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Plant Mitochondrial Omics: State-of-the-Art Knowledge

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PlantOmics: The Omics of Plant Science

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.

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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

    CAS  PubMed  Google Scholar 

  • Agrawal RK, Sharma MR (2012) Structural aspects of mitochondrial translational apparatus. Curr Opin Struct Biol 22(6):797–803

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Barrientos A (2002) In vivo and in organello assessment of OXPHOS activities. Methods 26(4):307–316

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Bennoun P, Delosme M (1999) Chloroplast suppressors that act on a mitochondrial mutation in Chlamydomonas reinhardtii. Mol Gen Gene MGG 262(1):85–89

    CAS  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • Berry EA, Guergova-Kuras M, Huang LS, Crofts AR (2000) Structure and function of cytochrome bc complexes. Annu Rev Biochem 69:1005–1075

    CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • Brennicke A, Marchfelder A, Binder S (1999) RNA editing. FEMS Microbiol Rev 23(3):297–316

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Capaldi RA (1990) Structure and assembly of cytochrome c oxidase. Arch Biochem Biophys 280(2):252–262

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Cheetham GM, Jeruzalmi D, Steitz TA (1999) Structural basis for initiation of transcription from an RNA polymerase-promoter complex. Nature 399(6731):80–83

    CAS  PubMed  Google Scholar 

  • Choquet Y, Wollman FA (2002) Translational regulations as specific traits of chloroplast gene expression. FEBS Lett 529(1):39–42

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • Claros MG, Vincens P (1996) Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur J Biochem 241(3):779–786

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • Farre JC, Aknin C, Araya A, Castandet B (2012) RNA editing in mitochondrial trans-introns is required for splicing. PLoS One 7(12):20

    Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • Fukuda H (2000) Programmed cell death of tracheary elements as a paradigm in plants. Plant Mol Biol 44(3):245–253

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • Giege P, Hoffmann M, Binder S, Brennicke A (2000) RNA degradation buffers asymmetries of transcription in Arabidopsis mitochondria. EMBO Rep 1(2):164–170

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • Greenberg JT, Yao N (2004) The role and regulation of programmed cell death in plant-pathogen interactions. Cell Microbiol 6(3):201–211

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • Handa H (2008) Linear plasmids in plant mitochondria: peaceful coexistences or malicious invasions? Mitochondrion 8(1):15–25

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Heath MC (2000) Nonhost resistance and nonspecific plant defenses. Curr Opin Plant Biol 3(4):315–319

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  PubMed  Google Scholar 

  • Hedtke B, Borner T, Weihe A (1997) Mitochondrial and chloroplast phage-type RNA polymerases in Arabidopsis. Science 277(5327):809–811

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Hedtke B, Borner T, Weihe A (2000) One RNA polymerase serving two genomes. EMBO Rep 1(5):435–440

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Herrmann JM, Funes S (2005) Biogenesis of cytochrome oxidase-sophisticated assembly lines in the mitochondrial inner membrane. Gene 354:43–52

    CAS  PubMed  Google Scholar 

  • Hess WR, Borner T (1999) Organellar RNA polymerases of higher plants. Int Rev Cytol 190:1–59

    CAS  PubMed  Google Scholar 

  • Hiesel R, Wissinger B, Schuster W, Brennicke A (1989) RNA editing in plant mitochondria. Science 246(4937):1632–1634

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Holec S, Lange H, Canaday J, Gagliardi D (2008) Coping with cryptic and defective transcripts in plant mitochondria. Biochim Biophys Acta 9:566–573

    Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Horsefield R, Iwata S, Byrne B (2004) Complex II from a structural perspective. Curr Protein Pept Sci 5(2):107–118

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Jacques JP, Hausmann S, Kolakofsky D (1994) Paramyxovirus mRNA editing leads to G deletions as well as insertions. EMBO J 13(22):5496–5503

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Kerr JF (2002) History of the events leading to the formulation of the apoptosis concept. Toxicology 181–182:471–474

    PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  Google Scholar 

  • Kubo T, Newton KJ (2008) Angiosperm mitochondrial genomes and mutations. Mitochondrion 8(1):5–14

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Lambowitz AM, Zimmerly S (2004) Mobile group II introns. Annu Rev Genet 38:1–35

    CAS  PubMed  Google Scholar 

  • Lambowitz AM, Zimmerly S (2011) Group II introns: mobile ribozymes that invade DNA. Cold Spring Harb Perspect Biol 3(8):a003616

    Google Scholar 

  • Lang BF, Gray MW, Burger G (1999) Mitochondrial genome evolution and the origin of eukaryotes. Annu Rev Genet 33:351–397

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Leister D (2012) Retrograde signaling in plants: from simple to complex scenarios. Front Plant Sci 3(135):19

    Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Mackenzie S, McIntosh L (1999) Higher plant mitochondria. Plant Cell 11(4):571–586

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • McCabe PF, Leaver CJ (2000) Programmed cell death in cell cultures. Plant Mol Biol 44(3):359–368

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Millar AH, Sweetlove LJ, Giege P, Leaver CJ (2001) Analysis of the Arabidopsis mitochondrial proteome. Plant Physiol 127(4):1711–1727

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Millar AH, Whelan J, Soole KL, Day DA (2011) Organization and regulation of mitochondrial respiration in plants. Annu Rev Plant Biol 62:79–104

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • Osteryoung KW, Nunnari J (2003) The division of endosymbiotic organelles. Science 302(5651):1698–1704. doi:10.1126/science.1082192

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Patel S, Dinesh-Kumar SP (2008) Arabidopsis ATG6 is required to limit the pathogen-associated cell death response. Autophagy 4(1):20–27

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Peters K, Belt K, Braun HP (2013) 3D gel map of Arabidopsis complex I. Front Plant Sci 4(153)

    Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Rochaix JD (2001) Assembly, function, and dynamics of the photosynthetic machinery in Chlamydomonas reinhardtii. Plant Physiol 127(4):1394–1398

    PubMed Central  CAS  PubMed  Google Scholar 

  • Rolland F, Moore B, Sheen J (2002) Sugar sensing and signaling in plants. Plant Cell 14(205):S185–S205

    PubMed Central  CAS  PubMed  Google Scholar 

  • Rutter J, Winge DR, Schiffman JD (2010) Succinate dehydrogenase—assembly, regulation and role in human disease. Mitochondrion 10(4):393–401

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Senior DJ, Tsai CS (1990) Esterase activity of high-Km aldehyde dehydrogenase from rat liver mitochondria. Biochem Cell Biol 68(4):758–763

    CAS  PubMed  Google Scholar 

  • Shikanai T (2006) RNA editing in plant organelles: machinery, physiological function and evolution. Cell Mol Life Sci 63(6):698–708

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • Soll J, Schleiff E (2004) Protein import into chloroplasts. Nat Rev Mol Cell Biol 5(3):198–208

    CAS  PubMed  Google Scholar 

  • Sousa R (1996) Structural and mechanistic relationships between nucleic acid polymerases. Trends Biochem Sci 21(5):186–190

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Thomas SG, Franklin-Tong VE (2004) Self-incompatibility triggers programmed cell death in Papaver pollen. Nature 429(6989):305–309. doi:10.1038/nature02540

    CAS  PubMed  Google Scholar 

  • Thompson CB (1995) Apoptosis in the pathogenesis and treatment of disease. Science 267(5203):1456–1462

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • Toro N, Jimenez-Zurdo JI, Garcia-Rodriguez FM (2007) Bacterial group II introns: not just splicing. FEMS Microbiol Rev 31(3):342–358

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Tzagoloff A (1995) Ubiquinol-cytochrome-c oxidoreductase from Saccharomyces cerevisiae. Methods Enzymol 260:51–63

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Velours J, Arselin G (2000) The Saccharomyces cerevisiae ATP synthase. J Bioenerg Biomembr 32(4):383–390

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Vicens Q, Cech TR (2006) Atomic level architecture of group I introns revealed. Trends Biochem Sci 31(1):41–51

    CAS  PubMed  Google Scholar 

  • Vogel RO, Smeitink JA, Nijtmans LG (2007) Human mitochondrial complex I assembly: a dynamic and versatile process. Biochim Biophys Acta 10(27):9

    Google Scholar 

  • Vothknecht UC, Westhoff P (2001) Biogenesis and origin of thylakoid membranes. Biochim Biophys Acta 12:1–2

    Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • Wallace DC (2005a) The mitochondrial genome in human adaptive radiation and disease: on the road to therapeutics and performance enhancement. Gene 354:169–180

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • Werhahn W, Braun HP (2002) Biochemical dissection of the mitochondrial proteome from Arabidopsis thaliana by three-dimensional gel electrophoresis. Electrophoresis 23(4):640–646

    CAS  PubMed  Google Scholar 

  • Wheeler DS (2009) Death to sepsis: targeting apoptosis pathways in sepsis. Crit Care 13(6):1010. doi:10.1186/cc8162

    PubMed Central  PubMed  Google Scholar 

  • 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

    CAS  Google Scholar 

  • Woodson JD, Chory J (2008) Coordination of gene expression between organellar and nuclear genomes. Nat Rev Genet 9(5):383–395

    CAS  PubMed  Google Scholar 

  • Xiong Y, Contento AL, Bassham DC (2007a) Disruption of autophagy results in constitutive oxidative stress in Arabidopsis. Autophagy 3(3):257–258

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

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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

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