Abstract
The semi-autonomous nature of mitochondria provides avenues to understand the evolution of cellular functions, genome and regulatory circuit connecting gene expression and functions. The mitochondria compromised its genome size for functional compatibility of cell, and this transition has been started approximately three billion years ago, when bacteria with unique energy-producing capabilities took residence in a proto-eukaryotic cell. In the course of evolution of this symbiotic relationship, the bacterium transferred many of its genes to the host nucleus, creating the modern nuclear DNA (nDNA) genome. Since their discovery in 1840 (called bioblast), great progress has been made in understanding the central role of mitochondria in the regulation of energy metabolism and nonetheless as a key determinant of cellular fate. The mitochondrial genomic sequence database is available for majority of species used as scientific model to address current scientific questions. Herein mitochondrial omics give an edge to understand regulation at transcriptional, post-transcriptional (splicing and RNA editing), translational and post-translational level, energy complex composition, biogenesis and cell death. Where necessary, the readers are referred to related detailed studies.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Adams KL, Palmer JD (2003) Evolution of mitochondrial gene content: gene loss and transfer to the nucleus. Mol Phylogenet Evol 29(3):380–395
Agrawal RK, Sharma MR (2012) Structural aspects of mitochondrial translational apparatus. Curr Opin Struct Biol 22(6):797–803
Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJ, Staden R, Young IG (1981) Sequence and organization of the human mitochondrial genome. Nature 290(5806):457–465
Attallah CV, Welchen E, Pujol C, Bonnard G, Gonzalez DH (2007) Characterization of Arabidopsis thaliana genes encoding functional homologues of the yeast metal chaperone Cox19p, involved in cytochrome c oxidase biogenesis. Plant Mol Biol 65(3):343–355. doi:10.1007/s11103-007-9224-1
Balk J, Leaver CJ (2001) The PET1-CMS mitochondrial mutation in sunflower is associated with premature programmed cell death and cytochrome c release. Plant Cell 13(8):1803–1818
Balk J, Leaver CJ, McCabe PF (1999) Translocation of cytochrome c from the mitochondria to the cytosol occurs during heat-induced programmed cell death in cucumber plants. FEBS Lett 463(1–2):151–154
Bardel J, Louwagie M, Jaquinod M, Jourdain A, Luche S, Rabilloud T, Macherel D, Garin J, Bourguignon J (2002) A survey of the plant mitochondrial proteome in relation to development. Proteomics 2(7):880–898
Barrientos A (2002) In vivo and in organello assessment of OXPHOS activities. Methods 26(4):307–316
Barrientos A, Fontanesi F, Diaz F (2009) Evaluation of the mitochondrial respiratory chain and oxidative phosphorylation system using polarography and spectrophotometric enzyme assays. Curr Protoc Hum Genet Jonathan L Haines [et al] Chapter 19:Unit19 13. doi:10.1002/0471142905.hg1903s63
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(1):335–344
Benne R, Van den Burg J, Brakenhoff JP, Sloof P, Van Boom JH, Tromp MC (1986) Major transcript of the frameshifted coxII gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA. Cell 46(6):819–826
Bennoun P, Delosme M (1999) Chloroplast suppressors that act on a mitochondrial mutation in Chlamydomonas reinhardtii. Mol Gen Gene MGG 262(1):85–89
Ben-Shem A, Garreau de Loubresse N, Melnikov S, Jenner L, Yusupova G, Yusupov M (2011) The structure of the eukaryotic ribosome at 3.0 A resolution. Science 334(6062):1524–1529
Bentolila S, Babina AM, Germain A, Hanson MR (2013) Quantitative trait locus mapping identifies REME2, a PPR-DYW protein required for editing of specific C targets in Arabidopsis mitochondria. RNA Biol 10:9
Berget SM, Moore C, Sharp PA (1977) Spliced segments at the 5’ terminus of adenovirus 2 late mRNA. Proc Natl Acad Sci U S A 74(8):3171–3175
Berry DL, Baehrecke EH (2007) Growth arrest and autophagy are required for salivary gland cell degradation in Drosophila. Cell 131(6):1137–1148. doi:10.1016/j.cell.2007.10.048
Berry EA, Guergova-Kuras M, Huang LS, Crofts AR (2000) Structure and function of cytochrome bc complexes. Annu Rev Biochem 69:1005–1075
Binder S, Hölzle A, Jonietz C (2011) RNA processing and RNA stability in plant mitochondria. In: Kempken F (ed) Plant mitochondria, vol 1, Advances in plant biology. Springer, New York, pp 107–130. doi:10.1007/978-0-387-89781-3_5
Brennicke A, Marchfelder A, Binder S (1999) RNA editing. FEMS Microbiol Rev 23(3):297–316
Cacas JL, Diamond M (2009) Is the autophagy machinery an executioner of programmed cell death in plants? Trends Plant Sci 14(6):299–300. doi:10.1016/j.tplants.2009.02.008, author reply 300–291
Capaldi RA (1990) Structure and assembly of cytochrome c oxidase. Arch Biochem Biophys 280(2):252–262
Cardol P (2011) Mitochondrial NADH: ubiquinone oxidoreductase (complex I) in eukaryotes: a highly conserved subunit composition highlighted by mining of protein databases. Biochim Biophys Acta 1807(11):1390–1397. doi:10.1016/j.bbabio.2011.06.015
Cardol P, Vanrobaeys F, Devreese B, Van Beeumen J, Matagne RF, Remacle C (2004) Higher plant-like subunit composition of mitochondrial complex I from Chlamydomonas reinhardtii: 31 conserved components among eukaryotes. Biochim Biophys Acta 4(3):212–224
Cardol P, Gonzalez-Halphen D, Reyes-Prieto A, Baurain D, Matagne RF, Remacle C (2005) The mitochondrial oxidative phosphorylation proteome of Chlamydomonas reinhardtii deduced from the Genome Sequencing Project. Plant Physiol 137(2):447–459. doi:10.1104/pp. 104.054148
Castandet B, Choury D, Begu D, Jordana X, Araya A (2010) Intron RNA editing is essential for splicing in plant mitochondria. Nucleic Acids Res 38(20):7112–7121
Chapdelaine Y, Bonen L (1991) The wheat mitochondrial gene for subunit I of the NADH dehydrogenase complex: a trans-splicing model for this gene-in-pieces. Cell 65(3):465–472
Chaw SM, Shih AC, Wang D, Wu YW, Liu SM, Chou TY (2008) The mitochondrial genome of the gymnosperm Cycas taitungensis contains a novel family of short interspersed elements, Bpu sequences, and abundant RNA editing sites. Mol Biol Evol 25(3):603–615
Cheetham GM, Jeruzalmi D, Steitz TA (1999) Structural basis for initiation of transcription from an RNA polymerase-promoter complex. Nature 399(6731):80–83
Choquet Y, Wollman FA (2002) Translational regulations as specific traits of chloroplast gene expression. FEBS Lett 529(1):39–42
Chow LT, Gelinas RE, Broker TR, Roberts RJ (1977) An amazing sequence arrangement at the 5’ ends of adenovirus 2 messenger RNA. Cell 12(1):1–8
Christensen AC, Lyznik A, Mohammed S, Elowsky CG, Elo A, Yule R, Mackenzie SA (2005) Dual-domain, dual-targeting organellar protein presequences in Arabidopsis can use non-AUG start codons. Plant Cell 17(10):2805–2816
Claros MG, Vincens P (1996) Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur J Biochem 241(3):779–786
Courtois F, Merendino L, Demarsy E, Mache R, Lerbs-Mache S (2007) Phage-type RNA polymerase RPOTmp transcribes the rrn operon from the PC promoter at early developmental stages in Arabidopsis. Plant Physiol 145(3):712–721
Crosti P, Malerba M, Bianchetti R (2001) Tunicamycin and Brefeldin A induce in plant cells a programmed cell death showing apoptotic features. Protoplasma 216(1–2):31–38
Cui J, Liu J, Li Y, Shi T (2011) Integrative identification of Arabidopsis mitochondrial proteome and its function exploitation through protein interaction network. PLoS One 6(1):0016022
Diaz S, Renault T, Villalba A, Carballal MJ (2011) Disseminated neoplasia in cockles Cerastoderma edule: ultrastructural characterisation and effects on haemolymph cell parameters. Dis Aquat Org 96(2):157–167. doi:10.3354/dao02384
Doelling JH, Walker JM, Friedman EM, Thompson AR, Vierstra RD (2002) The APG8/12-activating enzyme APG7 is required for proper nutrient recycling and senescence in Arabidopsis thaliana. J Biol Chem 277(36):33105–33114. doi:10.1074/jbc.M204630200
Dombrowski S, Hoffmann M, Guha C, Binder S (1999) Continuous primary sequence requirements in the 18-nucleotide promoter of dicot plant mitochondria. J Biol Chem 274(15):10094–10099
Dutilleul C, Driscoll S, Cornic G, De Paepe R, Foyer CH, Noctor G (2003a) Functional mitochondrial complex I is required by tobacco leaves for optimal photosynthetic performance in photorespiratory conditions and during transients. Plant Physiol 131(1):264–275. doi:10.1104/pp. 011155
Dutilleul C, Garmier M, Noctor G, Mathieu C, Chetrit P, Foyer CH, de Paepe R (2003b) Leaf mitochondria modulate whole cell redox homeostasis, set antioxidant capacity, and determine stress resistance through altered signaling and diurnal regulation. Plant Cell 15(5):1212–1226
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(4):1005–1016
Eubel H, Jansch L, Braun HP (2003) New insights into the respiratory chain of plant mitochondria. Supercomplexes and a unique composition of complex II. Plant Physiol 133(1):274–286
Farre JC, Aknin C, Araya A, Castandet B (2012) RNA editing in mitochondrial trans-introns is required for splicing. PLoS One 7(12):20
Forner J, Weber B, Wietholter C, Meyer RC, Binder S (2005) Distant sequences determine 5’ end formation of cox3 transcripts in Arabidopsis thaliana ecotype C24. Nucleic Acids Res 33(15):4673–4682
Forner J, Weber B, Thuss S, Wildum S, Binder S (2007) Mapping of mitochondrial mRNA termini in Arabidopsis thaliana: t-elements contribute to 5’ and 3’ end formation. Nucleic Acids Res 35(11):3676–3692
Fuentes D, Meneses M, Nunes-Nesi A, Araujo WL, Tapia R, Gomez I, Holuigue L, Gutierrez RA, Fernie AR, Jordana X (2011) A deficiency in the flavoprotein of Arabidopsis mitochondrial complex II results in elevated photosynthesis and better growth in nitrogen-limiting conditions. Plant Physiol 157(3):1114–1127. doi:10.1104/pp. 111.183939
Fujii S, Toda T, Kikuchi S, Suzuki R, Yokoyama K, Tsuchida H, Yano K, Toriyama K (2011) Transcriptome map of plant mitochondria reveals islands of unexpected transcribed regions. BMC Genomics 12(279):1471–2164
Fukuda H (2000) Programmed cell death of tracheary elements as a paradigm in plants. Plant Mol Biol 44(3):245–253
Gagliardi D, Leaver CJ (1999) Polyadenylation accelerates the degradation of the mitochondrial mRNA associated with cytoplasmic male sterility in sunflower. EMBO J 18(13):3757–3766
Ghezzi D, Goffrini P, Uziel G, Horvath R, Klopstock T, Lochmuller H, D’Adamo P, Gasparini P, Strom TM, Prokisch H, Invernizzi F, Ferrero I, Zeviani M (2009) SDHAF1, encoding a LYR complex-II specific assembly factor, is mutated in SDH-defective infantile leukoencephalopathy. Nat Genet 41(6):654–656
Giege P, Brennicke A (1999) RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs. Proc Natl Acad Sci U S A 96(26):15324–15329
Giege P, Hoffmann M, Binder S, Brennicke A (2000) RNA degradation buffers asymmetries of transcription in Arabidopsis mitochondria. EMBO Rep 1(2):164–170
Giege P, Sweetlove LJ, Cognat V, Leaver CJ (2005) Coordination of nuclear and mitochondrial genome expression during mitochondrial biogenesis in Arabidopsis. Plant Cell 17(5):1497–1512
Glanz S, Kuck U (2009) Trans-splicing of organelle introns–a detour to continuous RNAs. BioEssays: News Rev Mol, Cell Dev Biol 31(9):921–934
Gleason C, Huang S, Thatcher LF, Foley RC, Anderson CR, Carroll AJ, Millar AH, Singh KB (2011) Mitochondrial complex II has a key role in mitochondrial-derived reactive oxygen species influence on plant stress gene regulation and defense. Proc Natl Acad Sci U S A 108(26):10768–10773
Greenberg JT, Yao N (2004) The role and regulation of programmed cell death in plant-pathogen interactions. Cell Microbiol 6(3):201–211
Grewe F, Viehoever P, Weisshaar B, Knoop V (2009) A trans-splicing group I intron and tRNA-hyperediting in the mitochondrial genome of the lycophyte Isoetes engelmannii. Nucleic Acids Res 37(15):5093–5104
Grivell LA, Artal-Sanz M, Hakkaart G, de Jong L, Nijtmans LG, van Oosterum K, Siep M, van der Spek H (1999) Mitochondrial assembly in yeast. FEBS Lett 452(1–2):57–60
Gueguen V, Macherel D, Jaquinod M, Douce R, Bourguignon J (2000) Fatty acid and lipoic acid biosynthesis in higher plant mitochondria. J Biol Chem 275(7):5016–5025
Hall DH, Gu G, Garcia-Anoveros J, Gong L, Chalfie M, Driscoll M (1997) Neuropathology of degenerative cell death in Caenorhabditis elegans. J Neurosci 17(3):1033–1045
Hamasur B, Glaser E (1992) Plant mitochondrial F0F1 ATP synthase. Identification of the individual subunits and properties of the purified spinach leaf mitochondrial ATP synthase. Eur J Biochem 205(1):409–416
Hanaoka H, Noda T, Shirano Y, Kato T, Hayashi H, Shibata D, Tabata S, Ohsumi Y (2002) Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene. Plant Physiol 129(3):1181–1193. doi:10.1104/pp. 011024
Handa H (2003) The complete nucleotide sequence and RNA editing content of the mitochondrial genome of rapeseed (Brassica napus L.): comparative analysis of the mitochondrial genomes of rapeseed and Arabidopsis thaliana. Nucleic Acids Res 31(20):5907–5916
Handa H (2008) Linear plasmids in plant mitochondria: peaceful coexistences or malicious invasions? Mitochondrion 8(1):15–25
Hao HX, Khalimonchuk O, Schraders M, Dephoure N, Bayley JP, Kunst H, Devilee P, Cremers CW, Schiffman JD, Bentz BG, Gygi SP, Winge DR, Kremer H, Rutter J (2009) SDH5, a gene required for flavination of succinate dehydrogenase, is mutated in paraganglioma. Science 325(5944):1139–1142
Heath MC (2000) Nonhost resistance and nonspecific plant defenses. Curr Opin Plant Biol 3(4):315–319
Heazlewood JL, Howell KA, Millar AH (2003a) Mitochondrial complex I from Arabidopsis and rice: orthologs of mammalian and fungal components coupled with plant-specific subunits. Biochim Biophys Acta 1604(3):159–169
Heazlewood JL, Howell KA, Whelan J, Millar AH (2003b) Towards an analysis of the rice mitochondrial proteome. Plant Physiol 132(1):230–242. doi:10.1104/pp. 102.018986
Heazlewood JL, Millar AH, Day DA, Whelan J (2003c) What makes a mitochondrion? Genome Biol 4(6):218. doi:10.1186/gb-2003-4-6-218
Hedtke B, Borner T, Weihe A (1997) Mitochondrial and chloroplast phage-type RNA polymerases in Arabidopsis. Science 277(5327):809–811
Hedtke B, Wagner I, Borner T, Hess WR (1999) Inter-organellar crosstalk in higher plants: impaired chloroplast development affects mitochondrial gene and transcript levels. Plant J 19(6):635–643
Hedtke B, Borner T, Weihe A (2000) One RNA polymerase serving two genomes. EMBO Rep 1(5):435–440
Hedtke B, Legen J, Weihe A, Herrmann RG, Borner T (2002) Six active phage-type RNA polymerase genes in Nicotiana tabacum. Plant J 30(6):625–637
Heineke D, Bykova N, Gardestrom P, Bauwe H (2001) Metabolic response of potato plants to an antisense reduction of the P-protein of glycine decarboxylase. Planta 212(5–6):880–887
Herald VL, Heazlewood JL, Day DA, Millar AH (2003) Proteomic identification of divalent metal cation binding proteins in plant mitochondria. FEBS Lett 537(1–3):96–100
Herrmann JM, Funes S (2005) Biogenesis of cytochrome oxidase-sophisticated assembly lines in the mitochondrial inner membrane. Gene 354:43–52
Hess WR, Borner T (1999) Organellar RNA polymerases of higher plants. Int Rev Cytol 190:1–59
Hiesel R, Wissinger B, Schuster W, Brennicke A (1989) RNA editing in plant mitochondria. Science 246(4937):1632–1634
Hiesel R, Combettes B, Brennicke A (1994) Evidence for RNA editing in mitochondria of all major groups of land plants except the Bryophyta. Proc Natl Acad Sci U S A 91(2):629–633
Hoch B, Maier RM, Appel K, Igloi GL, Kossel H (1991) Editing of a chloroplast mRNA by creation of an initiation codon. Nature 353(6340):178–180
Hofius D, Schultz-Larsen T, Joensen J, Tsitsigiannis DI, Petersen NH, Mattsson O, Jorgensen LB, Jones JD, Mundy J, Petersen M (2009) Autophagic components contribute to hypersensitive cell death in Arabidopsis. Cell 137(4):773–783. doi:10.1016/j.cell.2009.02.036
Holec S, Lange H, Canaday J, Gagliardi D (2008) Coping with cryptic and defective transcripts in plant mitochondria. Biochim Biophys Acta 9:566–573
Holt IJ, He J, Mao CC, Boyd-Kirkup JD, Martinsson P, Sembongi H, Reyes A, Spelbrink JN (2007) Mammalian mitochondrial nucleoids: organizing an independently minded genome. Mitochondrion 7 (5):311–321
Horsefield R, Iwata S, Byrne B (2004) Complex II from a structural perspective. Curr Protein Pept Sci 5(2):107–118
Huang S, Taylor NL, Narsai R, Eubel H, Whelan J, Millar AH (2009) Experimental analysis of the rice mitochondrial proteome, its biogenesis, and heterogeneity. Plant Physiol 149(2):719–734
Igamberdiev AU, Bykova NV, Lea PJ, Gardestrom P (2001) The role of photorespiration in redox and energy balance of photosynthetic plant cells: a study with a barley mutant deficient in glycine decarboxylase. Physiol Plant 111(4):427–438
Islam MS, Studer B, Byrne SL, Farrell JD, Panitz F, Bendixen C, Moller IM, Asp T (2013) The genome and transcriptome of perennial ryegrass mitochondria. BMC Genomics 14(1):202
Jacoby RP, Li L, Huang S, Pong Lee C, Millar AH, Taylor NL (2012) Mitochondrial composition, function and stress response in plants. J Integr Plant Biol 54(11):887–906
Jacques JP, Hausmann S, Kolakofsky D (1994) Paramyxovirus mRNA editing leads to G deletions as well as insertions. EMBO J 13(22):5496–5503
Jansch L, Kruft V, Schmitz UK, Braun HP (1996) New insights into the composition, molecular mass and stoichiometry of the protein complexes of plant mitochondria. Plant J 9(3):357–368
Johanningmeier U, Howell SH (1984) Regulation of light-harvesting chlorophyll-binding protein mRNA accumulation in Chlamydomonas reinhardi. Possible involvement of chlorophyll synthesis precursors. J Biol Chem 259(21):13541–13549
Kabeya Y, Sato N (2005) Unique translation initiation at the second AUG codon determines mitochondrial localization of the phage-type RNA polymerases in the moss Physcomitrella patens. Plant Physiol 138(1):369–382
Kawai-Yamada M, Ohori Y, Uchimiya H (2004) Dissection of Arabidopsis Bax inhibitor-1 suppressing Bax-, hydrogen peroxide-, and salicylic acid-induced cell death. Plant Cell 16(1):21–32. doi:10.1105/tpc.014613
Kempken F, Mullen JA, Pring DR, Tang HV (1991) RNA editing of sorghum mitochondrial atp6 transcripts changes 15 amino acids and generates a carboxy-terminus identical to yeast. Curr Genet 20(5):417–422
Kerr JF (2002) History of the events leading to the formulation of the apoptosis concept. Toxicology 181–182:471–474
Kim SR, Yang JI, Moon S, Ryu CH, An K, Kim KM, Yim J, An G (2009) Rice OGR1 encodes a pentatricopeptide repeat-DYW protein and is essential for RNA editing in mitochondria. Plant J 59(5):738–749
Kleffmann T, Russenberger D, von Zychlinski A, Christopher W, Sjolander K, Gruissem W, Baginsky S (2004) The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions. Curr Biol 14(5):354–362
Klodmann J, Braun HP (2011) Proteomic approach to characterize mitochondrial complex I from plants. Phytochemistry 72(10):1071–1080. doi:10.1016/j.phytochem.2010.11.012
Klodmann J, Sunderhaus S, Nimtz M, Jansch L, Braun HP (2010) Internal architecture of mitochondrial complex I from Arabidopsis thaliana. Plant Cell 22(3):797–810
Knaapen MW, Davies MJ, De Bie M, Haven AJ, Martinet W, Kockx MM (2001) Apoptotic versus autophagic cell death in heart failure. Cardiovasc Res 51(2):304–312
Kobayashi Y, Dokiya Y, Kumazawa Y, Sugita M (2002) Non-AUG translation initiation of mRNA encoding plastid-targeted phage-type RNA polymerase in Nicotiana sylvestris. Biochem Biophys Res Commun 299(1):57–61
Kropat J, Oster U, Rudiger W, Beck CF (1997) Chlorophyll precursors are signals of chloroplast origin involved in light induction of nuclear heat-shock genes. Proc Natl Acad Sci U S A 94(25):14168–14172
Kruft V, Eubel H, Jansch L, Werhahn W, Braun HP (2001) Proteomic approach to identify novel mitochondrial proteins in Arabidopsis. Plant Physiol 127(4):1694–1710
Kubo T, Mikami T (2007) Organization and variation of angiosperm mitochondrial genome. Physiol Plant 129(1):6–13. doi:10.1111/j.1399-3054.2006.00768.x
Kubo T, Newton KJ (2008) Angiosperm mitochondrial genomes and mutations. Mitochondrion 8(1):5–14
Kugita M, Yamamoto Y, Fujikawa T, Matsumoto T, Yoshinaga K (2003) RNA editing in hornwort chloroplasts makes more than half the genes functional. Nucleic Acids Res 31(9):2417–2423
Kuhn K, Weihe A, Borner T (2005) Multiple promoters are a common feature of mitochondrial genes in Arabidopsis. Nucleic Acids Res 33(1):337–346
Kuhn K, Bohne AV, Liere K, Weihe A, Borner T (2007) Arabidopsis phage-type RNA polymerases: accurate in vitro transcription of organellar genes. Plant Cell 19(3):959–971
Kuhn K, Richter U, Meyer EH, Delannoy E, de Longevialle AF, O’Toole N, Borner T, Millar AH, Small ID, Whelan J (2009) Phage-type RNA polymerase RPOTmp performs gene-specific transcription in mitochondria of Arabidopsis thaliana. Plant Cell 21(9):2762–2779
Kwasniak M, Majewski P, Skibior R, Adamowicz A, Czarna M, Sliwinska E, Janska H (2013) Silencing of the nuclear RPS10 gene encoding mitochondrial ribosomal protein alters translation in Arabidopsis mitochondria. Plant Cell 25(5):1855–1867
Lenz H, Rudinger M, Volkmar U, Fischer S, Herres S, Grewe F, Knoop V (2010) Introducing the plant RNA editing prediction and analysis computer tool PREPACT and an update on RNA editing site nomenclature. Curr Genet 56(2):189–201
Lambowitz AM, Zimmerly S (2004) Mobile group II introns. Annu Rev Genet 38:1–35
Lambowitz AM, Zimmerly S (2011) Group II introns: mobile ribozymes that invade DNA. Cold Spring Harb Perspect Biol 3(8):a003616
Lang BF, Gray MW, Burger G (1999) Mitochondrial genome evolution and the origin of eukaryotes. Annu Rev Genet 33:351–397
Lapuente-Brun E, Moreno-Loshuertos R, Acin-Perez R, Latorre-Pellicer A, Colas C, Balsa E, Perales-Clemente E, Quiros PM, Calvo E, Rodriguez-Hernandez MA, Navas P, Cruz R, Carracedo A, Lopez-Otin C, Perez-Martos A, Fernandez-Silva P, Fernandez-Vizarra E, Enriquez JA (2013) Supercomplex assembly determines electron flux in the mitochondrial electron transport chain. Science 340(6140):1567–1570
Larkin RM, Alonso JM, Ecker JR, Chory J (2003) GUN4, a regulator of chlorophyll synthesis and intracellular signaling. Science 299(5608):902–906. doi:10.1126/science.1079978
Leist M, Jaattela M (2001) Four deaths and a funeral: from caspases to alternative mechanisms. Nat Rev Mol Cell Biol 2(8):589–598. doi:10.1038/35085008
Leister D (2012) Retrograde signaling in plants: from simple to complex scenarios. Front Plant Sci 3(135):19
Leon P, Arroyo A, Mackenzie S (1998) Nuclear control of plastid and mitochondrial development in higher plants. Annu Rev Plant Physiol Plant Mol Biol 49:453–480. doi:10.1146/annurev.arplant.49.1.453
Leon G, Holuigue L, Jordana X (2007) Mitochondrial complex II Is essential for gametophyte development in Arabidopsis. Plant Physiol 143(4):1534–1546. doi:10.1104/pp. 106.095158
Lerbs-Mache S (1993) The 110-kDa polypeptide of spinach plastid DNA-dependent RNA polymerase: single-subunit enzyme or catalytic core of multimeric enzyme complexes? Proc Natl Acad Sci U S A 90(12):5509–5513
Levine B, Goldman JE, Jiang HH, Griffin DE, Hardwick JM (1996) Bc1-2 protects mice against fatal alphavirus encephalitis. Proc Natl Acad Sci U S A 93(10):4810–4815
Liere K, Weihe A, Borner T (2011) The transcription machineries of plant mitochondria and chloroplasts: composition, function, and regulation. J Plant Physiol 168(12):1345–1360
Li-Pook-Than J, Bonen L (2006) Multiple physical forms of excised group II intron RNAs in wheat mitochondria. Nucleic Acids Res 34(9):2782–2790
Lister R, Chew O, Lee MN, Heazlewood JL, Clifton R, Parker KL, Millar AH, Whelan J (2004) A transcriptomic and proteomic characterization of the Arabidopsis mitochondrial protein import apparatus and its response to mitochondrial dysfunction. Plant Physiol 134(2):777–789. doi:10.1104/pp. 103.033910
Liu Y, Schiff M, Czymmek K, Talloczy Z, Levine B, Dinesh-Kumar SP (2005) Autophagy regulates programmed cell death during the plant innate immune response. Cell 121(4):567–577. doi:10.1016/j.cell.2005.03.007
Long M, Betran E, Thornton K, Wang W (2003) The origin of new genes: glimpses from the young and old. Nat Rev Genet 4(11):865–875
Mackenzie S, McIntosh L (1999) Higher plant mitochondria. Plant Cell 11(4):571–586
Mahendran R, Spottswood MS, Ghate A, Ling ML, Jeng K, Miller DL (1994) Editing of the mitochondrial small subunit rRNA in Physarum polycephalum. EMBO J 13(1):232–240
Malerba M, Cerana R, Crosti P (2004) Comparison between the effects of fusicoccin, Tunicamycin, and Brefeldin A on programmed cell death of cultured sycamore (Acer pseudoplatanus L.) cells. Protoplasma 224(1–2):61–70
McAllister WT (1993) Structure and function of the bacteriophage T7 RNA polymerase (or, the virtues of simplicity). Cell Mol Biol Res 39(4):385–391
McCabe PF, Leaver CJ (2000) Programmed cell death in cell cultures. Plant Mol Biol 44(3):359–368
McCabe MS, Power JB, de Laat AM, Davey MR (1997a) Detection of single-copy genes in DNA from transgenic plants by nonradioactive Southern blot analysis. Mol Biotechnol 7(1):79–84. doi:10.1007/BF02821545
McCabe PF, Valentine TA, Forsberg LS, Pennell RI (1997b) Soluble signals from cells identified at the cell wall establish a developmental pathway in carrot. Plant Cell 9(12):2225–2241
Mercer TR, Neph S, Dinger ME, Crawford J, Smith MA, Shearwood AM, Haugen E, Bracken CP, Rackham O, Stamatoyannopoulos JA, Filipovska A, Mattick JS (2011) The human mitochondrial transcriptome. Cell 146(4):645–658
Meyer EH, Taylor NL, Millar AH (2008) Resolving and identifying protein components of plant mitochondrial respiratory complexes using three dimensions of gel electrophoresis. J Proteome Res 7(2):786–794. doi:10.1021/pr700595p
Millar AH, Sweetlove LJ, Giege P, Leaver CJ (2001) Analysis of the Arabidopsis mitochondrial proteome. Plant Physiol 127(4):1711–1727
Millar AH, Eubel H, Jansch L, Kruft V, Heazlewood JL, Braun HP (2004) Mitochondrial cytochrome c oxidase and succinate dehydrogenase complexes contain plant specific subunits. Plant Mol Biol 56(1):77–90. doi:10.1007/s11103-004-2316-2
Millar AH, Whelan J, Soole KL, Day DA (2011) Organization and regulation of mitochondrial respiration in plants. Annu Rev Plant Biol 62:79–104
Mochizuki N, Brusslan JA, Larkin R, Nagatani A, Chory J (2001) Arabidopsis genomes uncoupled 5 (GUN5) mutant reveals the involvement of Mg-chelatase H subunit in plastid-to-nucleus signal transduction. Proc Natl Acad Sci U S A 98(4):2053–2058. doi:10.1073/pnas.98.4.2053
Moller 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
Mootha VK, Bunkenborg J, Olsen JV, Hjerrild M, Wisniewski JR, Stahl E, Bolouri MS, Ray HN, Sihag S, Kamal M, Patterson N, Lander ES, Mann M (2003) Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell 115(5):629–640
Notsu Y, Masood S, Nishikawa T, Kubo N, Akiduki G, Nakazono M, Hirai A, Kadowaki K (2002) The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants. Mol Genet Genomics 268(4):434–445
Op den Camp RG, Przybyla D, Ochsenbein C, Laloi C, Kim C, Danon A, Wagner D, Hideg E, Gobel C, Feussner I, Nater M, Apel K (2003) Rapid induction of distinct stress responses after the release of singlet oxygen in Arabidopsis. Plant Cell 15(10):2320–2332
Osteryoung KW, Nunnari J (2003) The division of endosymbiotic organelles. Science 302(5651):1698–1704. doi:10.1126/science.1082192
Parenteau J, Durand M, Morin G, Gagnon J, Lucier JF, Wellinger RJ, Chabot B, Elela SA (2011) Introns within ribosomal protein genes regulate the production and function of yeast ribosomes. Cell 147(2):320–331
Patel S, Dinesh-Kumar SP (2008) Arabidopsis ATG6 is required to limit the pathogen-associated cell death response. Autophagy 4(1):20–27
Peiffer WE, Ingle RT, Ferguson-Miller S (1990) Structurally unique plant cytochrome c oxidase isolated from wheat germ, a rich source of plant mitochondrial enzymes. Biochemistry 29(37):8696–8701
Peters K, Belt K, Braun HP (2013) 3D gel map of Arabidopsis complex I. Front Plant Sci 4(153)
Pfannschmidt T, Schutze K, Brost M, Oelmuller R (2001) A novel mechanism of nuclear photosynthesis gene regulation by redox signals from the chloroplast during photosystem stoichiometry adjustment. J Biol Chem 276(39):36125–36130. doi:10.1074/jbc.M105701200
Pursiheimo S, Mulo P, Rintamaki E, Aro EM (2001) Coregulation of light-harvesting complex II phosphorylation and lhcb mRNA accumulation in winter rye. Plant J 26(3):317–327
Qiu YL, Palmer JD (2004) Many independent origins of trans splicing of a plant mitochondrial group II intron. J Mol Evol 59(1):80–89
Raczynska KD, Le Ret M, Rurek M, Bonnard G, Augustyniak H, Gualberto JM (2006) Plant mitochondrial genes can be expressed from mRNAs lacking stop codons. FEBS Lett 580(24):5641–5646
Raghavendra AS, Padmasree K (2003) Beneficial interactions of mitochondrial metabolism with photosynthetic carbon assimilation. Trends Plant Sci 8(11):546–553. doi:10.1016/j.tplants.2003.09.015
Rebeille F, Macherel D, Mouillon JM, Garin J, Douce R (1997) Folate biosynthesis in higher plants: purification and molecular cloning of a bifunctional 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase/7,8-dihydropteroate synthase localized in mitochondria. EMBO J 16(5):947–957
Remacle C, Barbieri MR, Cardol P, Hamel PP (2008) Eukaryotic complex I: functional diversity and experimental systems to unravel the assembly process. Mol Genet Genomics 280(2):93–110. doi:10.1007/s00438-008-0350-5
Richter U, Kiessling J, Hedtke B, Decker E, Reski R, Borner T, Weihe A (2002) Two RpoT genes of Physcomitrella patens encode phage-type RNA polymerases with dual targeting to mitochondria and plastids. Gene 290(1–2):95–105
Robison MM, Ling X, Smid MP, Zarei A, Wolyn DJ (2009) Antisense expression of mitochondrial ATP synthase subunits OSCP (ATP5) and gamma (ATP3) alters leaf morphology, metabolism and gene expression in Arabidopsis. Plant Cell Physiol 50(10):1840–1850. doi:10.1093/pcp/pcp125
Rochaix JD (2001) Assembly, function, and dynamics of the photosynthetic machinery in Chlamydomonas reinhardtii. Plant Physiol 127(4):1394–1398
Rolland F, Moore B, Sheen J (2002) Sugar sensing and signaling in plants. Plant Cell 14(205):S185–S205
Rutter J, Winge DR, Schiffman JD (2010) Succinate dehydrogenase—assembly, regulation and role in human disease. Mitochondrion 10(4):393–401
Sabar M, De Paepe R, de Kouchkovsky Y (2000) Complex I impairment, respiratory compensations, and photosynthetic decrease in nuclear and mitochondrial male sterile mutants of Nicotiana sylvestris. Plant Physiol 124(3):1239–1250
Sabar M, Gagliardi D, Balk J, Leaver CJ (2003) ORFB is a subunit of F1F(O)-ATP synthase: insight into the basis of cytoplasmic male sterility in sunflower. EMBO Rep 4(4):381–386
Sabar M, Balk J, Leaver CJ (2005) Histochemical staining and quantification of plant mitochondrial respiratory chain complexes using blue-native polyacrylamide gel electrophoresis. Plant J 44(5):893–901. doi:10.1111/j.1365-313X.2005.02577.x
Senior DJ, Tsai CS (1990) Esterase activity of high-Km aldehyde dehydrogenase from rat liver mitochondria. Biochem Cell Biol 68(4):758–763
Shikanai T (2006) RNA editing in plant organelles: machinery, physiological function and evolution. Cell Mol Life Sci 63(6):698–708
Sickmann A, Reinders J, Wagner Y, Joppich C, Zahedi R, Meyer HE, Schonfisch B, Perschil I, Chacinska A, Guiard B, Rehling P, Pfanner N, Meisinger C (2003) The proteome of Saccharomyces cerevisiae mitochondria. Proc Natl Acad Sci U S A 100(23):13207–13212
Small I, Peeters N, Legeai F, Lurin C (2004) Predotar: a tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics 4(6):1581–1590
Smith PM, Fox JL, Winge DR (2012) Biogenesis of the cytochrome bc(1) complex and role of assembly factors. Biochim Biophys Acta 2:276–286
Soll J, Schleiff E (2004) Protein import into chloroplasts. Nat Rev Mol Cell Biol 5(3):198–208
Sousa R (1996) Structural and mechanistic relationships between nucleic acid polymerases. Trends Biochem Sci 21(5):186–190
Strand A, Asami T, Alonso J, Ecker JR, Chory J (2003) Chloroplast to nucleus communication triggered by accumulation of Mg-protoporphyrinIX. Nature 421(6918):79–83. doi:10.1038/nature01204
Surpin M, Zheng H, Morita MT, Saito C, Avila E, Blakeslee JJ, Bandyopadhyay A, Kovaleva V, Carter D, Murphy A, Tasaka M, Raikhel N (2003) The VTI family of SNARE proteins is necessary for plant viability and mediates different protein transport pathways. Plant Cell 15(12):2885–2899. doi:10.1105/tpc.016121
Sweetlove LJ, Heazlewood JL, Herald V, Holtzapffel R, Day DA, Leaver CJ, Millar AH (2002) The impact of oxidative stress on Arabidopsis mitochondria. Plant J 32(6):891–904
Takemura M, Oda K, Yamato K, Ohta E, Nakamura Y, Nozato N, Akashi K, Ohyama K (1992) Gene clusters for ribosomal proteins in the mitochondrial genome of a liverwort, Marchantia polymorpha. Nucleic Acids Res 20(12):3199–3205
Takenaka M, Verbitskiy D, van der Merwe JA, Zehrmann A, Brennicke A (2008) The process of RNA editing in plant mitochondria. Mitochondrion 8(1):35–46
Talla E, Anthouard V, Bouchier C, Frangeul L, Dujon B (2005) The complete mitochondrial genome of the yeast Kluyveromyces thermotolerans. FEBS Lett 579(1):30–40
Taylor SW, Fahy E, Zhang B, Glenn GM, Warnock DE, Wiley S, Murphy AN, Gaucher SP, Capaldi RA, Gibson BW, Ghosh SS (2003) Characterization of the human heart mitochondrial proteome. Nat Biotechnol 21(3):281–286
Taylor NL, Heazlewood JL, Millar AH (2011) The Arabidopsis thaliana 2-D gel mitochondrial proteome: refining the value of reference maps for assessing protein abundance, contaminants and post-translational modifications. Proteomics 11(9):1720–1733
Thomas SG, Franklin-Tong VE (2004) Self-incompatibility triggers programmed cell death in Papaver pollen. Nature 429(6989):305–309. doi:10.1038/nature02540
Thompson CB (1995) Apoptosis in the pathogenesis and treatment of disease. Science 267(5203):1456–1462
Toor N, Robart AR, Christianson J, Zimmerly S (2006) Self-splicing of a group IIC intron: 5’ exon recognition and alternative 5’ splicing events implicate the stem-loop motif of a transcriptional terminator. Nucleic Acids Res 34(22):6461–6471
Toro N, Jimenez-Zurdo JI, Garcia-Rodriguez FM (2007) Bacterial group II introns: not just splicing. FEMS Microbiol Rev 31(3):342–358
Townley HE, McDonald K, Jenkins GI, Knight MR, Leaver CJ (2005) Ceramides induce programmed cell death in Arabidopsis cells in a calcium-dependent manner. Biol Chem 386(2):161–166. doi:10.1515/BC.2005.020
Tseng CC, Lee CJ, Chung YT, Sung TY, Hsieh MH (2013) Differential regulation of Arabidopsis plastid gene expression and RNA editing in non-photosynthetic tissues. Plant Mol Biol 82(4–5):375–392
Tzagoloff A (1995) Ubiquinol-cytochrome-c oxidoreductase from Saccharomyces cerevisiae. Methods Enzymol 260:51–63
Ugalde C, Vogel R, Huijbens R, Van Den Heuvel B, Smeitink J, Nijtmans L (2004) Human mitochondrial complex I assembles through the combination of evolutionary conserved modules: a framework to interpret complex I deficiencies. Hum Mol Genet 13(20):2461–2472. doi:10.1093/hmg/ddh262
Unseld M, Marienfeld JR, Brandt P, Brennicke A (1997) The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides. Nat Genet 15(1):57–61. doi:10.1038/ng0197-57
Vacca RA, de Pinto MC, Valenti D, Passarella S, Marra E, De Gara L (2004) Production of reactive oxygen species, alteration of cytosolic ascorbate peroxidase, and impairment of mitochondrial metabolism are early events in heat shock-induced programmed cell death in tobacco Bright-Yellow 2 cells. Plant Physiol 134(3):1100–1112. doi:10.1104/pp. 103.035956
Vandenabeele S, Vanderauwera S, Vuylsteke M, Rombauts S, Langebartels C, Seidlitz HK, Zabeau M, Van Montagu M, Inze D, Van Breusegem F (2004) Catalase deficiency drastically affects gene expression induced by high light in Arabidopsis thaliana. Plant J 39(1):45–58
Velours J, Arselin G (2000) The Saccharomyces cerevisiae ATP synthase. J Bioenerg Biomembr 32(4):383–390
Verbitskiy D, Zehrmann A, van der Merwe JA, Brennicke A, Takenaka M (2010) The PPR protein encoded by the LOVASTATIN INSENSITIVE 1 gene is involved in RNA editing at three sites in mitochondria of Arabidopsis thaliana. Plant J 61(3):446–455
Vicens Q, Cech TR (2006) Atomic level architecture of group I introns revealed. Trends Biochem Sci 31(1):41–51
Vogel RO, Smeitink JA, Nijtmans LG (2007) Human mitochondrial complex I assembly: a dynamic and versatile process. Biochim Biophys Acta 10(27):9
Vothknecht UC, Westhoff P (2001) Biogenesis and origin of thylakoid membranes. Biochim Biophys Acta 12:1–2
Wagner RW, Smith JE, Cooperman BS, Nishikura K (1989) A double-stranded RNA unwinding activity introduces structural alterations by means of adenosine to inosine conversions in mammalian cells and Xenopus eggs. Proc Natl Acad Sci U S A 86(8):2647–2651
Wallace DC (2005a) The mitochondrial genome in human adaptive radiation and disease: on the road to therapeutics and performance enhancement. Gene 354:169–180
Wallace DC (2005b) A mitochondrial paradigm of metabolic and degenerative diseases, aging, and cancer: a dawn for evolutionary medicine. Annu Rev Genet 39:359–407
Werhahn W, Braun HP (2002) Biochemical dissection of the mitochondrial proteome from Arabidopsis thaliana by three-dimensional gel electrophoresis. Electrophoresis 23(4):640–646
Wheeler DS (2009) Death to sepsis: targeting apoptosis pathways in sepsis. Crit Care 13(6):1010. doi:10.1186/cc8162
Wilde A, Mikolajczyk S, Alawady A, Lokstein H, Grimm B (2004) The gun4 gene is essential for cyanobacterial porphyrin metabolism. FEBS Lett 571(1–3):119–123. doi:10.1016/j.febslet.2004.06.063
Woodson JD, Chory J (2008) Coordination of gene expression between organellar and nuclear genomes. Nat Rev Genet 9(5):383–395
Xiong Y, Contento AL, Bassham DC (2007a) Disruption of autophagy results in constitutive oxidative stress in Arabidopsis. Autophagy 3(3):257–258
Xiong Y, Contento AL, Nguyen PQ, Bassham DC (2007b) Degradation of oxidized proteins by autophagy during oxidative stress in Arabidopsis. Plant Physiol 143(1):291–299. doi:10.1104/pp. 106.092106
Xu XW, Shi C, He ZQ, Ma CM, Chen WH, Shen YP, Guo Q, Shen CJ, Xu J (2008) Effects of phytoestrogen on mitochondrial structure and function of hippocampal CA1 region of ovariectomized rats. Cell Mol Neurobiol 28(6):875–886. doi:10.1007/s10571-008-9265-2
Xue S, Barna M (2012) Specialized ribosomes: a new frontier in gene regulation and organismal biology. Nat Rev Mol Cell Biol 13(6):355–369
Yagi Y, Tachikawa M, Noguchi H, Satoh S, Obokata J, Nakamura T (2013) Pentatricopeptide repeat proteins involved in plant organellar RNA editing. RNA Biol 10:9
Yao N, Imai S, Tada Y, Nakayashiki H, Tosa Y, Park P, Mayama S (2002) Apoptotic cell death is a common response to pathogen attack in oats. Mol Plant-Microbe Interact 15(10):1000–1007. doi:10.1094/MPMI.2002.15.10.1000
Yoshimoto K, Jikumaru Y, Kamiya Y, Kusano M, Consonni C, Panstruga R, Ohsumi Y, Shirasu K (2009) Autophagy negatively regulates cell death by controlling NPR1-dependent salicylic acid signaling during senescence and the innate immune response in Arabidopsis. Plant Cell 21(9):2914–2927. doi:10.1105/tpc.109.068635
Zehrmann A, Verbitskiy D, van der Merwe JA, Brennicke A, Takenaka M (2009) A DYW domain-containing pentatricopeptide repeat protein is required for RNA editing at multiple sites in mitochondria of Arabidopsis thaliana. Plant Cell 21(2):558–567
Zeng WH, Liao SC, Chang CC (2007) Identification of RNA editing sites in chloroplast transcripts of Phalaenopsis aphrodite and comparative analysis with those of other seed plants. Plant Cell Physiol 48(2):362–368
Zhang Z, Liu JJ, Yao FL, He H, Yang J, Xie HF, He T (2007) Morphological changes of non-apoptotic programmed cell death of polymorphonuclar neutrophils induced by ONO-AE-248. Xi bao yu fen zi mian yi xue za zhi Chin J Cell Mol Immunol 23(5):413–415
Zmudjak M, Colas des Francs-Small C, Keren I, Shaya F, Belausov E, Small I, Ostersetzer-Biran O (2013) mCSF1, a nucleus-encoded CRM protein required for the processing of many mitochondrial introns, is involved in the biogenesis of respiratory complexes I and IV in Arabidopsis. New Phytol 199(2):379–394. doi:10.1111/nph.12282
Zuzarte-Luis V, Hurle JM (2002) Programmed cell death in the developing limb. Int J Dev Biol 46(7):871–876
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer India
About this chapter
Cite this chapter
Ghulam, M.M., Kousar, S., Vardhan, H. (2015). Plant Mitochondrial Omics: State-of-the-Art Knowledge. In: Barh, D., Khan, M., Davies, E. (eds) PlantOmics: The Omics of Plant Science. Springer, New Delhi. https://doi.org/10.1007/978-81-322-2172-2_20
Download citation
DOI: https://doi.org/10.1007/978-81-322-2172-2_20
Published:
Publisher Name: Springer, New Delhi
Print ISBN: 978-81-322-2171-5
Online ISBN: 978-81-322-2172-2
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)