S-nitrosylation of proteins is the main mechanism through which nitric oxide (NO) regulates cellular function and likely represents the archetype redox-based signaling system across aerobic and anaerobic organisms. How NO generated by different nitric oxide synthase (NOS) isoforms leads to specificity of S-nitrosylation remains incompletely understood. This study aimed to identify proteins interacting with, and whose S-nitrosylation is mediated by, human NOS isoforms in the same cellular system, thereby illuminating the contribution of individual NOSs to specificity.
Results:
Of the hundreds of proteins interacting with each NOS, many were also S-nitrosylated. However, a large proportion of S-nitrosylated proteins (SNO-proteins) did not associate with NOS. Moreover, most NOS interactors and SNO-proteins were unique to each isoform. The amount of NO produced by each NOS isoform was unrelated to the numbers of SNO-proteins. Thus, NOSs promoted S-nitrosylation of largely distinct sets of target proteins. Different signaling pathways were enriched downstream of each NOS.
Innovation and Conclusion:
The interactomes and SNOomes of individual NOS isoforms were largely distinct. Only a small fraction of SNO-proteins interacted with their respective NOS. Amounts of S-nitrosylation were unrelated to the amount of NO generated by NOSs. These data argue against free diffusion of NO or NOS interactions as being necessary or sufficient for S-nitrosylation and favor roles for additional enzymes and/or regulatory elements in imparting SNO-protein specificity. Antioxid. Redox Signal. 39, 621–634.
Get full access to this article
View all access options for this article.
References
1.
AldertonWK, CooperCE, and KnowlesRG. Nitric oxide synthases: structure, function and inhibition. Biochem J, 357: 593–615, 2001.
2.
AnandP, HausladenA, WangYJ, ZhangGF, StomberskiC, BrunengraberH, HessDT, and StamlerJS. Identification of S-nitroso-CoA reductases that regulate protein S-nitrosylation. Proc Natl Acad Sci U S A, 111: 18572–18577, 2014.
3.
AndrewPJ and MayerB. Enzymatic function of nitric oxide synthases. Cardiovasc Res, 43: 521–531, 1999.
4.
AngeloM, SingelDJ, and StamlerJS. An S-nitrosothiol (SNO) synthase function of hemoglobin that utilizes nitrite as a substrate. Proc Natl Acad Sci U S A, 103: 8366–8371, 2006.
5.
BenharM, ForresterMT, and HessDT, StamlerJS. Regulated protein denitrosylation by cytosolic and mitochondrial thioredoxins. Science, 320: 1050–1054, 2008.
6.
BombicinoSS, IglesiasDE, ZaobornyjT, BoverisA, and ValdezLB. Mitochondrial nitric oxide production supported by reverse electron transfer. Arch Biochem Biophys, 607: 8–19, 2016.
7.
BroniowskaKA, KeszlerA, BasuS, Kim-ShapiroDB, and HoggN. Cytochrome c-mediated formation of S-nitrosothiol in cells. Biochem J, 442: 191–197, 2012.
8.
BustamanteJ, CzerniczyniecA, and Lores-ArnaizS. Brain nitric oxide synthases and mitochondrial function. Front Biosci, 12: 1034–1040, 2007.
9.
CaoS, YaoJ, McCabeTJ, YaoQ, KatusicZS, SessaWC, and ShahV. Direct interaction between endothelial nitric-oxide synthase and dynamin-2. Implications for nitric-oxide synthase function. J Biol Chem, 276: 14249–14256, 2001.
10.
ChatterjiA, BanerjeeD, BilliarTR, and SenguptaR. Understanding the role of S-nitrosylation/nitrosative stress in inflammation and the role of cellular denitrosylases in inflammation modulation: Implications in health and diseases. Free Radic Biol Med, 172: 604–621, 2021.
11.
ChenL, KongX, FuJ, XuY, FangS, HuaP, LuoL, and YinZ. CHIP facilitates ubiquitination of inducible nitric oxide synthase and promotes its proteasomal degradation. Cell Immunol, 258: 38–43, 2009.
12.
ChungHS, KimGE, HolewinskiRJ, VenkatramanV, ZhuG, BedjaD, KassDA, and Van EykJE. Transient receptor potential channel 6 regulates abnormal cardiac S-nitrosylation in Duchenne muscular dystrophy. Proc Natl Acad Sci U S A, 114: E10763–E10771, 2017.
13.
ForresterMT, ThompsonJW, FosterMW, NogueiraL, MoseleyMA, and StamlerJS. Proteomic analysis of S-nitrosylation and denitrosylation by resin-assisted capture. Nature Biotech, 27: 557–559, 2009.
14.
FosterMW, ThompsonJW, ForresterMT, ShaY, McMahonTJ, BowlesDE, MoseleyMA, and MarshallHE. Proteomic analysis of the NOS2 interactome in human airway epithelial cells. Nitric Oxide, 34: 37–46, 2013.
15.
HessDT, MatsumotoA, KimS-O, MarshallHE, and StamlerJS. Protein S-nitrosylation: purview and parameters. Nat Rev Mol Cell Biol, 6: 150–166, 2005.
16.
HyndmanKA, MusallJB, XueJ, and PollockJS. Dynamin activates NO production in rat renal inner medullary collecting ducts via protein-protein interaction with NOS1. Am J Physiol Renal Physiol, 301: F118–124, 2011.
17.
JiaJ, ArifA, TerenziF, WillardB, PlowEF, HazenSL, and FoxPL. Target-selective protein S-nitrosylation by sequence motif recognition. Cell, 159: 623–634, 2014.
18.
JiangJ, CyrD, BabbittRW, SessaWC, and PattersonC. Chaperone-dependent regulation of endothelial nitric-oxide synthase intracellular trafficking by the co-chaperone/ubiquitin ligase CHIP. J Biol Chem, 278: 49332–49341, 2003.
19.
KanaiAJ, PearceLL, ClemensPR, BirderLA, VanBibberMM, ChoiS-Y, de GroatWC, and PetersonJ. Identification of a neuronal nitric oxide synthase in isolated cardiac mitochondria using electrochemical detection. Proc Natl Acad Sci U S A, 98: 14126–14131, 2001.
20.
KanehisaM and GotoS. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res, 28: 27–30, 2000.
21.
KimDI, JensenSC, NobleKA, KcB, RouxKH, MotamedchabokiK, and RouxKJ. An improved smaller biotin ligase for BioID proximity labeling. Mol Biol Cell, 27: 1188–1196, 2016.
22.
LancasterJRJr. How are nitrosothiols formed de novo in vivo?. Arch Biochem Biophys, 617: 137–144, 2017.
23.
LeziE and SwerdlowRH. Mitochondria in neurodegeneration. Adv Exp Med Biol, 942: 269–286, 2012.
24.
LiS, YuK, WuG, ZhangQ, WangP, ZhengJ, LiuZ-X, WangJ, GaoX, and ChengH. pCysMod: Prediction of multiple cysteine modifications based on deep learning framework. Front Cell Dev Biol, 9: 617366, 2021.
25.
LiuL, HausladenA, ZengM, QueL, HeitmanJ, and StamlerJS. A metabolic enzyme for S-nitrosothiol conserved from bacteria to humans. Nature, 410: 490–494, 2001.
26.
LiuYW, SurkaMC, SchroeterT, LukiyanchukV, and SchmidSL. Isoform and splice-variant specific functions of dynamin-2 revealed by analysis of conditional knock-out cells. Mol Biol Cell, 19: 5347–5359, 2008.
27.
LundbergJO and WeitzbergE. Nitric oxide signaling in health and disease. Cell, 185: 2853–2878, 2022.
28.
MarmorsteinR and ZhouMM. Writers and readers of histone acetylation: structure, mechanism, and inhibition. Cold Spring Harb Perspect Biol, 6: a018762, 2014.
29.
MatsumotoA, ComatasKE, LiuL, and StamlerJS. Screening for nitric oxide-dependent protein-protein interactions. Science, 301: 657–661, 2003.
30.
MorrealeFE and WaldenH. Types of ubiquitin ligases. Cell, 165: 248.e241–248.e241, 2016.
31.
NakamuraT and LiptonSA. Emerging role of protein-protein transnitrosylation in cell signaling pathways. Antioxid Redox Signal, 18: 239–249, 2012.
32.
NakamuraT and LiptonSA. ‘SNO’-storms compromise protein activity and mitochondrial metabolism in neurodegenerative disorders. Trends Endocrinol Metab, 28: 879–892, 2017.
33.
NakamuraT, TuS, AkhtarMW, SunicoCR, OkamotoS, and LiptonSA. Aberrant protein S-nitrosylation in neurodegenerative diseases. Neuron, 78: 596–614, 2013.
34.
OhCK, SultanA, PlatzerJ, DolatabadiN, SoldnerF, McClatchyDB, DiedrichJK, YatesJR, AmbasudhanR, NakamuraT, JaenischR, and LiptonSA. S-nitrosylation of PINK1 attenuates PINK1/Parkin-dependent mitophagy in hiPSC-basedParkinson's disease. models. Cell Rep, 21: 2171–2182, 2017.
35.
OzawaK, WhalenEJ, NelsonCD, MuY, HessDT, LefkowitzRJ, and StamlerJS. S-nitrosylation of beta-arrestin regulates beta-adrenergic receptor trafficking. Mol Cell, 31: 395–405, 2008.
36.
PadavannilA, Ayala-HernandezMG, Castellanos-SilvaEA, and LettsJA. The mysterious multitude: Structural perspective on the accessory subunits of respiratory complex I. Front Mol Biosci, 8: 798353, 2021.
37.
PartovianC, ZhuangZ, MoodieK, LinM, OuchiN, SessaWC, WalshK, and SimonsM. PKC-alpha activates eNOS and increases arterial blood flow in vivo. Circ Res, 97: 482–487, 2005.
38.
PengHM, MorishimaY, JenkinsGJ, DunbarAY, LauM, PattersonC, PrattWB, and OsawaY. Ubiquitylation of neuronal nitric-oxide synthase byCHIP, a chaperone-dependentE. ligase. J Biol Chem, 279: 52970–52977, 2004.
39.
RizzaS and FilomeniG. Chronicles of a reductase: Biochemistry, genetics and physio-pathological role of GSNOR. Free Radic Biol Med, 110: 19–30, 2017.
40.
SethD, HessDT, HausladenA, WangL, WangY-J, and StamlerJS. A multiplex enzymatic machinery for cellular protein S-nitrosylation. Mol Cell, 69: 451–464.e456, 2018.
41.
SethP, HsiehPN, JamalS, WangL, GygiSP, JainMK, CollerJ, and StamlerJS. Regulation of microRNA machinery and development by interspecies S-nitrosylation. Cell, 176: 1014–1025.e1012, 2019.
42.
SowaG. Caveolae, caveolins, cavins, and endothelial cell function: New insights. Front Physiol, 2: 120, 2012.
43.
StamlerJS, SimonDI, OsborneJA, MullinsME, JarakiO, MichelT, SingelDJ, and LoscalzoJ. S-nitrosylation of proteins with nitric oxide: synthesis and characterization of biologically active compounds. Proc Natl Acad Sci U S A, 89: 444–448, 1992.
44.
StomberskiCT, HessDT, and StamlerJS. Protein S-nitrosylation: Determinants of specificity and enzymatic regulation ofS-nitrosothiol-based. signaling. Antioxid Redox Signal, 30: 1331–1351, 2017.
StoyanovskyDA, TyurinaYY, TyurinVA, AnandD, MandaviaDN, GiusD, IvanovaJ, PittB, BilliarTR, and KaganVE. Thioredoxin and lipoic acid catalyze the denitrosation of low molecular weight and protein S-nitrosothiols. J Am Chem Soc, 127: 15815–15823, 2005.
47.
SuY. Regulation of endothelial nitric oxide synthase activity by protein-protein interaction. Curr Pharm Des, 20: 3514–3520, 2014.
48.
SunicoCR, NakamuraT, RockensteinE, ManteM, AdameA, ChanSF, NewmeyerTF, MasliahE, NakanishiN, and LiptonSA. S-nitrosylation of parkin as a novel regulator of p53-mediated neuronal cell death in sporadic Parkinson's disease. Mol Neurodegener, 8: 29, 2013.
49.
SzklarczykD, GableAL, LyonD, JungeA, WyderS, Huerta-CepasJ, SimonovicM, DonchevaNT, MorrisJH, BorkP, JensenLJ, and MeringCV. STRING v11: Protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucl Acids Res, 47: D607–D613, 2019.
50.
TejeroJ, ShivaS, and GladwinMT. Sources of vascular nitric oxide and reactive oxygen species and their regulation. Physiol Rev, 99: 311–379, 2018.
51.
XieY, LuoX, LiY, ChenL, MaW, HuangJ, CuiJ, ZhaoY, XueY, ZuoZ, and RenJ. DeepNitro: Prediction of protein nitration and nitrosylation sites by deep learning. Genomics Proteomics Bioinformics, 16: 294–306, 2018.
52.
YeH, WuJ, LiangZ, ZhangY, and HuangZ. Protein S-nitrosation: Biochemistry, identification, molecular mechanisms, and therapeutic applications. J Med Chem, 65: 5902–5925, 2022.
Supplementary Material
Please find the following supplemental material available below.
For Open Access articles published under a Creative Commons License, all supplemental material carries the same license as the article it is associated with.
For non-Open Access articles published, all supplemental material carries a non-exclusive license, and permission requests for re-use of supplemental material or any part of supplemental material shall be sent directly to the copyright owner as specified in the copyright notice associated with the article.
