<i>S</i>-nitroso proteome of<i>Mycobacterium tuberculosis</i>: Enzymes of intermediary metabolism and antioxidant defense

Rhee, Kyu Y.; Erdjument‐Bromage, Hediye; Tempst, Paul; Nathan, Carl

doi:10.1073/pnas.0406133102

Cited by 158 publications

(144 citation statements)

References 55 publications

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“…These new thiols are then marked by introduction of a mixed-disulfide bond with a biotin-tagging reagent, captured on immobilized avidin, and selectively released from avidin by reduction of the disulfide linker. Several laboratories have used the biotin-switch method in combination with 1D or 2D PAGE and in-gel trypsinolysis for identification of SNO proteins by mass spectrometry (10)(11)(12)(13)(14). To extend the capability of this approach, we introduced a proteolytic digestion step before avidin capture.…”

Section: Snosid a Proteomic Methods For Identification Of Cysteine S-mentioning

confidence: 99%

SNOSID, a proteomic method for identification of cysteine S-nitrosylation sites in complex protein mixtures

Hao

Derakhshan

Shi

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

315

320

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Reversible addition of NO to Cys-sulfur in proteins, a modification termed S-nitrosylation, has emerged as a ubiquitous signaling mechanism for regulating diverse cellular processes. A key first-step toward elucidating the mechanism by which S-nitrosylation modulates a protein's function is specification of the targeted Cys (SNO-Cys) residue. To date, S-nitrosylation site specification has been laboriously tackled on a protein-by-protein basis. Here we describe a high-throughput proteomic approach that enables simultaneous identification of SNO-Cys sites and their cognate proteins in complex biological mixtures. The approach, termed SNOSID (SNO Site Identification), is a modification of the biotin-swap technique [Jaffrey, S. R., Erdjument-Bromage, H., Ferris, C. D., Tempst, P. & Snyder, S. H. (2001) Nat. Cell. Biol. 3, 193–197], comprising biotinylation of protein SNO-Cys residues, trypsinolysis, affinity purification of biotinylated-peptides, and amino acid sequencing by liquid chromatography tandem MS. With this approach, 68 SNO-Cys sites were specified on 56 distinct proteins in S -nitrosoglutathione-treated (2–10 μM) rat cerebellum lysates. In addition to enumerating these S-nitrosylation sites, the method revealed endogenous SNO-Cys modification sites on cerebellum proteins, including α-tubulin, β-tubulin, GAPDH, and dihydropyrimidinase-related protein-2. Whereas these endogenous SNO proteins were previously recognized, we extend prior knowledge by specifying the SNO-Cys modification sites. Considering all 68 SNO-Cys sites identified, a machine learning approach failed to reveal a linear Cys-flanking motif that predicts stable transnitrosation by S -nitrosoglutathione under test conditions, suggesting that undefined 3D structural features determine S-nitrosylation specificity. SNOSID provides the first effective tool for unbiased elucidation of the SNO proteome, identifying Cys residues that undergo reversible S-nitrosylation.

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Section: Snosid a Proteomic Methods For Identification Of Cysteine S-mentioning

confidence: 99%

SNOSID, a proteomic method for identification of cysteine S-nitrosylation sites in complex protein mixtures

Hao

Derakhshan

Shi

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

315

320

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“…For instance, DLDH was found to be modified by 4-hydroxynonenal (HNE) in the ventilatory muscles of rats challenged by lipopolysaccharide (Hussain, et al, 2006), and found to be nitrosylated in rat liver (Foster and Stamler, 2004) and in Mycobacterium tuberculosis (Rhee, et al, 2005). Because DLDH activity was not measured in these studies, it is not yet known whether or not the HNE modification or nitrosylation had any significant inhibitory effects.…”

Section: Discussionmentioning

confidence: 99%

Changes in dihydrolipoamide dehydrogenase expression and activity during postnatal development and aging in the rat brain

Thangthaeng

Forster

2008

Mechanisms of Ageing and Development

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Brain energy metabolism is increased during postnatal development and diminished in neurodegenerative diseases linked to senescence. The objective of this study was to determine if these conditions could involve postnatal or senescence-related shifts in activity or expression of dihydrolipoamide dehydrogenase (DLDH), a key mitochondrial oxidoreductase. Rats ranging from 10 to 60 days of age were used in studies of postnatal development, whereas rats aged 5 or 30 months were used in the aging studies. The expression of DLDH was determined by Western blot analysis using anti-DLDH antibodies and DLDH diaphorase activity was measured by an in-gel activity staining method using nitroblue tetrazolium (NBT)/NADH. Activity of DLDH dehydrogenase was measured as NAD + oxidation of dihydrolipoamide. When these measures were considered in separate groups of 10-, 20-, 30-, or 60-day-old rats, all three showed an increase between 10 and 20 days of age. However, dehydrogenase activity of DLDH showed a further, progressive increase from 20 days to adulthood, in the absence of any further change in DLDH expression or diaphorase activity. No age-related decline in DLDH activity or expression was evident over the period from 5 to 30 months of age. Moreover, aging did not render DLDH more susceptible to oxidative inactivation by mitochondria-generated reactive oxygen species (ROS). Taken together, results of the present study indicate that (1) brain DLDH expression and activity undergo independent postnatal maturational increases; (2) Senescence does not confer any detectable change in the activity of DLDH or its susceptibility to inactivation by mitochondrial oxidative stress.

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“…Whereas many enzymes are subject to inhibition by peroxynitrite, the contribution of tyrosine nitration, S-nitrosation, and other mechanisms to inactivation varies considerably [67][68][69][70]. DTT only partially protected against PDHC inhibition, suggesting that tyrosine nitration is the primary mechanism of inactivation.…”

Section: Nih-pa Author Manuscriptmentioning

confidence: 99%

Postischemic hyperoxia reduces hippocampal pyruvate dehydrogenase activity

Richards

Rosenthal

Kristián

et al. 2006

Free Radical Biology and Medicine

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The pyruvate dehydrogenase complex (PDHC) is a mitochondrial matrix enzyme that catalyzes the oxidative decarboxylation of pyruvate and represents the sole bridge between anaerobic and aerobic cerebral energy metabolism. Previous studies demonstrating loss of PDHC enzyme activity and immunoreactivity during reperfusion after cerebral ischemia suggest that oxidative modifications are involved. This study tested the hypothesis that hyperoxic reperfusion exacerbates loss of PDHC enzyme activity, possibly due to tyrosine nitration or S-nitrosation. We used a clinically relevant canine ventricular fibrillation cardiac arrest model in which, after resuscitation and ventilation on either 100% O 2 (hyperoxic) or 21-30% O 2 (normoxic), animals were sacrificed at 2 h reperfusion and the brains removed for enzyme activity and immunoreactivity measurements. Animals resuscitated under hyperoxic conditions exhibited decreased PDHC activity and elevated 3-nitrotyrosine immunoreactivity in the hippocampus but not the cortex, compared to nonischemic controls. These measures were unchanged in normoxic animals. In vitro exposure of purified PDHC to peroxynitrite resulted in a dose-dependent loss of activity and increased nitrotyrosine immunoreactivity. These results support the hypothesis that oxidative stress contributes to loss of hippocampal PDHC activity during cerebral ischemia and reperfusion and suggest that PDHC is a target of peroxynitrite. KeywordsMitochondria; Hyperoxia; Nitrotyrosine; Normoxia; Oxidative stress; Global ischemia; Selective vulnerability; Free radicals Global cerebral ischemia and reperfusion cause severe neurochemical alterations, including oxidative modifications to lipids, proteins, and DNA. These and other covalent modifications can impair enzyme activities, including those necessary for energy metabolism. Alterations in these enzyme activities can limit postischemic aerobic metabolism and cellular ATP regeneration, thereby contributing to the pathophysiology of delayed neuronal cell death [1][2][3][4]. One enzyme known to be targeted and inactivated by reactive oxygen species is the pyruvate dehydrogenase complex (PDHC) [5]. Effects of ischemia/reperfusion on the PDHC can be particularly devastating because this enzyme forms the bridge between glycolysis and the Krebs cycle and can be the rate-limiting step in aerobic cerebral energy metabolism. NIH Public Access Author ManuscriptFree Radic Biol Med. Author manuscript; available in PMC 2008 October 21. Published in final edited form as:Free Radic Biol Med. 2006 June 1; 40(11): 1960-1970. doi:10.1016/j.freeradbiomed.2006.01.022. NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author ManuscriptThe PDHC is located exclusively in the mitochondrial matrix and catalyzes the oxidative decarboxylation of pyruvate to form NADH and acetyl coenzyme A-the primary form of carbon that enters the Krebs cycle in the adult brain. Several laboratories have shown that PDHC enzyme activity is lost during cerebral ischemia/reperfusion [6][7][8]. PDHC im...

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S-nitroso proteome ofMycobacterium tuberculosis: Enzymes of intermediary metabolism and antioxidant defense

Cited by 158 publications

References 55 publications

SNOSID, a proteomic method for identification of cysteine S-nitrosylation sites in complex protein mixtures

SNOSID, a proteomic method for identification of cysteine S-nitrosylation sites in complex protein mixtures

Changes in dihydrolipoamide dehydrogenase expression and activity during postnatal development and aging in the rat brain

Postischemic hyperoxia reduces hippocampal pyruvate dehydrogenase activity

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