Science326, 1109–1111 (2009). ArticleCASPubMed Google Scholar
Paulsen, C. E. et al. Peroxide-dependent sulfenylation of the EGFR catalytic site enhances kinase activity. Nat. Chem. Biol.8, 57–64 (2011). ArticleCASPubMedPubMed Central Google Scholar
Kulathu, Y. et al. Regulation of A20 and other OTU deubiquitinases by reversible oxidation. Nat. Commun.4, 1569 (2013). ArticleCASPubMed Google Scholar
Seo, Y. H. & Carroll, K. S. Profiling protein thiol oxidation in tumor cells using sulfenic acid-specific antibodies. Proc. Natl. Acad. Sci. USA106, 16163–16168 (2009). ArticleCASPubMedPubMed Central Google Scholar
Jacob, C., Holme, A. L. & Fry, F. H. The sulfinic acid switch in proteins. Org. Biomol. Chem.2, 1953–1956 (2004). ArticleCASPubMed Google Scholar
Woo, H. A. et al. Reversible oxidation of the active site cysteine of peroxiredoxins to cysteine sulfinic acid: immunoblot detection with antibodies specific for the hyperoxidized cysteine-containing sequence. J. Biol. Chem.278, 47361–47364 (2003). ArticleCASPubMed Google Scholar
Wood, Z. A., Poole, L. B. & Karplus, P. A. Peroxiredoxin evolution and the regulation of hydrogen peroxide signaling. Science300, 650–653 (2003). ArticleCASPubMed Google Scholar
Biteau, B., Labarre, J. & Toledano, M. B. ATP-dependent reduction of cysteine-sulphinic acid by S. cerevisiae sulphiredoxin. Nature425, 980–984 (2003). ArticleCASPubMed Google Scholar
Chang, T. S. et al. Characterization of mammalian sulfiredoxin and its reactivation of hyperoxidized peroxiredoxin through reduction of cysteine sulfinic acid in the active site to cysteine. J. Biol. Chem.279, 50994–51001 (2004). ArticleCASPubMed Google Scholar
Woo, H. A. et al. Reduction of cysteine sulfinic acid by sulfiredoxin is specific to 2-cys peroxiredoxins. J. Biol. Chem.280, 3125–3128 (2005). ArticleCASPubMed Google Scholar
Lo Conte, M. & Carroll, K. S. The redox biochemistry of protein sulfenylation and sulfinylation. J. Biol. Chem.288, 26480–26488 (2013). ArticleCASPubMedPubMed Central Google Scholar
Canet-Aviles, R. M. et al. The Parkinson’s disease protein DJ-1 is neuroprotective due to cysteine-sulfinic acid-driven mitochondrial localization. Proc. Natl. Acad. Sci. USA101, 9103–9108 (2004). ArticleCASPubMedPubMed Central Google Scholar
Blackinton, J. et al. Formation of a stabilized cysteine sulfinic acid is critical for the mitochondrial function of the parkinsonism protein DJ-1. J. Biol. Chem.284, 6476–6485 (2009). ArticleCASPubMedPubMed Central Google Scholar
Kil et al. Circadian oscillation of sulfiredoxin in the mitochondria. Mol. Cell.59, 651–663 (2015). ArticleCASPubMed Google Scholar
Dickinson, B. C. & Chang, C. J. Chemistry and biology of reactive oxygen species in signaling or stress responses. Nat. Chem. Biol.7, 504–511 (2011). ArticleCASPubMedPubMed Central Google Scholar
Wei, Q., Jiang, H., Matthews, C. P. & Colburn, N. H. Sulfiredoxin is an AP-1 target gene that is required for transformation and shows elevated expression in human skin malignancies. Proc. Natl. Acad. Sci. USA105, 19738–19743 (2008). ArticleCASPubMedPubMed Central Google Scholar
Wei, Q. et al. Sulfiredoxin-peroxiredoxin IV axis promotes human lung cancer progression through modulation of specific phosphokinase signaling. Proc. Natl. Acad. Sci. USA108, 7004–7009 (2011). ArticleCASPubMedPubMed Central Google Scholar
Kim, H. et al. Sulfiredoxin inhibitor induces preferential death of cancer cells through reactive oxygen species-mediated mitochondrial damage. Free Rad. Biol. Med.91, 264–274 (2016). ArticleCASPubMed Google Scholar
Woo, H. A. & Rhee, S. G. in Methods inRedoxSignaling (ed. Das, D.) Ch. 4, 19–23 (Mary Ann Liebert, New Rochelle, NY, USA, 2010).
Lee, C. F., Paull, T. T. & Person, M. D. Proteome-wide detection and quantitative analysis of irreversible cysteine oxidation using long column UPLC-pSRM. J. Prot. Res.12, 4302–4315 (2013). ArticleCAS Google Scholar
Lo Conte, M. & Carroll, K. S. Chemoselective ligation of sulfinic acids with aryl-nitroso compounds. Angew. Chem. Int. Ed.51, 6502–6505 (2012). ArticleCAS Google Scholar
Lo Conte, M., Lin, J., Wilson, M. A. & Carroll, K. S. A chemical approach for the detection of protein sulfinylation. ACS Chem. Biol.10, 1825–1830 (2015). ArticleCASPubMedPubMed Central Google Scholar
Majmudar, J. D. et al. Harnessing redox cross-reactivity to profile distinct cysteine modifications. J. Am. Chem. Soc.138, 1852–1859 (2016). ArticleCASPubMedPubMed Central Google Scholar
Mitroka, S. et al. Direct and nitroxyl (HNO)-mediated reactions of acyloxy nitroso compounds with the thiol-containing proteins glyceraldehyde 3-phosphate dehydrogenase and alkyl hydroperoxide reductase subunit C. J. Med. Chem.56, 6583–6592 (2013). ArticleCASPubMedPubMed Central Google Scholar
Schlick, T. L., Ding, Z., Kovacs, E. W. & Francis, M. B. Dual-surface modification of the tobacco mosaic virus. J. Am. Chem. Soc.127, 3718–3723 (2005). ArticleCASPubMed Google Scholar
Delaunay, A., Pflieger, D., Barrault, M. B., Vinh, J. & Toledano, M. B. A thiol peroxidase is an H2O2 receptor and redox-transducer in gene activation. Cell111, 471–481 (2002). ArticleCASPubMed Google Scholar
Baek, J. Y. et al. Sulfiredoxin protein is critical for redox balance and survival of cells exposed to low steady-state levels of H2O2. J. Biol. Chem.287, 81–89 (2012). ArticleCASPubMed Google Scholar
Kim, K. H., Lee, W. & Kim, E. E. Crystal structures of human peroxiredoxin 6 in different oxidation states. Biochem. Biophys. Res. Comm.477, 717–722 (2016). ArticleCASPubMed Google Scholar
van Montfort, R. L., Congreve, M., Tisi, D., Carr, R. & Jhoti, H. Oxidation state of the active-site cysteine in protein tyrosine phosphatase 1B. Nature423, 773–777 (2003). ArticleCASPubMed Google Scholar
Mullen, L., Hanschmann, E. M., Lillig, C. H., Herzenberg, L. A. & Ghezzi, P. Cysteine oxidation targets peroxiredoxins 1 and 2 for exosomal release through a novel mechanism of redox-dependent secretion. Mol. Med.21, 98–108 (2015). ArticleCASPubMedPubMed Central Google Scholar
Szabo-Taylor, K. et al. Oxidative and other posttranslational modifications in extracellular vesicle biology. Semin. Cell Dev. Biol.40, 8–16 (2015). ArticleCASPubMed Google Scholar
Porta, C., Moroni, M., Guallini, P., Torri, C. & Marzatico, F. Antioxidant enzymatic system and free radicals pathway in two different human cancer cell lines. Anticancer. Res.16, 2741–2747 (1996). CASPubMed Google Scholar
Chauvin, J. R. & Pratt, D. A. On the reactions of thiols, sulfenic acids, and sulfinic acids with hydrogen peroxide. Angew. Chem. Int. Ed.56, 6255–6259 (2017). ArticleCAS Google Scholar
Li, H. et al. Crystal structure and substrate specificity of PTPN12. Cell Rep.15, 1345–1358 (2016). ArticleCASPubMed Google Scholar
Jönsson, T. J. et al. Structural basis for the retroreduction of inactivated peroxiredoxins by human sulfiredoxin. Biochemistry44, 8634–8642 (2005). ArticleCASPubMed Google Scholar
Klamt, F. et al. Oxidant-induced apoptosis is mediated by oxidation of the actin-regulatory protein cofilin. Nat. Cell Biol.11, 1241–1246 (2009). ArticleCASPubMedPubMed Central Google Scholar
Cameron, J. M. et al. Polarized cell motility induces hydrogen peroxide to inhibit cofilin via cysteine oxidation. Curr. Biol.25, 1520–1525 (2015). ArticleCASPubMedPubMed Central Google Scholar
Hamann, M., Zhang, T., Hendrich, S. & Thomas, J. A. Quantitation of protein sulfinic and sulfonic acid, irreversibly oxidized protein cysteine sites in cellular proteins. Methods. Enzymol.348, 146–156 (2002). ArticleCASPubMed Google Scholar
White, M. D. et al. Plant cysteine oxidases are dioxygenases that directly enable arginyl transferase-catalysed arginylation of N-end rule targets. Nat. Commun.8, 14690 (2017). ArticleCASPubMedPubMed Central Google Scholar
Schroder, K. NADPH oxidases in redox regulation of cell adhesion and migration. Antioxid. Redox Signal.20, 2043–2058 (2014). ArticleCASPubMed Google Scholar
Li, X. et al. Mitochondria-translocated PGK1 functions as a protein kinase to coordinate glycolysis and the TCA cycle in tumorigenesis. Mol. Cell61, 705–719 (2016). ArticleCASPubMedPubMed Central Google Scholar
Sun, T. et al. Activation of multiple proto-oncogenic tyrosine kinases in breast cancer via loss of the PTPN12 phosphatase. Cell144, 703–718 (2011).
Paulsen, C. E. & Carroll, K. S. Chemical dissection of an essential redox switch in yeast. Chem. Biol.16, 217–225 (2009). ArticleCASPubMed Google Scholar
Cheng, H., Donahue, J. L., Battle, S. E., Ray, W. K. & Larson, T. J. Biochemical and genetic characterization of PspE and GlpE, two single-domain sulfurtransferases of Escherichia coli. Open Microbiol. J.2, 18–28 (2008). ArticleCASPubMedPubMed Central Google Scholar
Chi, H. et al. pFind-Alioth: a novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data. J. Proteomics125, 89–97 (2015). ArticleCASPubMed Google Scholar
Li, D. et al. pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry. Bioinformatics21, 3049–3050 (2005). ArticleCASPubMed Google Scholar
Wang, L. H. et al. pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry. Rapid Commun. Mass Spectrom.21, 2985–2991 (2007). ArticleCASPubMed Google Scholar
Tan, D. et al. Trifunctional cross-linker for mapping protein-protein interaction networks and comparing protein conformational states. eLife5, e12509 (2016).
Liu, C. et al. pQuant improves quantitation by keeping out interfering signals and evaluating the accuracy of calculated ratios. Anal. Chem.86, 5286–5294 (2014). ArticleCASPubMed Google Scholar
Ma, Y., McClatchy, D. B., Barkallah, S., Wood, W. W. & Yates, J. R. 3rd HILAQ: a novel strategy for newly synthesized protein quantification. J. Proteome Res.16, 2213–2220 (2017). ArticleCASPubMedPubMed Central Google Scholar
Garcia, F. J. & Carroll, K. S. Redox-based probes as tools to monitor oxidized protein tyrosine phosphatases in living cells. Eur. J. Med. Chem.17, 28–33 (2014). ArticleCAS Google Scholar