The proteome of higher plant mitochondria

Mitochondrion - Tập 33 - Trang 22-37 - 2017
R.S.P. Rao1, F. Salvato2, B. Thal3, H. Eubel3, J.J. Thelen4, I.M. Møller5
1Biostatistics and Bioinformatics Division, Yenepoya Research Center, Yenepoya University, Mangalore 575018, India
2Institute of Biology, Department of Plant Biology, University of Campinas, Cidade Universitária Zeferino Vaz - Barão Geraldo, Campinas CEP: 13083-970, São Paulo, Brazil
3Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, DE-30419 Hannover, Germany
4Department of Biochemistry, University of Missouri-Columbia, Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
5Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark

Tài liệu tham khảo

Adams, 2002, Genes for two mitochondrial ribosomal proteins in flowering plants are derived from their cytosolic or plastid counterparts, Plant Cell, 14, 931, 10.1105/tpc.010483 Ahsan, 2012, Scanning mutagenesis of the amino acid sequences flanking phosphorylation site 1 of the mitochondrial pyruvate dehydrogenase complex, Front. Plant Sci., 3, 153, 10.3389/fpls.2012.00153 Alban, 2011, Biotin (vitamin B8) synthesis in plants, Adv. Bot. Res., 59, 39, 10.1016/B978-0-12-385853-5.00005-2 Arrieta-Montiel, 2011, Plant mitochondrial genomes and recombination. Chapter 3, 65 Balk, 2014, Iron cofactor assembly in plants, Annu. Rev. Plant Biol., 65, 125, 10.1146/annurev-arplant-050213-035759 Bannai, 2002, Extensive feature detection of N-terminal protein sorting signals, Bioinformatics, 18, 298, 10.1093/bioinformatics/18.2.298 Bardel, 2002, A survey of the plant mitochondrial proteome in relation to development, Proteomics, 2, 880, 10.1002/1615-9861(200207)2:7<880::AID-PROT880>3.0.CO;2-0 Bartoli, 2000, Ascorbate biosynthesis in mitochondria is linked to the electron transport chain between complexes III and IV, Plant Physiol., 123, 335, 10.1104/pp.123.1.335 Bedhomme, 2005, Folate metabolism in plants: an Arabidopsis homolog of the mammalian mitochondrial folate transporter mediates folate import into chloroplasts, J. Biol. Chem., 280, 34823, 10.1074/jbc.M506045200 Bergman, 1980, Method to obtain a chlorophyll-free preparation of intact mitochondria from spinach leaves, Plant Physiol., 66, 442, 10.1104/pp.66.3.442 Blancquaert, 2010, Folates and folic acid: from fundamental research toward sustainable health, Crit. Rev. Plant Sci., 29, 14, 10.1080/07352680903436283 Brand, 2010, The sites and topology of mitochondrial superoxide production, Exp. Gerontol., 45, 466, 10.1016/j.exger.2010.01.003 Braun, 2014, The life of plant mitochondrial complex I, Mitochondrion, 19, 295, 10.1016/j.mito.2014.02.006 Budde, 1988, Regulation of steady state pyruvate dehydrogenase complex activity in plant mitochondria: reactivation constraints, Plant Physiol., 88, 1026, 10.1104/pp.88.4.1026 Bykova, 2001, Involvement of matrix NADP turnover in the oxidation of NAD-linked substrates by pea leaf mitochondria, Physiol. Plant., 111, 448, 10.1034/j.1399-3054.2001.1110404.x Bykova, 2003, Identification of 14 new phosphoproteins involved in important plant mitochondrial processes, FEBS Lett., 540, 141, 10.1016/S0014-5793(03)00250-3 Calamita, 2005, The inner mitochondrial membrane has aquaporin-8 water channels and is highly permeable to water, J. Biol. Chem., 280, 17149, 10.1074/jbc.C400595200 Calvo, 2010, The mitochondrial proteome and human disease, Annu. Rev. Genomics Hum. Genet., 11, 25, 10.1146/annurev-genom-082509-141720 Calvo, 2016, MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins, Nucleic Acids Res., 44, D1251, 10.1093/nar/gkv1003 Carraretto, 2016, Ion channels in plant bioenergetic organelles, chloroplasts and mitochondria: from molecular identification to function, Mol. Plant, 9, 371, 10.1016/j.molp.2015.12.004 Carrie, 2009, Protein transport in organelles: dual targeting of proteins to mitochondria and chloroplasts, FEBS J., 276, 1187, 10.1111/j.1742-4658.2009.06876.x Casteilla, 2011, Control of mitochondrial volume by mitochondrial metabolic water, Mitochondrion, 11, 862, 10.1016/j.mito.2011.06.008 Cavalcanti, 2014, Evolution and functional implications of the tricarboxylic acid cycle as revealed by phylogenetic analysis, Genome Biol. Evol., 6, 2830, 10.1093/gbe/evu221 Chen, 2011, Malonyl-CoA synthetase, encoded by ACYL ACTIVATING ENZYME13, is essential for growth and development of Arabidopsis, Plant Cell, 23, 2247, 10.1105/tpc.111.086140 Chen, 2009, Mitochondrial proteome during salt stress-induced programmed cell death in rice, Plant Physiol. Biochem., 47, 407, 10.1016/j.plaphy.2008.12.021 Chou, 2010, A new method for predicting the subcellular localization of eukaryotic proteins with both single and multiple sites: Euk-mPLoc 2.0, PLoS ONE, 5, 10.1371/journal.pone.0009931 Chou, 2010, Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization, PLoS ONE, 5, 10.1371/journal.pone.0011335 Claros, 1995, MitoProt, a Macintosh application for studying mitochondrial proteins, Comput. Appl. Biosci., 11, 441 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 Considine, 2003, Superoxide stimulates a proton leak in potato mitochondria that is related to the activity of uncoupling protein, J. Biol. Chem., 278, 22298, 10.1074/jbc.M301075200 Cui, 2011, Integrative identification of Arabidopsis mitochondrial proteome and its function exploitation through protein interaction network, PLoS ONE, 6, 10.1371/journal.pone.0016022 Dahan, 2014, Disruption of the cytochrome c oxidase deficient1 gene leads to cytochrome c oxidase depletion and reorchestrated respiratory metabolism in Arabidopsis, Plant Physiol., 166, 1788, 10.1104/pp.114.248526 Day, 1985, Biochemical characterization of chlorophyll-free mitochondria from pea leaves, Aust. J. Plant Physiol., 12, 219 Deryabina, 2004, Mitochondrial calcium transport systems: properties, regulation, and taxonomic features, Biochem. Mosc., 69, 91, 10.1023/B:BIRY.0000016357.17251.7b Desler, 2009, In silico screening for functional candidates amongst hypothetical proteins, BMC Bioinf., 10, 289, 10.1186/1471-2105-10-289 Douce, 1985 Dubinin, 2011, The mitochondrial proteome of the model legume Medicago truncatula, Biochim. Biophys. Acta, 1814, 1658, 10.1016/j.bbapap.2011.08.008 Duncan, 2011, Multiple lines of evidence localize signaling, morphology, and lipid biosynthesis machinery to the mitochondrial outer membrane of Arabidopsis, Plant Physiol., 157, 1093, 10.1104/pp.111.183160 Emanuelsson, 2000, Predicting subcellular localization of proteins based on their N-terminal amino acid sequence, J. Mol. Biol., 300, 1005, 10.1006/jmbi.2000.3903 Eubel, 2007, Free-flow electrophoresis for purification of plant mitochondria by surface charge, Plant J., 52, 583, 10.1111/j.1365-313X.2007.03253.x Foyer, 2003, Redox sensing and signalling associated with reactive oxygen in chloroplasts, peroxisomes and mitochondria, Physiol. Plant., 119, 355, 10.1034/j.1399-3054.2003.00223.x Fromm, 2016, Mitochondrial gamma carbonic anhydrases are required for complex I assembly and plant reproductive development, New Phytol., 10.1111/nph.13886 Fujii, 2011, The evolution of RNA editing and pentatricopeptide repeat genes, New Phytol., 191, 37, 10.1111/j.1469-8137.2011.03746.x Fukasawa, 2015, MitoFates: improved prediction of mitochondrial targeting sequences and their cleavage sites, Mol. Cell. Proteomics, 14, 1113, 10.1074/mcp.M114.043083 Gabaldón, 2004, Shaping the mitochondrial proteome, Biochim. Biophys. Acta, 1659, 212, 10.1016/j.bbabio.2004.07.011 Gardeström, 2016, The origin of cytosolic ATP in photosynthetic cells, Physiol. Plant., 10.1111/ppl.12455 Gasteiger, 2003, ExPASy: the proteomics server for in-depth protein knowledge and analysis, Nucleic Acids Res., 31, 3784, 10.1093/nar/gkg563 Gawryluk, 2014, Compositional complexity of the mitochondrial proteome of a unicellular eukaryote (Acanthamoeba castellanii, supergroup Amoebozoa) rivals that of animals, fungi, and plants, J. Proteomics, 109, 400, 10.1016/j.jprot.2014.07.005 Gibon, 2000, Proline accumulation in canola leaf discs subjected to osmotic stress is related to the loss of chlorophylls and to the decrease of mitochondrial activity, Physiol. Plant., 110, 469, 10.1111/j.1399-3054.2000.1100407.x Glaser, 2011, Protein import into plant mitochondria. Chapter 11, 261 Haferkamp, 2012, The plant mitochondrial carrier family: functional and evolutionary aspects, Front. Plant Sci., 3, 2, 10.3389/fpls.2012.00002 Hatzfeld, 2000, Beta-cyanoalanine synthase is a mitochondrial cysteine synthase-like protein in spinach and Arabidopsis, Plant Physiol., 123, 1163, 10.1104/pp.123.3.1163 Havelund, 2013, Biochemistry and proteomics of mitochondria from non-photosynthetic tissues, Front. Plant Sci., 4, 51, 10.3389/fpls.2013.00051 Heazlewood, 2005, AMPDB: the Arabidopsis mitochondrial protein database, Nucleic Acids Res., 33, D605, 10.1093/nar/gki048 Heazlewood, 2004, Experimental analysis of the Arabidopsis mitochondrial proteome highlights signaling and regulatory components, provides assessment of targeting prediction programs, and indicates plant-specific mitochondrial proteins, Plant Cell, 16, 241, 10.1105/tpc.016055 Hildebrandt, 2015, Amino acid catabolism in plants, Mol. Plant, 8, 1563, 10.1016/j.molp.2015.09.005 Hiraga, 1980, The mitochondrial glycine cleavage system. Purification and properties of glycine decarboxylase from chicken liver mitochondria, J. Biol. Chem., 255, 11664, 10.1016/S0021-9258(19)70183-5 Hoefnagel, 1998, Interdependence between chloroplasts and mitochondria in the light and the dark, BBA-Bioenergetics, 1366, 235, 10.1016/S0005-2728(98)00126-1 Hong, 2012, Mitochondrial proteomic analysis of CAM plants, Ananas comosus and Kalanchoë pinnata, Ann. Biol. Res., 3, 88 Hooper, 2014, SUBAcon: a consensus algorithm for unifying the subcellular localization data of the Arabidopsis proteome, Bioinformatics, 30, 3356, 10.1093/bioinformatics/btu550 Horton, 2007, WoLF PSORT: protein localization predictor, Nucleic Acids Res., 35, W585, 10.1093/nar/gkm259 Hosp, 2017, Lysine acetylation in mitochondria: from inventory to function, Mitochondrion, 33, 58, 10.1016/j.mito.2016.07.012 Howell, 2007, Oxygen initiation of respiration and mitochondrial biogenesis in rice, J. Biol. Chem., 282, 15619, 10.1074/jbc.M609866200 Huang, 2009, Experimental analysis of the rice mitochondrial proteome, its biogenesis, and heterogeneity, Plant Physiol., 149, 719, 10.1104/pp.108.131300 Huang, 2009, Refining the definition of plant mitochondrial presequences through analysis of sorting signals, N-terminal modifications, and cleavage motifs, Plant Physiol., 150, 1272, 10.1104/pp.109.137885 Ito, 2009, A survey of the Arabidopsis thaliana mitochondrial phosphoproteome, Proteomics, 9, 4229, 10.1002/pmic.200900064 Jackson, 1979, Separation of mitochondria from contaminating subcellular structures utilizing silica sol gradient centrifugation, Plant Physiol., 64, 150, 10.1104/pp.64.1.150 Jacoby, 2010, Wheat mitochondrial proteomes provide new links between antioxidant defense and plant salinity tolerance, J. Proteome Res., 9, 6595, 10.1021/pr1007834 Jacoby, 2013, Investigating the role of respiration in plant salinity tolerance by analyzing mitochondrial proteomes from wheat and a salinity-tolerant amphiploid (wheat×Lophopyrum elongatum), J. Proteome Res., 12, 4807, 10.1021/pr400504a Jacome, 2015, N-terminome analysis of the human mitochondrial proteome, Proteomics, 15, 2519, 10.1002/pmic.201400617 Jarmuszkiewicz, 2010, Potassium channels in the mitochondria of unicellular eukaryotes and plants, FEBS Lett., 584, 2057, 10.1016/j.febslet.2010.01.023 Kim, 2009, PCHM: a bioinformatic resource for high-throughput human mitochondrial proteome searching and comparison, Comput. Biol. Med., 39, 689, 10.1016/j.compbiomed.2009.05.006 Kim, 2014, Profiling of mitochondrial proteome in wheat roots, Mol. Biol. Rep., 41, 5359, 10.1007/s11033-014-3407-z Kinraide, 2010, The surface charge density of plant cell membranes (sigma): an attempt to resolve conflicting values for intrinsic sigma, J. Exp. Bot., 61, 2507, 10.1093/jxb/erq082 Klodmann, 2011, Defining the protein complex proteome of plant mitochondria, Plant Physiol., 157, 587, 10.1104/pp.111.182352 Krömer, 1995, Respiration during photosynthesis, Annu. Rev. Plant Physiol. Plant Mol. Biol., 46, 45, 10.1146/annurev.pp.46.060195.000401 Kruft, 2001, Proteomic approach to identify novel mitochondrial proteins in Arabidopsis, Plant Physiol., 127, 1694, 10.1104/pp.010474 Kruse, 2017, Mitochondrial phosphoproteomics, Mitochondrion, 33, 45, 10.1016/j.mito.2016.08.004 Kubo, 2008, Angiosperm mitochondrial genomes and mutations, Mitochondrion, 8, 5, 10.1016/j.mito.2007.10.006 Kühn, 2011, The RCC1 family protein RUG3 is required for splicing of nad2 and complex I biogenesis in mitochondria of Arabidopsis thaliana, Plant J., 67, 1067, 10.1111/j.1365-313X.2011.04658.x Lee, 2006, A role for mitochondrial aquaporins in cellular life-and-death decisions?, Am. J. Phys. Cell Physiol., 291, C195, 10.1152/ajpcell.00641.2005 Lee, 2008, Heterogeneity of the mitochondrial proteome for photosynthetic and non-photosynthetic Arabidopsis metabolism, Mol. Cell. Proteomics, 7, 1297, 10.1074/mcp.M700535-MCP200 Lee, 2011, Combining proteomics of root and shoot mitochondria and transcript analysis to define constitutive and variable components in plant mitochondria, Phytochemistry, 72, 1092, 10.1016/j.phytochem.2010.12.004 Lee, 2012, Mitochondrial proteome heterogeneity between tissues from the vegetative and reproductive stages of Arabidopsis thaliana development, J. Proteome Res., 11, 3326, 10.1021/pr3001157 Lee, 2013, Recent advances in the composition and heterogeneity of the Arabidopsis mitochondrial proteome, Front. Plant Sci., 4, 4, 10.3389/fpls.2013.00004 Lee, 2013, Cellular responses to l-serine in Saccharomyces cerevisiae: roles of general amino acid control, compartmentalization, and aspartate synthesis, FEMS Yeast Res., 13, 618, 10.1111/1567-1364.12063 Lightowlers, 2013, Human pentatricopeptide proteins, RNA Biol., 10, 1433, 10.4161/rna.24770 Logan, 2004, Mitochondrial morphology, dynamics and inheritance, 13 Lorenz, 2015, In vitro analyses of mitochondrial ATP/phosphate carriers from Arabidopsis thaliana revealed unexpected Ca2+-effects, BMC Plant Biol., 15, 285, 10.1186/s12870-015-0616-0 Lyubushkina, 2011, The role of mitochondria in response of wild grass Elymus sibiricus L. seedlings to temperature stress, water deficiency and hydrogen peroxide exposure, J. Stress Physiol. Biochem., 7, 97 Mackenzie, 1999, Higher plant mitochondria, Plant Cell, 11, 571, 10.1105/tpc.11.4.571 Manna, 2015, An overview of pentatricopeptide repeat proteins and their applications, Biochimie, 113, 93, 10.1016/j.biochi.2015.04.004 Matamoros, 2013, Mitochondria are an early target of oxidative modifications in senescing legume nodules, New Phytol., 197, 873, 10.1111/nph.12049 Maxwell, 1999, The alternative oxidase lowers mitochondrial reactive oxygen production in plant cells, Proc. Natl. Acad. Sci. U. S. A., 96, 8271, 10.1073/pnas.96.14.8271 Meinken, 2012, Computational prediction of protein subcellular locations in eukaryotes: an experience report, Comput. Mol. Biol., 2, 1 Meyer, 2011, Insights into the composition and assembly of the membrane arm of plant complex I through analysis of subcomplexes in Arabidopsis mutant lines, J. Biol. Chem., 286, 26081, 10.1074/jbc.M110.209601 Millar, 2003, Genomic and proteomic analysis of mitochondrial carrier proteins in Arabidopsis, Plant Physiol., 131, 443, 10.1104/pp.009985 Millar, 2004, Mitochondrial cytochrome c oxidase and succinate dehydrogenase complexes contain plant specific subunits, Plant Mol. Biol., 56, 77, 10.1007/s11103-004-2316-2 Millar, 2003, Control of ascorbate synthesis by respiration and its implications for stress responses, Plant Physiol., 133, 443, 10.1104/pp.103.028399 Millar, 2001, Analysis of the Arabidopsis mitochondrial proteome, Plant Physiol., 127, 1711, 10.1104/pp.010387 Millar, 2004, Changes in the mitochondrial proteome during the anoxia to air transition in rice focus around cytochrome-containing respiratory complexes, J. Biol. Chem., 279, 39471, 10.1074/jbc.M406015200 Mittler, 2004, Reactive oxygen gene network of plants, Trends Plant Sci., 9, 490, 10.1016/j.tplants.2004.08.009 Miyaji, 2015, AtPHT4;4 is a chloroplast-localized ascorbate transporter in Arabidopsis, Nat. Commun., 6, 5928, 10.1038/ncomms6928 Møller, 1975, Unpublished observation Møller, 2001, Plant mitochondria and oxidative stress. Electron transport, NADPH turnover and metabolism of reactive oxygen species, Annu. Rev. Plant Physiol. Plant Mol. Biol., 52, 561, 10.1146/annurev.arplant.52.1.561 Møller, 2016, What is hot in plant mitochondria?, Physiol. Plant., 10.1111/ppl.12456 Møller, 1998, The role of NADP in the mitochondrial matrix, Trends Plant Sci., 3, 21, 10.1016/S1360-1385(97)01156-4 Møller, 2010, ROS signalling – specificity is required, Trends Plant Sci., 15, 370, 10.1016/j.tplants.2010.04.008 Møller, 1981, 9-Aminoacridine as a fluorescent probe of the electrical diffuse layer associated with the membranes of plant mitochondria, Biochem. J., 193, 37, 10.1042/bj1930037 Møller, 2015, The potato tuber mitochondrial proteome further expanded Møller, 2007, Oxidative modifications to cellular components in plants, Annu. Rev. Plant Biol., 58, 459, 10.1146/annurev.arplant.58.032806.103946 Møller, 2011, Protein carbonylation and metal-catalyzed protein oxidation in a cellular perspective, J. Proteomics, 74, 2228, 10.1016/j.jprot.2011.05.004 Mooney, 2002, The complex fate of alpha-ketoacids, Annu. Rev. Plant Biol., 53, 357, 10.1146/annurev.arplant.53.100301.135251 Munoz-Montesino, 2014, Mitochondrial ascorbic acid transport is mediated by a low-affinity form of the sodium-coupled ascorbic acid transporter-2, Free Radic. Biol. Med., 70, 241, 10.1016/j.freeradbiomed.2014.02.021 Nakai, 1999, PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization, Trends Biochem. Sci., 24, 34, 10.1016/S0968-0004(98)01336-X Nakai, 1992, A knowledge base for predicting protein localization sites in eukaryotic cells, Genomics, 14, 897, 10.1016/S0888-7543(05)80111-9 Neuburger, 1982, Purification of plant mitochondria by isopycnic centrifugation in density gradients of Percoll, Arch. Biochem. Biophys., 217, 312, 10.1016/0003-9861(82)90507-0 Ng, 2014, Anterograde and retrograde regulation of nuclear genes encoding mitochondrial proteins during growth, development, and stress, Mol. Plant, 7, 1075, 10.1093/mp/ssu037 Nietzel, 2017, Redox regulation of mitochondrial proteins and proteomes by cysteine thiol switches, Mitochondrion, 33, 72, 10.1016/j.mito.2016.07.010 Oliver, 1994, The glycine decarboxylase complex from plant mitochondria, Annu. Rev. Plant Physiol. Plant Mol. Biol., 45, 323, 10.1146/annurev.pp.45.060194.001543 Palmieri, 2011, Evolution, structure and function of mitochondrial carriers: a review with new insights, Plant J., 66, 161, 10.1111/j.1365-313X.2011.04516.x Pastore, 1999, The existence of the K+ channel in plant mitochondria, J. Biol. Chem., 274, 26683, 10.1074/jbc.274.38.26683 Pertoft, 1978, Density gradients prepared from colloidal silica particles coated by polyvinylpyrrolidone (Percoll), Anal. Biochem., 88, 271, 10.1016/0003-2697(78)90419-0 Pertoft, 2000, Fractionation of cells and subcellular particles with Percoll, J. Biochem. Biophys. Methods, 44, 1, 10.1016/S0165-022X(00)00066-X Peters, 2012, Complex I-complex II ratio strongly differs in various organs of Arabidopsis thaliana, Plant Mol. Biol., 79, 273, 10.1007/s11103-012-9911-4 Picault, 2004, The growing family of mitochondrial carriers in Arabidopsis, Trends Plant Sci., 9, 138, 10.1016/j.tplants.2004.01.007 Pineau, 2008, l-Galactono-1,4-lactone dehydrogenase is required for the accumulation of plant respiratory complex I, J. Biol. Chem., 283, 32500, 10.1074/jbc.M805320200 Piper, 2002, Regulation of the yeast glycine cleavage genes is responsive to the availability of multiple nutrients, FEMS Yeast Res., 2, 59, 10.1016/S1567-1356(01)00061-7 Radi, 1991, Detection of catalase in rat heart mitochondria, J. Biol. Chem., 266, 22028, 10.1016/S0021-9258(18)54740-2 Rasmusson, 2011, Mitochondrial electron transport and plant stress. Chapter 14, 357 Rasmusson, 2008, The multiplicity of dehydrogenases in the electron transport chain of plant mitochondria, Mitochondrion, 8, 47, 10.1016/j.mito.2007.10.004 Rizzuto, 2000, Mitochondria as all-round players of the calcium game, J. Physiol., 529, 37, 10.1111/j.1469-7793.2000.00037.x Robert, 2012, Voltage-dependent-anion-channels (VDACs) in Arabidopsis have a dual localization in the cell but show a distinct role in mitochondria, Plant Mol. Biol., 78, 431, 10.1007/s11103-012-9874-5 Rode, 2011, GelMap - a novel software tool for building and presenting proteome reference maps, J Proteomics, 74, 2214, 10.1016/j.jprot.2011.06.017 Rubin, 1977, Regulation of plant pyruvate dehydrogenase complex by phosphorylation, Plant Physiol., 60, 34, 10.1104/pp.60.1.34 Ruy, 2004, A highly active ATP-insensitive K+ import pathway in plant mitochondria, J. Bioenerg. Biomembr., 36, 195, 10.1023/B:JOBB.0000023623.70126.04 Salvato, 2014, The potato tuber mitochondrial proteome, Plant Physiol., 164, 637, 10.1104/pp.113.229054 Savojardo, 2014, TPpred2: improving the prediction of mitochondrial targeting peptide cleavage sites by exploiting sequence motifs, Bioinformatics, 30, 2973, 10.1093/bioinformatics/btu411 Saxena, 2005, Cloning and characterization of a mitochondrial glyoxalase II from Brassica juncea that is upregulated by NaCl, Zn, and ABA, Biochem. Biophys. Res. Commun., 336, 813, 10.1016/j.bbrc.2005.08.178 Schaedler, 2014, A conserved mitochondrial ATP-binding cassette transporter exports glutathione polysulfide for cytosolic metal cofactor assembly, J. Biol. Chem., 289, 23264, 10.1074/jbc.M114.553438 Schertl, 2014, Biochemical characterization of proline dehydrogenase in Arabidopsis mitochondria, FEBS J., 281, 2794, 10.1111/febs.12821 Schwitzguébel, 1981, Changes in density of mitochondria and glyoxysomes from Neurospora crassa: a reevaluation utilizing silica sol gradient centrifugation, J. Gen. Microbiol., 126, 289 Small, 2000, The PPR motif: a TPR-related motif prevalent in plant organellar proteins, Trends Biochem. Sci., 25, 46, 10.1016/S0968-0004(99)01520-0 Small, 2004, Predotar: a tool for rapidly screening proteomes for N-terminal targeting sequences, Proteomics, 4, 1581, 10.1002/pmic.200300776 Smith, 2016, MitoMiner v3.1, an update on the mitochondrial proteomics database, Nucleic Acids Res., 44, D1258, 10.1093/nar/gkv1001 Soto, 2010, TIP5;1 is an aquaporin specifically targeted to pollen mitochondria and is probably involved in nitrogen remobilization in Arabidopsis thaliana, Plant J., 64, 1038, 10.1111/j.1365-313X.2010.04395.x Srere, 1980, The infrastructure of the mitochondrial matrix, Trends Biochem. Sci., 5, 120, 10.1016/0968-0004(80)90051-1 Stover, 1990, Serine hydroxymethyltransferase catalyzes the hydrolysis of 5,10-methenyltetrahydrofolate to 5-formyltetrahydrofolate, J. Biol. Chem., 265, 14227, 10.1016/S0021-9258(18)77290-6 Struglics, 1993, The presence of a short redox chain in the membrane of potato tuber peroxisomes and the association of malate dehydrogenase with the membrane, Physiol. Plant., 88, 19, 10.1111/j.1399-3054.1993.tb01755.x Svensson, 2001, Light-dependent gene expression for proteins in the respiratory chain of potato leaves, Plant J., 28, 73, 10.1046/j.1365-313X.2001.01128.x Svensson, 2002, Cold stress decreases the capacity for respiratory NADH oxidation in potato leaves, FEBS Lett., 517, 79, 10.1016/S0014-5793(02)02581-4 Szarka, 2004, Facilitated glucose and dehydroascorbate transport in plant mitochondria, Arch. Biochem. Biophys., 428, 73, 10.1016/j.abb.2004.05.011 2014 Tan, 2012, Components of mitochondrial oxidative phosphorylation vary in abundance following exposure to cold and chemical stresses, J. Proteome Res., 11, 3860, 10.1021/pr3003535 Taylor, 2005, Differential impact of environmental stresses on the pea mitochondrial proteome, Mol. Cell. Proteomics, 4, 1122, 10.1074/mcp.M400210-MCP200 Thal, 2015, Functional and proteomic comparison of V. faba root and symbiotic root nodule mitochondria Thelen, 2000, Pyruvate dehydrogenase kinase from Arabidopsis thaliana: a protein histidine kinase that phosphorylates serine residues, Biochem. J., 349, 195, 10.1042/bj3490195 Thelen, 1998, Molecular analysis of two pyruvate dehydrogenase kinases from maize, J. Biol. Chem., 273, 26618, 10.1074/jbc.273.41.26618 Vauclare, 1996, Regulation of the expression of the glycine decarboxylase complex during pea leaf development, Plant Physiol., 112, 1523, 10.1104/pp.112.4.1523 Veena, 1999, Glyoxalase I from Brassica juncea: molecular cloning, regulation and its over-expression confer tolerance in transgenic tobacco under stress, Plant J., 17, 385, 10.1046/j.1365-313X.1999.00390.x Wagner, 2015, The EF-hand Ca2+ binding protein MICU choreographs mitochondrial Ca2+ dynamics in Arabidopsis, Plant Cell, 27, 3190, 10.1105/tpc.15.00509 Waller, 2012, Mitochondrial and plastidial COG0354 proteins have folate-dependent functions in iron-sulphur cluster metabolism, J. Exp. Bot., 63, 403, 10.1093/jxb/err286 Wang, 2015, Comparative studies of mitochondrial proteomics reveal an intimate protein network of male sterility in wheat (Triticum aestivum L.), J. Exp. Bot., 66, 6191, 10.1093/jxb/erv322 Welchen, 2014, Coordination of plant mitochondrial biogenesis: keeping pace with cellular requirements, Front. Plant Sci., 4, 551, 10.3389/fpls.2013.00551 Werhahn, 2002, Biochemical dissection of the mitochondrial proteome from Arabidopsis thaliana by three-dimensional gel electrophoresis, Electrophoresis, 23, 640, 10.1002/1522-2683(200202)23:4<640::AID-ELPS640>3.0.CO;2-F Wiedemann, 2004, The protein import machinery of mitochondria, J. Biol. Chem., 279, 14473, 10.1074/jbc.R400003200 Wydro, 2013, The evolutionarily conserved iron-sulfur protein INDH is required for complex I assembly and mitochondrial translation in Arabidopsis, Plant Cell, 25, 4014, 10.1105/tpc.113.117283 Yasuno, 1998, Biosynthesis of lipoic acid in Arabidopsis: cloning and characterization of the cDNA for lipoic acid synthase, Plant Physiol., 118, 935, 10.1104/pp.118.3.935 Yasuno, 2004, Identification and molecular characterization of the beta-ketoacyl-acyl carrier protein synthase component of the Arabidopsis mitochondrial fatty acid synthase, J. Biol. Chem., 279, 8242, 10.1074/jbc.M308894200 Zanin, 2010, Evidence that core histone H3 is targeted to the mitochondria in Brassica oleracea, Cell Biol. Int., 34, 997, 10.1042/CBI20090281 Zhou, 1998, Effect of hypoxia on sugar accumulation, respiration, activities of amylase and starch phosphorylase, and induction of alternative oxidase and acid invertase during storage of potato tubers (Solanum tuberosum cv. Russet Burbank) at 1 °C, Physiol. Plant., 104, 255, 10.1034/j.1399-3054.1998.1040214.x