Mitochondrial Chemical Biology: New Probes Elucidate the Secrets of the Powerhouse of the Cell

Cell Chemical Biology - Tập 23 - Trang 917-927 - 2016
Simon Wisnovsky1, Eric K. Lei1, Sae Rin Jean2, Shana O. Kelley1,2,3
1Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
2Department of Chemistry, Faculty of Arts and Science, University of Toronto, Toronto, ON M5S 3H6, Canada
3Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada

Tài liệu tham khảo

Abbate, 2015, Dual selective iron chelating probes with a potential to monitor mitochondrial labile iron pools, Chem. Commun., 52, 784, 10.1039/C5CC06170A Adlam, 2005, Targeting an antioxidant to mitochondria decreases cardiac ischemia-reperfusion injury, FASEB J., 19, 1088, 10.1096/fj.05-3718com Bacman, 2013, Specific elimination of mutant mitochondrial genomes in patient-derived cells by mitoTALENs, Nat. Med., 19, 1111, 10.1038/nm.3261 Bralha, 2015, Targeting mitochondrial RNA polymerase in acute myeloid leukemia, Oncotarget, 6, 37216, 10.18632/oncotarget.6129 Calvo, 2010, The mitochondrial proteome and human disease, Annu. Rev. Genomics Hum. Genet., 11, 25, 10.1146/annurev-genom-082509-141720 Calvo, 2015, MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins, Nucleic Acids Res., 44, 1251, 10.1093/nar/gkv1003 Carreon, 2004, Thiazole orange−peptide conjugates:  sensitivity of DNA binding to chemical structure, Org. Lett., 6, 517, 10.1021/ol0362818 Chalmers, 2012, Selective uncoupling of individual mitochondria within a cell using a mitochondria-targeted photoactivated protonophore, J. Am. Chem. Soc., 134, 758, 10.1021/ja2077922 Chamberlain, 2013, Targeted delivery of doxorubicin to mitochondria, ACS Chem. Biol., 8, 1389, 10.1021/cb400095v Chang, 2002, A genome-wide screen for methyl methanesulfonate-sensitive mutants reveals genes required for S phase progression in the presence of DNA damage, Proc. Natl. Acad. Sci. USA, 99, 16934, 10.1073/pnas.262669299 Cheng, 2013, A highly specific BODIPY-based probe localized in mitochondria for HClO imaging, Analyst, 138, 6091, 10.1039/c3an01152f Cheung-Ong, 2013, DNA-damaging agents in cancer chemotherapy: serendipity and chemical biology, Chem. Biol., 20, 648, 10.1016/j.chembiol.2013.04.007 Chouchani, 2013, Cardioprotection by S-nitrosation of a cysteine switch on mitochondrial complex I, Nat. Med., 19, 753, 10.1038/nm.3212 Chyan, 2014, Reaction-based fluorescent sensor for investigating mobile Zn2+ in mitochondria of healthy versus cancerous prostate cells, Proc. Natl. Acad. Sci. USA, 111, 143, 10.1073/pnas.1310583110 Claros, 1996, Computational method to predict mitochondrially imported proteins and their targeting sequences, Eur. J. Biochem., 241, 779, 10.1111/j.1432-1033.1996.00779.x Cocheme, 2011, Measurement of H2O2 within living Drosophila during aging using a ratiometric mass spectrometry probe targeted to the mitochondrial matrix, Cell Metab., 13, 340, 10.1016/j.cmet.2011.02.003 Cole, 2015, Inhibition of the mitochondrial protease ClpP as a therapeutic strategy for human acute myeloid leukemia, Cancer Cell, 27, 864, 10.1016/j.ccell.2015.05.004 Cossarizza, 1993, A new method for the cytofluorometric analysis of mitochondrial membrane potential using the J-aggregate forming lipophilic cation 5,5′,6,6′-tetrachloro-1,1′,3,3′-tetraethylbenzimidazolcarbocyanine iodide (JC-1), Biochem. Biophys. Res. Commun., 197, 40, 10.1006/bbrc.1993.2438 Cullen, 2007, Mitochondria as a critical target of the chemotherapeutic agent cisplatin in head and neck cancer, J. Bioenerg. Biomembr., 39, 43, 10.1007/s10863-006-9059-5 Dickinson, 2008, A targetable fluorescent probe for imaging hydrogen peroxide in the mitochondria of living cells, J. Am. Chem. Soc., 130, 9638, 10.1021/ja802355u Dodani, 2011, A targetable fluorescent sensor reveals that copper-deficient SCO1 and SCO2 patient cells prioritize mitochondrial copper homeostasis, J. Am. Chem. Soc., 133, 8606, 10.1021/ja2004158 Duchen, 2004, Mitochondria in health and disease: perspectives on a new mitochondrial biology, Mol. Aspects Med., 25, 365, 10.1016/j.mam.2004.03.001 Emanuelsson, 2007, Locating proteins in the cell using TargetP, SignalP and related tools, Nat. Protoc., 2, 953, 10.1038/nprot.2007.131 Fonseca, 2011, Rerouting chlorambucil to mitochondria combats drug deactivation and resistance in cancer cells, Chem. Biol., 18, 445, 10.1016/j.chembiol.2011.02.010 Frezza, 2007, Organelle isolation: functional mitochondria from mouse liver, muscle and cultured fibroblasts, Nat. Protoc., 2, 287, 10.1038/nprot.2006.478 Gammage, 2014, Mitochondrially targeted ZFNs for selective degradation of pathogenic mitochondrial genomes bearing large-scale deletions or point mutations, EMBO Mol. Med., 6, 458, 10.1002/emmm.201303672 Giepmans, 2006, The fluorescent toolbox for assessing protein location and function, Science, 312, 217, 10.1126/science.1124618 Harbauer, 2014, The protein import machinery of mitochondria—a regulatory hub in metabolism, stress, and disease, Cell Metab., 19, 357, 10.1016/j.cmet.2014.01.010 Hashimoto, 2015, MitoTALEN: a general approach to reduce mutant mtDNA loads and restore oxidative phosphorylation function in mitochondrial diseases, Mol. Ther., 23, 1592, 10.1038/mt.2015.126 Helleday, 2008, DNA repair pathways as targets for cancer therapy, Nat. Rev. Cancer, 8, 193, 10.1038/nrc2342 Holt, 1988, Deletions of muscle mitochondrial DNA in patients with mitochondrial myopathies, Nature, 331, 717, 10.1038/331717a0 Hoogeweijs, 2016, Assessing the delivery of molecules to the mitochondrial matrix using click chemistry, ChemBioChem, 10.1002/cbic.201600188 Horton, 2008, Mitochondria-penetrating peptides, Chem. Biol., 15, 375, 10.1016/j.chembiol.2008.03.015 Hu, 2015, Fluorescent probe HKSOX-1 for imaging and detection of endogenous superoxide in live cells and in vivo, J. Am. Chem. Soc., 137, 6837, 10.1021/jacs.5b01881 Huber, 2003, Organelle proteomics: implications for subcellular fractionation in proteomics, Circul. Res., 92, 962, 10.1161/01.RES.0000071748.48338.25 Ishikawa, 2008, ROS-generating mitochondrial DNA mutations can regulate tumor cell metastasis, Science, 320, 661, 10.1126/science.1156906 Jean, 2015, Mitochondrial targeting of doxorubicin eliminates nuclear effects associated with cardiotoxicity, ACS Chem. Biol., 10, 2007, 10.1021/acschembio.5b00268 Jhas, 2013, Metabolic adaptation to chronic inhibition of mitochondrial protein synthesis in acute myeloid leukemia cells, PLoS One, 8, e58367, 10.1371/journal.pone.0058367 Jo, 2015, Efficient mitochondrial genome editing by CRISPR/Cas9, Biomed. Res. Int., 2015, 305716, 10.1155/2015/305716 Kang, 2009, Combinatorial drug design targeting multiple cancer signaling networks controlled by mitochondrial Hsp90, J. Clin. Invest., 119, 454, 10.1172/JCI37613 Kang, 2010, Preclinical characterization of mitochondria-targeted small molecule Hsp90 inhibitors, gamitrinibs, in advanced prostate cancer, Clin. Cancer Res., 16, 4779, 10.1158/1078-0432.CCR-10-1818 Kazak, 2012, Minimizing the damage: repair pathways keep mitochondrial DNA intact, Nat. Rev. Mol. Cell Biol., 13, 659, 10.1038/nrm3439 Kim, 2015, Tumor Necrosis Factor Receptor-associated Protein 1 (TRAP1) mutation and TRAP1 inhibitor gamitrinib-triphenylphosphonium (G-TPP) induce a Forkhead box O (FOXO)-dependent cell protective signal from mitochondria, J. Biol. Chem., 291, 1841, 10.1074/jbc.M115.656934 Kojima, 2009, Construction of highly reactive probes for abasic site detection by introduction of an aromatic and a guanidine residue into an aminooxy group, J. Am. Chem. Soc., 131, 13208, 10.1021/ja904767k Koopman, 2005, Inhibition of complex I of the electron transport chain causes O2-.-mediated mitochondrial outgrowth, Am. J. Physiol. Cell Physiol., 288, C1440, 10.1152/ajpcell.00607.2004 Kovtun, 2007, OGG1 initiates age-dependent CAG trinucleotide expansion in somatic cells, Nature, 447, 447, 10.1038/nature05778 Kujoth, 2005, Mitochondrial DNA mutations, oxidative stress, and apoptosis in mammalian aging, Science, 309, 481, 10.1126/science.1112125 Lewis, 2003, Mitochondrial toxicity of NRTI antiviral drugs: an integrated cellular perspective, Nat. Rev. Drug Discov., 2, 812, 10.1038/nrd1201 Li, 2013, Mitochondria-targeted reaction-based two-photon fluorescent probe for imaging of superoxide anion in live cells and in vivo, Anal. Chem., 85, 9877, 10.1021/ac402409m Li, 2014, A near-infrared-emitting fluorescent probe for monitoring mitochondrial pH, Chem. Commun., 50, 7184, 10.1039/c4cc01390e Lin, 2006, Mitochondrial dysfunction and oxidative stress in neurodegenerative diseases, Nature, 443, 787, 10.1038/nature05292 Logan, 2016, Assessing the mitochondrial membrane potential in cells and in vivo using targeted click chemistry and mass spectrometry, Cell Metab., 23, 379, 10.1016/j.cmet.2015.11.014 Mahon, 2007, Deconvolution of the cellular oxidative stress response with organelle-specific peptide conjugates, Chem. Biol., 14, 923, 10.1016/j.chembiol.2007.07.011 Marrache, 2014, Detouring of cisplatin to access mitochondrial genome for overcoming resistance, Proc. Natl. Acad. Sci. USA, 111, 10444, 10.1073/pnas.1405244111 Miao, 2014, Novel fluorescent probes for highly selective two-photon imaging of mitochondria in living cells, Biosens. Bioelectron., 55, 423, 10.1016/j.bios.2013.12.044 Murphy, 2008, Targeting lipophilic cations to mitochondria, Biochim. Biophys. Acta, 1777, 1028, 10.1016/j.bbabio.2008.03.029 Pinto, 2015, Mechanisms linking mtDNA damage and aging, Free Radic. Biol. Med., 85, 250, 10.1016/j.freeradbiomed.2015.05.005 Podratz, 2011, Cisplatin induced mitochondrial DNA damage in dorsal root ganglion neurons, Neurobiol. Dis., 41, 661, 10.1016/j.nbd.2010.11.017 Polyzos, 2016, Mitochondrial targeting of XJB-5-131 attenuates or improves pathophysiology in HdhQ150 animals with well-developed disease phenotypes, Hum. Mol. Genet., 10.1093/hmg/ddw051 Prime, 2012, A ratiometric fluorescent probe for assessing mitochondrial phospholipid peroxidation within living cells, Free Radic. Biol. Med., 53, 544, 10.1016/j.freeradbiomed.2012.05.033 Reddy, 2015, Selective elimination of mitochondrial mutations in the germline by genome editing, Cell, 161, 459, 10.1016/j.cell.2015.03.051 Ren, 2015, A membrane-activatable near-infrared fluorescent probe with ultra-photostability for mitochondrial membrane potentials, Analyst, 141, 3679, 10.1039/C5AN01860A Rhee, 2013, Proteomic mapping of mitochondria in living cells via spatially-restricted enzymatic tagging, Science, 339, 1328, 10.1126/science.1230593 Rizzuto, 2012, Mitochondria as sensors and regulators of calcium signalling, Nat. Rev. Mol. Cell Biol., 13, 566, 10.1038/nrm3412 Robb, 2015, Selective superoxide generation within mitochondria by the targeted redox cycler MitoParaquat, Free Radic. Biol. Med., 89, 883, 10.1016/j.freeradbiomed.2015.08.021 Roux, 2012, A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells, J. Cell Biol., 196, 801, 10.1083/jcb.201112098 Schmidt, 2010, Mitochondrial protein import: from proteomics to functional mechanisms, Nat. Rev. Mol. Cell Biol., 11, 655, 10.1038/nrm2959 Schon, 2012, Human mitochondrial DNA: roles of inherited and somatic mutations, Nat. Rev. Genet., 13, 878, 10.1038/nrg3275 Sena, 2012, Physiological roles of mitochondrial reactive oxygen species, Mol. Cell, 48, 158, 10.1016/j.molcel.2012.09.025 Škrtić, 2011, Inhibition of mitochondrial translation as a therapeutic strategy for human acute myeloid leukemia, Cancer Cell, 20, 674, 10.1016/j.ccr.2011.10.015 Smith, 2016, MitoMiner v3.1, an update on the mitochondrial proteomics database, Nucleic Acids Res., 44, D1258, 10.1093/nar/gkv1001 Smith, 2012, Mitochondrial pharmacology, Trends Pharmacol. Sci., 33, 341, 10.1016/j.tips.2012.03.010 Tait, 2010, Mitochondria and cell death: outer membrane permeabilization and beyond, Nat. Rev. Mol. Cell Biol., 11, 621, 10.1038/nrm2952 Taki, 2014, A mitochondria-targeted turn-on fluorescent probe based on a rhodol platform for the detection of copper(I), Org. Biomol. Chem., 12, 4999, 10.1039/C4OB00527A Titov, 2016, Complementation of mitochondrial electron transport chain by manipulation of the NAD+/NADH ratio, Science, 352, 231, 10.1126/science.aad4017 Wen, 2015, Mitochondria-directed fluorescent probe for the detection of hydrogen peroxide near mitochondrial DNA, Anal. Chem., 87, 10579, 10.1021/acs.analchem.5b03326 Williams, 2014, Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling, Science, 346, 748, 10.1126/science.1257522 Wisnovsky, 2013, Targeting mitochondrial DNA with a platinum-based anticancer agent, Chem. Biol., 20, 1323, 10.1016/j.chembiol.2013.08.010 Wisnovsky, 2016, Mitochondrial DNA repair and replication proteins revealed by targeted chemical probes, Nat. Chem. Biol., 12, 567, 10.1038/nchembio.2102 Xiao, 2015, A fast-responsive mitochondria-targeted fluorescent probe detecting endogenous hypochlorite in living RAW 264.7 cells and nude mouse, Chem. Commun., 51, 1442, 10.1039/C4CC07411D Xu, 2008, Manipulating the metazoan mitochondrial genome with targeted restriction enzymes, Science, 321, 575, 10.1126/science.1160226 Xu, 2016, Mitochondria-targeted fluorescent probe for imaging hydrogen peroxide in living cells, Anal. Chem., 88, 1455, 10.1021/acs.analchem.5b04424 Yakes, 1997, Mitochondrial DNA damage is more extensive and persists longer than nuclear DNA damage in human cells following oxidative stress, Proc. Natl. Acad. Sci. USA, 94, 514, 10.1073/pnas.94.2.514 Yasueda, 2016, A set of organelle-localizable reactive molecules for mitochondrial chemical proteomics in living cells and brain tissues, J. Am. Chem. Soc., 138, 7592, 10.1021/jacs.6b02254 Yin, 2016, Mitochondria-targeted molecules MitoQ and SS31 reduce mutant huntingtin-induced mitochondrial toxicity and synaptic damage in Huntington's disease, Hum. Mol. Genet., 10.1093/hmg/ddw045 Yu, 2013, Reversible near-infrared fluorescent probe introducing tellurium to mimetic glutathione peroxidase for monitoring the redox cycles between peroxynitrite and glutathione in vivo, J. Am. Chem. Soc., 135, 7674, 10.1021/ja401360a Zhang, 2012, Identification of the molecular basis of doxorubicin-induced cardiotoxicity, Nat. Med., 18, 1, 10.1038/nm.2919 Zhang, 2015, Visualizing changes in mitochondrial Mg2+during apoptosis with organelle-targeted triazole-based ratiometric fluorescent sensors, Chem. Sci., 6, 6841, 10.1039/C5SC02442K Zhang, 2015, A mitochondria-targetable fluorescent probe for peroxynitrite: fast response and high selectivity, Chem. Commun., 51, 2721, 10.1039/C4CC09122A Zhao, 2004, Cell-permeable peptide antioxidants targeted to inner mitochondrial membrane inhibit mitochondrial swelling, oxidative cell death, and reperfusion injury, J. Biol. Chem., 279, 34682, 10.1074/jbc.M402999200 Zhou, 2002, Transcriptional regulation of mitotic genes by camptothecin-induced DNA damage microarray analysis of dose-and time-dependent effects, Cancer Res., 62, 1688