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  • Adam Z, Ostersetzer O. 2001. Degradation of unassembled and damaged thylakoid proteins. Biochemical Society Transactions 29: 427430.
  • Adams KL, Qiu Y-L, Stoutemyer M, Palmer JD. 2002. Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. PNAS 99: 99059912.
  • Asakura Y, Barkan A. 2006. Arabidopsis orthologs of maize chloroplast splicing factors promote splicing of orthologous and species-specific group II introns. Plant Physiology 142: 16561663.
  • Asakura Y, Barkan A. 2007. A CRM domain protein functions dually in group I and group II intron splicing in land plant chloroplasts. Plant Cell 19: 38643875.
  • Asakura Y, Bayraktar OA, Barkan A. 2008. Two CRM protein subfamilies cooperate in the splicing of group IIB introns in chloroplasts. RNA 14: 23192332.
  • Baerenfaller K, Hirsch-Hoffmann M, Svozil J, Hull R, Russenberger D, Bischof S, Lu QT, Gruissem W, Baginsky S. 2011. pep2pro: a new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in Arabidopsis thaliana. Integrative Biology 3: 225237.
  • Barkan A. 2011. Expression of plastid genes: organelle-specific elaborations on a prokaryotic scaffold. Plant Physiology 155: 15201532.
  • Barkan A, Klipcan L, Ostersetzer O, Kawamura T, Asakura Y, Watkins KP. 2007. The CRM domain: an RNA binding module derived from an ancient ribosome-associated protein. RNA 13: 5564.
  • Barrientos A, Zambrano A, Tzagoloff A. 2004. Mss51p and Cox14p jointly regulate mitochondrial Cox1p expression in Saccharomyces cerevisiae. EMBO Journal 23: 34723482.
  • Berg M, Rogers R, Muralla R, Meinke D. 2005. Requirement of aminoacyl-tRNA synthetases for gametogenesis and embryo development in Arabidopsis. Plant Journal 44: 866878.
  • Bonen L. 2008. Cis- and trans-splicing of group II introns in plant mitochondria. Mitochondrion 8: 2634.
  • Bonen L, Vogel J. 2001. The ins and outs of group II introns. Trends in Genetics 17: 322331.
  • Brangeon J, Sabar M, Gutierres S, Combettes B, Bove J, Gendy C, Chetrit P, Colas des Francs-Small C, Pla M, Vedel F et al. 2000. Defective splicing of the first nad4 intron is associated with lack of several complex I subunits in the Nicotiana sylvestris NMS1 nuclear mutant. Plant Journal 21: 269280.
  • Carrie C, Giraud E, Duncan O, Xu L, Wang Y, Huang SB, Clifton R, Murcha M, Filipovska A, Rackham O et al. 2010. Conserved and novel functions for Arabidopsis thaliana MIA40 in assembly of proteins in mitochondria and peroxisomes. Journal of Biological Chemistry 285: 3613836148.
  • Carrie C, Murcha MW, Kuehn K, Duncan O, Barthet M, Smith PM, Eubel H, Meyer E, Day DA, Millar AH et al. 2008. Type II NAD(P)H dehydrogenases are targeted to mitochondria and chloroplasts or peroxisomes in Arabidopsis thaliana. FEBS Letters 582: 30733079.
  • Cech TR. 1986. The generality of self-splicing RNA: relationship to nuclear messenger-RNA splicing. Cell 44: 207210.
  • Clifton R, Lister R, Parker K, Sappl P, Elhafez D, Millar A, Day D, Whelan J. 2005. Stress-induced co-expression of alternative respiratory chain components in Arabidopsis thaliana. Plant Molecular Biology 58: 193212.
  • Clifton SW, Minx P, Fauron CM-R, Gibson M, Allen JO, Sun H, Thompson M, Barbazuk WB, Kanuganti S, Tayloe C et al. 2004. Sequence and comparative analysis of the maize NB mitochondrial genome. Plant Physiology 136: 34863503.
  • Clough SJ, Bent AF. 1998. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant Journal 16: 735743.
  • Colas des Francs-Small C, Kroeger T, Zmudjak M, Ostersetzer-Biran O, Rahimi N, Small I, Barkan A. 2011. A PORR domain protein required for rpl2 and ccmFc intron splicing and for the biogenesis of c-type cytochromes in Arabidopsis mitochondria. Plant Journal 69: 9961005.
  • Dai LX, Toor N, Olson R, Keeping A, Zimmerly S. 2003. Database for mobile group II introns. Nucleic Acids Research 31: 424426.
  • Das G, Varshney U. 2006. Peptidyl-tRNA hydrolase and its critical role in protein biosynthesis. Microbiology 152: 21912195.
  • Dlakic M, Mushegian A. 2011. Prp8, the pivotal protein of the spliceosomal catalytic center, evolved from a retroelement-encoded reverse transcriptase. RNA 17: 799808.
  • Emanuelsson O, Nielsen H, Brunak S, Heijne Gv. 2000. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. Journal of Molecular Biology 300: 10051016.
  • Falcon de Longevialle A, Meyer EH, Andres C, Taylor NL, Lurin C, Millar AH, Small ID. 2007. The pentatricopeptide repeat gene OTP43 is required for trans-splicing of the mitochondrial nad1 intron 1 in Arabidopsis thaliana. Plant Cell 19: 32563265.
  • Gagliardi D, Binder S. 2007. Expression of the plant mitochondrial genome. In: Logan D, ed. Plant mitochondria. Oxford, UK: Blackwell Publishing, 5095.
  • Galej WP, Oubridge C, Newman AJ, Nagai K. 2013. Crystal structure of Prp8 reveals active site cavity of the spliceosome. Nature 493: 638643.
  • Garmier M, Carroll AJ, Delannoy E, Vallet C, Day DA, Small ID, Millar AH. 2008. Complex I dysfunction redirects cellular and mitochondrial metabolism in Arabidopsis. Plant Physiology 148: 13241341.
  • Gleave AP. 1992. A versatile binary vector system with a T-DNA organizational-structure conducive to efficient integration of cloned DNA into the plant genome. Plant Molecular Biology 20: 12031207.
  • 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 Research 31: 59075916.
  • Hazle T, Bonen L. 2007. Comparative analysis of sequences preceding protein-coding mitochondrial genes in flowering plants. Molecular Biology and Evolution 24: 11011112.
  • Heazlewood JL, Verboom RE, Tonti-Filippini J, Small I, Millar AH. 2007. SUBA: the Arabidopsis subcellular database. Nucleic Acids Research 35: D213D218.
  • Horan S, Bourges I, Taanman JW, Meunier B. 2005. Analysis of COX2 mutants reveals cytochrome oxidase subassemblies in yeast. Biochemical Journal 390: 703708.
  • Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem W, Zimmermann P. 2008. Genevestigator V3: a reference expression database for the meta-analysis of transcriptomes. Advances in Bioinformatics 2008: 420747420751.
  • Huang S, Taylor NL, Ströher E, Fenske R, Millar HA. 2012. Succinate dehydrogenase assembly factor 2 is needed for assembly and activity of mitochondrial complex II and for normal root elongation in Arabidopsis. Plant Journal 73: 429441.
  • Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ. 1998. Multiple sequence alignment with Clustal X. Trends in Biochemical Sciences 23: 403405.
  • Jenkins BD, Barkan A. 2001. Recruitment of a peptidyl-tRNA hydrolase as a facilitator of group II intron splicing in chloroplasts. EMBO Journal 20: 872879.
  • Jenkins BD, Kulhanek DJ, Barkan A. 1997. Nuclear mutations that block group II RNA splicing in maize chloroplasts reveal several intron classes with distinct requirements for splicing factors. Plant Cell 9: 283296.
  • Keren I, Bezawork-Geleta A, Kolton M, Maayan I, Belausov E, Levy M, Mett A, Gidoni D, Shaya F, Ostersetzer-Biran O. 2009. AtnMat2, a nuclear-encoded maturase required for splicing of group-II introns in Arabidopsis mitochondria. RNA 15: 22992311.
  • Keren I, Klipcan L, Bezawork-Geleta A, Kolton M, Shaya F, Ostersetzer-Biran O. 2008. Characterization of the molecular basis of group II intron RNA recognition by CRS1-CRM domains. Journal of Biological Chemistry 283: 2333323342.
  • Keren I, Tal L, des Francs-Small CC, Araújo WL, Shevtsov S, Shaya F, Fernie AR, Small I, Ostersetzer-Biran O. 2012. nMAT1, a Nuclear-encoded Maturase involved in the trans-splicing of nad1 intron 1, is essential for mitochondrial complex I assembly and function. Plant Journal 71: 413426.
  • Keser M, Langer T. 2000. Protein degradation in mitochondria. Seminars in Cell & Developmental Biology 11: 181190.
  • Klodmann J, Sunderhaus S, Nimtz M, Jänsch L, Braun H-P. 2010. Internal architecture of mitochondrial complex I from Arabidopsis thaliana. Plant Cell 22: 797810.
  • Knoop V. 2004. The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective. Current Genetics 46: 123139.
  • Knoop V. 2012. Seed plant mitochondrial genomes: complexity evolving. In: Bock R, Knoop V, eds. Genomics of chloroplasts and mitochondria. Dordrecht, Netherlands: Springer, 175200.
  • Köhler D, Schmidt-Gattung S, Binder S. 2010. The DEAD-box protein PMH2 is required for efficient group II intron splicing in mitochondria of Arabidopsis thaliana. Plant Molecular Biology 72: 459467.
  • Koprivova A, Colas des Francs-Small C, Calder G, Mugford ST, Tanz S, Lee B-R, Zechmann B, Small I, Kopriva S. 2010. Identification of a pentatricopeptide repeat protein implicated in splicing of intron 1 of mitochondrial nad7 transcripts. Journal of Biological Chemistry 285: 3219232199.
  • Kubo T, Nishizawa S, Sugawara A, Itchoda N, Estiati A, Mikami T. 2000. The complete nucleotide sequence of the mitochondrial genome of sugar beet (Beta vulgaris L.) reveals a novel gene for tRNA(Cys)(GCA). Nucleic Acids Research 28: 25712576.
  • Kühn K, Carrie C, Giraud E, Wang Y, Meyer EH, Narsai R, Colas des Francs-Small C, Zhang B, Murcha MW, Whelan J. 2011. The RCC1 family protein RUG3 is required for splicing of nad2 and complex I biogenesis in mitochondria of Arabidopsis thaliana. Plant Journal 67: 10671080.
  • Kühn K, Richter U, Meyer EH, Delannoy E, Falcon de Longevialle A, O'Toole N, Börner 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: 27622779.
  • Laemmli UK. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227: 680685.
  • Lamattina L, Gonzalez D, Gualberto J, Grienenberger J-M. 1993. Higher plant mitochondria encode an homologue of the nuclear-encoded 30-kDa subunit of bovine mitochondrial complex I. European Journal of Biochemistry 217: 831838.
  • Lambowitz AM, Zimmerly S. 2004. Mobile group II introns. Annual Review of Genetics 38: 135.
  • Law SR, Narsai R, Taylor NL, Delannoy E, Carrie C, Giraud E, Millar AH, Small I, Whelan J. 2012. Nucleotide and RNA metabolism prime translational initiation in the earliest events of mitochondrial biogenesis during Arabidopsis germination. Plant Physiology 158: 16101627.
  • Li L, Carrie C, Nelson C, Whelan J, Millar AH. 2012. Accumulation of newly synthesized F1 in vivo in Arabidopsis mitochondria provides evidence for modular assembly of the plant F1Fo ATP synthase. Journal of Biological Chemistry 287: 2574925757.
  • Liu Y, He J, Chen Z, Ren X, Hong X, Gong Z. 2010. ABA overly-sensitive 5 (ABO5), encoding a pentatricopeptide repeat protein required for cis-splicing of mitochondrial nad2 intron 3, is involved in the abscisic acid response in Arabidopsis. Plant Journal 63: 749765.
  • Lynch M, Kewalramani A. 2003. Messenger RNA surveillance and the evolutionary proliferation of introns. Molecular Biology and Evolution 20: 563571.
  • Martin W, Koonin EV. 2006. Introns and the origin of nucleus-cytosol compartmentalization. Nature 440: 4145.
  • Matsuura M, Noah JW, Lambowitz AM. 2001. Mechanism of maturase-promoted group II intron splicing. EMBO Journal 20: 72597270.
  • Maurer LM, Yohannes E, Bondurant SS, Radmacher M, Slonczewski JL. 2005. pH regulates genes for flagellar motility, catabolism, and oxidative stress in Escherichia coli K-12. Journal of Bacteriology 187: 304319.
  • Meyer EH, Solheim C, Tanz SK, Bonnard G, Millar AH. 2011. Insights into the composition and assembly of the membrane arm of plant complex I through analysis of subcomplexes in Arabidopsis mutant lines. Journal of Biological Chemistry 286: 2608126092.
  • Meyer EH, Tomaz T, Carroll AJ, Estavillo G, Delannoy E, Tanz SK, Small ID, Pogson BJ, Millar AH. 2009. Remodeled respiration in ndufs4 with low phosphorylation efficiency suppresses Arabidopsis germination and growth and alters control of metabolism at night. Plant Physiology 151: 603619.
  • Mick DU, Fox TD, Rehling P. 2011. Inventory control: cytochrome c oxidase assembly regulates mitochondrial translation. Nature Reviews Molecular Cell Biology 12: 1420.
  • Millar AH, Whelan J, Soole KL, Day DA. 2011. Organization and regulation of mitochondrial respiration in plants. Annual Review of Plant Biology 62: 79104.
  • Minai L, Wostrikoff K, Wollman FA, Choquet Y. 2006. Chloroplast biogenesis of photosystem II cores involves a series of assembly-controlled steps that regulate translation. Plant Cell 18: 159175.
  • Narsai R, Law SR, Carrie C, Xu L, Whelan J. 2011. In depth temporal transcriptome profiling reveals a crucial developmental switch with roles for RNA processing and organelle metabolism that are essential for germination in Arabidopsis thaliana. Plant Physiology 157: 13421362.
  • 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. Molecular Genetics and Genomics 268: 434445.
  • Ogihara Y, Yamazaki Y, Murai K, Kanno A, Terachi T, Shiina T, Miyashita N, Nasuda S, Nakamura C, Mori N et al. 2005. Structural dynamics of cereal mitochondrial genomes as revealed by complete nucleotide sequencing of the wheat mitochondrial genome. Nucleic Acids Research 33: 62356250.
  • Ossowski S, Schwab R, Weigel D. 2008. Gene silencing in plants using artificial microRNAs and other small RNAs. Plant Journal 53: 674690.
  • Ostersetzer O, Cooke AM, Watkins KP, Barkan A. 2005. CRS1, a chloroplast group II intron splicing factor, promotes intron folding through specific interactions with two intron domains. Plant Cell 17: 241255.
  • Ostheimer GJ, Hadjivasiliou H, Kloer DP, Barkan A, Matthews BW. 2005. Structural analysis of the Group II Intron Splicing Factor CRS2 yields insights into its protein and RNA interaction surfaces. Journal of Molecular Biology 345: 5168.
  • Ostheimer GJ, Rojas M, Hadjivassiliou H, Barkan A. 2006. Formation of the CRS2-CAF2 group II Intron splicing complex Is mediated by a 22-amino acid motif in the COOH-terminal region of CAF2. Journal of Biological Chemistry 281: 47324738.
  • Ostheimer GJ, Williams-Carrier R, Belcher S, Osborne E, Gierke J, Barkan A. 2003. Group II intron splicing factors derived by diversification of an ancient RNA-binding domain. EMBO Journal 22: 39193929.
  • Perales M, Eubel H, Heinemeyer J, Colaneri A, Zabaleta E, Braun H-P. 2005. Disruption of a nuclear gene encoding a mitochondrial gamma carbonic anhydrase reduces complex I and supercomplex I+III2 levels and alters mitochondrial physiology in Arabidopsis. Journal of Molecular Biology 350: 263277.
  • Rasmusson AG, Geisler DA, Møller IM. 2008. The multiplicity of dehydrogenases in the electron transport chain of plant mitochondria. Mitochondrion 8: 4760.
  • Rigas S, Daras G, Laxa M, Marathias N, Fasseas C, Sweetlove LJ, Hatzopoulos P. 2009. Role of Lon1 protease in post-germinative growth and maintenance of mitochondrial function in Arabidopsis thaliana. New Phytologist 181: 588600.
  • Schwab R, Ossowski S, Riester M, Warthmann N, Weigel D. 2006. Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18: 11211133.
  • Sharp PA. 1985. On the origin of RNA splicing and introns. Cell 42: 397400.
  • Small I, Peeters N, Legeai F, Lurin C. 2004. Predotar: a tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics 4: 15811590.
  • Soto IC, Fontanesi F, Liu JJ, Barrientos A. 2012. Biogenesis and assembly of eukaryotic cytochrome c oxidase catalytic core. Biochimica et Biophysica Acta 1817: 883897.
  • Sugiyama Y, Watase Y, Nagase M, Makita N, Yagura S, Hirai A, Sugiura M. 2005. The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants. Molecular Genetics and Genomics 272: 603615.
  • Till B, Schmitz-Linneweber C, Williams-Carrier R, Barkan A. 2001. CRS1 is a novel group II intron splicing factor that was derived from a domain of ancient origin. RNA 7: 12271238.
  • Unseld M, Marienfeld JR, Brandt P, Brennicke A. 1997. The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides. Nature Genetics 15: 5761.
  • Wollman F-A, Minai L, Nechushtai R. 1999. The biogenesis and assembly of photosynthetic proteins in thylakoid membranes. Biochimica et Biophysica Acta 1411: 2185.
  • Yoshida K, Noguchi K. 2009. Differential gene expression profiles of the mitochondrial respiratory components in illuminated Arabidopsis leaves. Plant Cell Physiology 50: 14491462.