The potato tuber mitochondrial proteome

Plant Physiology

Volumn 164, Issue 2, 2014, Pages 637-653

  Salvato, Fernanda ^a,e   Havelund, Jesper F ^b,c   Chen, Mingjie ^a   Shyama Prasad Rao, R ^a   Rogowska Wrzesinska, Adelina ^c   Jensen, Ole N ^c   Gang, David R ^d   Thelen, Jay J ^a   Møller, Ian Max ^b  

^a University of Missouri   (United States)

^b AARHUS UNIVERSITY   (Denmark)

^c UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^d WASHINGTON STATE UNIVERSITY   (United States)

^e UNIVERSITY OF CAMPINAS   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL PROTEIN; PEPTIDE; PROTEOME; VEGETABLE PROTEIN;

ARABIDOPSIS; ARTICLE; CELL FRACTIONATION; CHEMISTRY; CYTOLOGY; FLUORESCENCE; LIQUID CHROMATOGRAPHY; METABOLISM; MITOCHONDRION; PLANT EPIDERMIS; PLANT TUBER; POTATO; PROTEIN DATABASE; PROTEIN PROCESSING; PROTEIN TRANSPORT; TANDEM MASS SPECTROMETRY; TOBACCO;

ARABIDOPSIS; CHROMATOGRAPHY, LIQUID; DATABASES, PROTEIN; FLUORESCENCE; MITOCHONDRIA; MITOCHONDRIAL PROTEINS; PEPTIDES; PLANT EPIDERMIS; PLANT PROTEINS; PLANT TUBERS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEIN TRANSPORT; PROTEOME; SOLANUM TUBEROSUM; SUBCELLULAR FRACTIONS; TANDEM MASS SPECTROMETRY; TOBACCO;

EID: 84893484597     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.113.229054     Document Type: Article

References (86)

1. Alban C (2011) Biotin (vitamin B8) synthesis in plants. Adv Bot Res 59: 39-66
2. Balbuena TS, Salas JJ, Martínez-Force E, Garcés R, Thelen JJ (2011) Proteome analysis of cold acclimation in sunflower. J Proteome Res 10: 2330-2346
3. Bannai H, Tamada Y, Maruyama O, Nakai K, Miyano S (2002) Extensive feature detection of N-terminal protein sorting signals. Bioinformatics 18: 298-305
4. Bartoli CG, Pastori GM, Foyer CH (2000) Ascorbate biosynthesis in mitochondria is linked to the electron transport chain between complexes III and IV. Plant Physiol 123: 335-344
5. Bjellqvist B, Basse B, Olsen E, Celis JE (1994) Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions. Electrophoresis 15: 529-539
6. Blancquaert D, Storozhenko S, Loizeau K, De Steur H, De Brouwer V, Viaene J, Ravanel S, Rébeillé F, Lambert W, Van Der Straeten D (2010) Folates and folic acid: from fundamental research toward sustainable health. Crit Rev Plant Sci 29: 14-35
7. Bykova NV, Møller IM (2001) Involvement of matrix NADP turnover in the oxidation of NAD-linked substrates by pea leaf mitochondria. Physiol Plant 111: 448-456
8. Calvo SE, Mootha VK (2010) The mitochondrial proteome and human disease. Annu Rev Genomics Hum Genet 11: 25-44
9. Carrari F, Coll-Garcia D, Schauer N, Lytovchenko A, Palacios-Rojas N, Balbo I, Rosso M, Fernie AR (2005) Deficiency of a plastidial adenylate kinase in Arabidopsis results in elevated photosynthetic amino acid biosynthesis and enhanced growth. Plant Physiol 137: 70-82
10. Chai MF, Wei PC, Chen QJ, An R, Chen J, Yang SH, Wang XC (2006) NADK3, a novel cytoplasmic source of NADPH, is required under conditions of oxidative stress and modulates abscisic acid responses in Arabidopsis. Plant J 47: 665-674
11. Chakrabarty R, Banerjee R, Chung SM, Farman M, Citovsky V, Hogenhout SA, Tzfira T, Goodin M (2007) PSITE vectors for stable integration or transient expression of autofluorescent protein fusions in plants: probing Nicotiana benthamiana-virus interactions. Mol Plant Microbe Interact 20: 740-750
12. Chew O, Whelan J, Millar AH (2003) Molecular definition of the ascorbateglutathione cycle in Arabidopsis mitochondria reveals dual targeting of antioxidant defenses in plants. J Biol Chem 278: 46869-46877
13. Claros MG, Vincens P (1996) Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur J Biochem 241: 779-786
14. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676
15. Considine MJ, Goodman M, Echtay KS, Laloi M, Whelan J, Brand MD, Sweetlove LJ (2003) Superoxide stimulates a proton leak in potato mitochondria that is related to the activity of uncoupling protein. J Biol Chem 278: 22298-22302
16. Cui JA, Liu JH, Li YH, Shi TL (2011) Integrative identification of Arabidopsis mitochondrial proteome and its function exploitation through protein interaction network. PLoS ONE 6: e16022
17. Dubin MJ, Bowler C, Benvenuto G (2008) A modified Gateway cloning strategy for overexpressing tagged proteins in plants. Plant Methods 4: 3
18. Duncan O, Taylor NL, Carrie C, Eubel H, Kubiszewski-Jakubiak S, Zhang B, Narsai R, Millar AH, Whelan J (2011) Multiple lines of evidence localize signaling, morphology, and lipid biosynthesis machinery to the mitochondrial outer membrane of Arabidopsis. Plant Physiol 157: 1093-1113
19. Emanuelsson O, Nielsen H, Brunak S, von Heijne G (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 300: 1005-1016
20. Eng JK, McCormack AL, Yates JR III (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 5: 976-989
21. Foyer CH, Noctor G (2003) Redox sensing and signalling associated with reactive oxygen in chloroplasts, peroxisomes and mitochondria. Physiol Plant 119: 355-364
22. Fujii S, Small I (2011) The evolution of RNA editing and pentatricopeptide repeat genes. New Phytol 191: 37-47
23. Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy server. In JM Walker, ed, The Proteomics Protocols Handbook, Humana Press, Totowa, NJ, pp 571-607
24. Giglione C, Meinnel T (2001) Organellar peptide deformylases: universality of the N-terminal methionine cleavage mechanism. Trends Plant Sci 6: 566-572
25. Havelund JF, Thelen JJ, Møller IM (2013) Biochemistry and proteomics of mitochondria from non-photosynthetic tissues. Front Plant Sci 4: 51
26. Heazlewood JL, Tonti-Filippini JS, Gout AM, Day DA, Whelan J, Millar AH (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: 241-256
27. Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res 35: W585-W587
28. Huang Y, Houston NL, Tovar-Mendez A, Stevenson SE, Miernyk JA, Randall DD, Thelen JJ (2010) A quantitative mass spectrometry-based approach for identifying protein kinase clients and quantifying kinase activity. Anal Biochem 402: 69-76
29. Islam MS, Studer B, Byrne SL, Farrell JD, Panitz F, Bendixen C, Møller IM, Asp T (2013) The genome and transcriptome of perennial ryegrass mitochondria. BMC Genomics 14: 202
30. Jimenez A, Hernandez JA, Del Rio LA, Sevilla F (1997) Evidence for the presence of the ascorbate-glutathione cycle in mitochondria and peroxisomes of pea leaves. Plant Physiol 114: 275-284
31. Kell DB (2009) Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases. BMC Med Genomics 2: 2
32. Kell DB (2010) Towards a unifying, systems biology understanding of large-scale cellular death and destruction caused by poorly liganded iron: Parkinson's, Huntington's, Alzheimer's, prions, bactericides, chemical toxicology and others as examples. Arch Toxicol 84: 825-889
33. Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJR, Pevzner PA (2010) The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search. Mol Cell Proteomics 9: 2840-2852
34. Kleffmann T, Russenberger D, von Zychlinski A, Christopher W, Sjölander K, Gruissem W, Baginsky S (2004) The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions. Curr Biol 14: 354-362
35. Klodmann J, Senkler M, Rode C, Braun HP (2011) Defining the protein complex proteome of plant mitochondria. Plant Physiol 157: 587-598
36. Kumar GN, Iyer S, Knowles NR (2007) Extraction of RNA from fresh, frozen, and lyophilized tuber and root tissues. J Agric Food Chem 55: 1674-1678
37. Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157: 105-132
38. Laemmli UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227: 680-685
39. Lee CP, Eubel H, Solheim C, Millar AH (2012) Mitochondrial proteome heterogeneity between tissues from the vegetative and reproductive stages of Arabidopsis thaliana development. J Proteome Res 11: 3326-3343
40. Li J, Cai T, Wu P, Cui Z, Chen X, Hou J, Xie Z, Xue P, Shi L, Liu P, et al (2009) Proteomic analysis of mitochondria from Caenorhabditis elegans. Proteomics 9: 4539-4553
41. Liu H, Sadygov RG, Yates JR III (2004) A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 76: 4193-4201
42. Löffler M, Fairbanks LD, Zameitat E, Marinaki AM, Simmonds HA (2005) Pyrimidine pathways in health and disease. Trends Mol Med 11: 430-437
43. Matros A, Kaspar S, Witzel K, Mock HP (2011) Recent progress in liquid chromatography-based separation and label-free quantitative plant proteomics. Phytochemistry 72: 963-974
44. Maxwell DP, Wang Y, McIntosh L (1999) The alternative oxidase lowers mitochondrial reactive oxygen production in plant cells. Proc Natl Acad Sci USA 96: 8271-8276
45. Millar AH, Heazlewood JL (2003) Genomic and proteomic analysis of mitochondrial carrier proteins in Arabidopsis. Plant Physiol 131: 443-453
46. Millar AH, Heazlewood JL, Kristensen BK, Braun HP, Møller IM (2005) The plant mitochondrial proteome. Trends Plant Sci 10: 36-43
47. Millar AH, Whelan J, Small I (2006) Recent surprises in protein targeting to mitochondria and plastids. Curr Opin Plant Biol 9: 610-615
48. Millar AH, Whelan J, Soole KL, Day DA (2011) Organization and regulation of mitochondrial respiration in plants. Annu Rev Plant Biol 62: 79-104
49. Møller IM (2001) Plant mitochondria and oxidative stress: electron transport, NADPH turnover and metabolism of reactive oxygen species. Annu Rev Plant Physiol Plant Mol Biol 52: 561-591
50. Møller IM (2007) Mitochondrial electron transport and oxidative stress. In DM Logan, ed, Plant Mitochondria. Annual Plant Reviews. Blackwell Publishing, Oxford, pp 185-211
51. Møller IM, Rasmusson AG (1998) The role of NADP in the mitochondrial matrix. Trends Plant Sci 3: 21-27
52. Møller IM, Rogowska-Wrzesinska A, Rao RS (2011) Protein carbonylation and metal-catalyzed protein oxidation in a cellular perspective. J Proteomics 74: 2228-2242
53. Nelson BK, Cai X, Nebenführ A (2007) A multicolored set of in vivo organelle markers for co-localization studies in Arabidopsis and other plants. Plant J 51: 1126-1136
54. Neuburger M, Day DA, Douce R (1985) Transport of NAD+ in Percollpurified potato tuber mitochondria: inhibition of NAD+ influx and efflux by N-4-azido-2-nitrophenyl-4-aminobutyryl-39-NAD+. Plant Physiol 78: 405-410
55. Neuburger M, Journet EP, Bligny R, Carde JP, Douce R (1982) Purification of plant mitochondria by isopycnic centrifugation in density gradients of Percoll. Arch Biochem Biophys 217: 312-323
56. O'Brien KM, Dirmeier R, Engle M, Poyton RO (2004) Mitochondrial protein oxidation in yeast mutants lacking manganese-(MnSOD) or copper-and zinc-containing superoxide dismutase (CuZnSOD). J Biol Chem 279: 51817-51827
57. Pagliarini DJ, Calvo SE, Chang B, Sheth SA, Vafai SB, Ong SE, Walford GA, Sugiana C, Boneh A, Chen WK, et al (2008) A mitochondrial protein compendium elucidates complex I disease biology. Cell 134: 112-123
58. Palmieri F, Pierri CL, De Grassi A, Nunes-Nesi A, Fernie AR (2011) Evolution, structure and function of mitochondrial carriers: a review with new insights. Plant J 66: 161-181
59. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20: 3551-3567
60. Pineau B, Layoune O, Danon A, De Paepe R (2008) L-Galactono-1,4-lactone dehydrogenase is required for the accumulation of plant respiratory complex I. J Biol Chem 283: 32500-32505
61. Premsler T, Zahedi RP, Lewandrowski U, Sickmann A (2009) Recent advances in yeast organelle and membrane proteomics. Proteomics 9: 4731-4743
62. Radi R, Turrens JF, Chang LY, Bush KM, Crapo JD, Freeman BA (1991) Detection of catalase in rat heart mitochondria. J Biol Chem 266: 22028-22034
63. Rasmusson AG, Møller IM (1990) NADP-utilizing enzymes in the matrix of plant mitochondria. Plant Physiol 94: 1012-1018
64. Rasmusson AG, Møller IM (2011) Mitochondrial electron transport and plant stress. In F Kempken, ed, Plant Mitochondria. Springer, New York, pp 357-381
65. Roberts JK, Aubert S, Gout E, Bligny R, Douce R (1997) Cooperation and competition between adenylate kinase, nucleoside diphosphokinase, electron transport, and ATP synthase in plant mitochondria studied by 31P-nuclear magnetic resonance. Plant Physiol 113: 191-199
66. Schneider G, Fechner U (2004) Advances in the prediction of protein targeting signals. Proteomics 4: 1571-1580
67. Schulze S, Mant A, Kossmann J, Lloyd JR (2004) Identification of an Arabidopsis inorganic pyrophosphatase capable of being imported into chloroplasts. FEBS Lett 565: 101-105
68. Small I, Peeters N, Legeai F, Lurin C (2004) Predotar: a tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics 4: 1581-1590
69. Small ID, Peeters N (2000) The PPR motif: a TPR-related motif prevalent in plant organellar proteins. Trends Biochem Sci 25: 46-47
70. Sparkes IA, Runions J, Kearns A, Hawes C (2006) Rapid, transient expression of fluorescent fusion proteins in tobacco plants and generation of stably transformed plants. Nat Protoc 1: 2019-2025
71. Stadtman ER, Van Remmen H, Richardson A, Wehr NB, Levine RL (2005) Methionine oxidation and aging. Biochim Biophys Acta 1703: 135-140
72. Stevenson SE, Chu Y, Ozias-Akins P, Thelen JJ (2009) Validation of gelfree, label-free quantitative proteomics approaches: applications for seed allergen profiling. J Proteomics 72: 555-566
73. Struglics A, Fredlund KM, Rasmusson AG, Møller IM (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: 19-28
74. Tan YF, Millar AH, Taylor NL (2012) Components of mitochondrial oxidative phosphorylation vary in abundance following exposure to cold and chemical stresses. J Proteome Res 11: 3860-3879
75. Tan YF, O'Toole N, Taylor NL, Millar AH (2010) Divalent metal ions in plant mitochondria and their role in interactions with proteins and oxidative stress-induced damage to respiratory function. Plant Physiol 152: 747-761
76. Taylor NL, Howell KA, Heazlewood JL, Tan TY, Narsai R, Huang S, Whelan J, Millar AH (2010) Analysis of the rice mitochondrial carrier family reveals anaerobic accumulation of a basic amino acid carrier involved in arginine metabolism during seed germination. Plant Physiol 154: 691-704
77. Thelen JJ, Miernyk JA (2012) The proteomic future: where mass spectrometry should be taking us. Biochem J 444: 169-181
78. Vizcaíno JA, Côté RG, Csordas A, Dianes JA, Fabregat A, Foster JM, Griss J, Alpi E, Birim M, Contell J, et al (2013) The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res 41: D1063-D1069
79. von Ballmoos C, Wiedenmann A, Dimroth P (2009) Essentials for ATP synthesis by F1F0 ATP synthases. Annu Rev Biochem 78: 649-672
80. Waller JC, Dhanoa PK, Schumann U, Mullen RT, Snedden WA (2010) Subcellular and tissue localization of NAD kinases from Arabidopsis: compartmentalization of de novo NADP biosynthesis. Planta 231: 305-317
81. Wenger CD, Phanstiel DH, Lee MV, Bailey DJ, Coon JJ (2011) COMPASS: a suite of pre-and post-search proteomics software tools for OMSSA. Proteomics 11: 1064-1074
82. Xu T, Venable JD, Park SK, Cociorva D, Lu B, Liao L, Wohlschlegel J, Hewel J, Yates JR (2006) ProLuCID, a fast and sensitive tandem mass spectra-based protein identification program. Mol Cell Proteomics 5: S174
83. Xu X, Pan S, Cheng S, Zhang B, Mu D, Ni P, Zhang G, Yang S, Li R, Wang J, et al (2011) Genome sequence and analysis of the tuber crop potato. Nature 475: 189-195
84. Ye H, Rouault TA (2010) Human iron-sulfur cluster assembly, cellular iron homeostasis, and disease. Biochemistry 49: 4945-4956
85. Zanin MK, Donohue JM, Everitt BA (2010) Evidence that core histone H3 is targeted to the mitochondria in Brassica oleracea. Cell Biol Int 34: 997-1003
86. Zhang Y, Wen Z, Washburn MP, Florens L (2010) Refinements to label free proteome quantitation: how to deal with peptides shared by multiple proteins. Anal Chem 82: 2272-2281