Expression Profiling of Organellar Genes

Adam Z (2007) Protein stability and degradation in plastids. Top Curr Genet 19:315–338CrossRefGoogle Scholar

Allison LA, Simon LD, Maliga P (1996) Deletion of rpoB reveals a second distinct transcription system in plastids of higher plants. EMBO J 15:2802–2809PubMedGoogle Scholar

Baena-González E, Allahverdiyeva Y, Svab Z, Maliga P, Josse EM, Kuntz M, Mäenpää P, Aro EM (2003) Deletion of the tobacco plastid psbA gene triggers an upregulation of the thylakoid-associated NAD(P)H dehydrogenase complex and the plastid terminal oxidase (PTOX). Plant J 35:704–716PubMedCrossRefGoogle Scholar

Baginsky S, Siddique A, Gruissem W (2004) Proteome analysis of tobacco bright yellow-2 (BY-2) cell culture plastids as a model for undifferentiated heterotrophic plastids. J Proteome Res 3:1128–1137PubMedCrossRefGoogle Scholar

Bancel E, Rogniaux H, Debiton C, Chambon C, Branlard G (2010) Extraction and proteome analysis of starch granule-associated proteins in mature wheat kernel (Triticum aestivum L.). J Proteome Res 9:3299–3310PubMedCrossRefGoogle Scholar

Barkan A (1989) Tissue-dependent plastid RNA splicing in maize: transcripts from four plastid genes are predominantly unspliced in leaf meristems and roots. Plant Cell 1:437–445PubMedGoogle Scholar

Barkan A (1993) Nuclear mutants of maize with defects in chloroplast polysome assembly have altered chloroplast RNA metabolism. Plant Cell 5:389–402PubMedGoogle Scholar

Barsan C, Sanchez-Bel P, Rombaldi C, Egea I, Rossignol M, Kuntz M, Zouine M, Latché A, Bouzayen M, Pech JC (2010) Characteristics of the tomato chromoplast revealed by proteomic analysis. J Exp Bot 61:2413–2431PubMedCrossRefGoogle Scholar

Baumgartner BJ, Rapp JC, Mullet JE (1989) Plastid transcription activity and DNA copy number increase early in barley chloroplast development. Plant Physiol 89:1011–1018PubMedCrossRefGoogle Scholar

Baumgartner BJ, Rapp JC, Mullet JE (1993) Plastid genes encoding the transcription/translation apparatus are differentially transcribed early in barley (Hordeum vulgare) chloroplast development (evidence for selective stabilization of psbA mRNA). Plant Physiol 101:781–791PubMedGoogle Scholar

Benne R, Van den Burg J, Brakenhoff J, Sloof P, Van Boom JH, Tromp MC (1986) Major transcript of the frameshift coxII from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA. Cell 46:819–826PubMedCrossRefGoogle Scholar

Bentolila S, Elliott LE, Hanson MR (2008) Genetic architecture of mitochondrial editing in Arabidopsis thaliana. Genetics 178:1693–1708PubMedCrossRefGoogle Scholar

Biehl A, Richly E, Noutsos C, Salamini F, Leister D (2005) Analysis of 101 nuclear transcriptomes reveals 23 distinct regulons and their relationship to metabolism, chromosomal gene distribution and co-ordination of nuclear and plastid gene expression. Gene 344:33–41PubMedCrossRefGoogle Scholar

Binder S, Brennicke A (1993) A transfer RNA gene transcription initiation site is similar to messenger RNA and rRNA promoters in plant mitochondria. Nucleic Acids Res 21:5012–5019PubMedCrossRefGoogle Scholar

Binder S, Marchfelder A, Brennicke A, Wissinger B (1992) RNA editing in trans-splicing intron sequences of nad2 mRNAs in Oenothera mitochondria. J Biol Chem 267:7615–7623PubMedGoogle Scholar

Bock R, Koop HU (1997) Extraplastidic site-specific factors mediate RNA editing in chloroplasts. EMBO J 16:3282–3288PubMedCrossRefGoogle Scholar

Bock R, Hagemann R, Kössel H, Kudla J (1993) Tissue- and stage-specific modulation of RNA editing of the psbF and psbL transcript from spinach plastids–a new regulatory mechanism? Mol Gen Genet 240:238–244PubMedCrossRefGoogle Scholar

Bock H, Brennicke A, Schuster W (1994a) Rps3 and rpl16 genes do not overlap in Oenothera mitochondria: GTG as a potential translation initiation codon in plant mitochondria? Plant Mol Biol 24:811–818PubMedCrossRefGoogle Scholar

Bock R, Kössel H, Maliga P (1994b) Introduction of a heterologous editing site into the tobacco plastid genome: the lack of RNA editing leads to a mutant phenotype. EMBO J 13:4623–4628PubMedGoogle Scholar

Bohne AV, Irihimovitch V, Weihe A, Stern DB (2006) Chlamydomonas reinhardtii encodes a single sigma70-like factor which likely functions in chloroplast transcription. Curr Genet 49:333–340PubMedCrossRefGoogle Scholar

Bollenbach T, Schuster G, Portnoy V, Stern D (2007) Processing, degradation, and polyadenylation of chloroplast transcripts. Top Curr Genet 19:175–211CrossRefGoogle Scholar

Bonen L, Vogel J (2001) The ins and outs of group II introns. Trends Genet 17:322–331PubMedCrossRefGoogle Scholar

Bouchez D, Höfte H (1998) Functional genomics in plants. Plant Physiol 118:725–732PubMedCrossRefGoogle Scholar

Bräutigam K, Dietzel L, Pfannschmidt T (2007) Plastid-nucleus communication: anterograde and retrograde signalling in the development and function of plastids. Top Curr Genet 19:409–456CrossRefGoogle Scholar

Brosch M, Krause K, Falk J, Krupinska K (2007) Analysis of gene expression in amyloplasts of potato tubers. Planta 227:91–99PubMedCrossRefGoogle Scholar

Buchanan BB, Gruissem W, Jones RL (eds) (2000) Biochemistry & molecular biology of plants. American Society of Plant Physiologists, RockwilleGoogle Scholar

Cahoon AB, Harris FM, Stern DB (2004) Analysis of developing maize plastids reveals two mRNA stability classes correlating with RNA polymerase type. EMBO Rep 5:801–806PubMedCrossRefGoogle Scholar

Cahoon AB, Takacs EM, Sharpe RM, Stern DB (2008) Nuclear, chloroplast, and mitochondrial transcript abundance along a maize leaf developmental gradient. Plant Mol Biol 66:33–46PubMedCrossRefGoogle Scholar

Canino G, Bocian E, Barbezier N, Echeverría M, Forner J, Binder S, Marchfelder A (2009) Arabidopsis encodes four tRNase Z enzymes. Plant Physiol 150:1494–1502PubMedCrossRefGoogle Scholar

Carrillo C, Bonen L (1997) RNA editing status of nad7 intron domains in wheat mitochondria. Nucleic Acids Res 25:403–409PubMedCrossRefGoogle Scholar

Carter ML, Smith AC, Kobayashi H, Purton S, Herrin DL (2004) Structure, circadian regulation and bioinformatic analysis of the unique sigma factor gene in Chlamydomonas reinhardtii. Photosynth Res 82:339–349PubMedCrossRefGoogle Scholar

Chang CC, Stern DB (1999) DNA-binding factors assemble in a sequence-specific manner on the maize mitochondrial atpA promoter. Curr Genet 35:506–511PubMedCrossRefGoogle 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 65:465–472PubMedCrossRefGoogle Scholar

Chateigner-Boutin AL, Hanson MR (2003) Developmental co-variation of RNA editing extent of plastid editing sites exhibiting similar cis-elements. Nucleic Acids Res 31:2586–2594PubMedCrossRefGoogle Scholar

Chateigner-Boutin AL, Small I (2007) A rapid high-throughput method for the detection and quantification of RNA editing based on high-resolution melting of amplicons. Nucleic Acids Res 35:e114PubMedCrossRefGoogle Scholar

Chateigner-Boutin AL, Ramos-Vega M, Guevara-García A, Andrés C, de la Luz Gutiérrez-Nava M, Cantero A, Delannoy E, Jiménez LF, Lurin C, Small I, León P (2008) CLB19, a pentatricopeptide repeat protein required for editing of rpoA and clpP chloroplast transcripts. Plant J 56:590–602PubMedCrossRefGoogle Scholar

Chaudhuri S, Carrer H, Maliga P (1995) Site-specific factor involved in the editing of the psbL mRNA in tobacco plastids. EMBO J 14:2951–2957PubMedGoogle Scholar

Chelm BK, Hallick RB (1976) Changes in the expression of the chloroplast genome of Euglena gracilis during chloroplast development. Biochemistry 15:593–599PubMedCrossRefGoogle Scholar

Chelm BK, Hallick RB, Gray PW (1979) Transcription program of the chloroplast genome of Euglena gracilis during chloroplast development. Proc Natl Acad Sci USA 76:2258–2262PubMedCrossRefGoogle Scholar

Cheung F, Haas BJ, Goldberg SM, May GD, Xiao Y, Town CD (2006) Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology. BMC Genomics 7:272PubMedCrossRefGoogle Scholar

Cho Y, Qiu Y-L, Kuhlman P, Palmer JD (1998) Explosive invasion of plant mitochondria by a group I intron. Proc Natl Acad Sci USA 95:14244–14249PubMedCrossRefGoogle Scholar

Cho WK, Geimer S, Meurer J (2009) Cluster analysis and comparison of various chloroplast transcriptomes and genes in Arabidopsis thaliana. DNA Res 16:31–44PubMedCrossRefGoogle Scholar

Clarke AK, MacDonald TM, Sjögren LLE (2005) The ATP-dependent Clp protease in chloroplasts of higher plants. Physiol Plant 123:406–412CrossRefGoogle Scholar

Corneille S, Lutz K, Maliga P (2000) Conservation of RNA editing between rice and maize plastids: are most editing events dispensable? Mol Gen Genet 264:419–424PubMedCrossRefGoogle Scholar

Covello PS, Gray MW (1989) RNA editing in plant mitochondria. Nature 341:662–666PubMedCrossRefGoogle Scholar

Daher Z, Recorbet G, Valot B, Robert F, Balliau T, Potin S, Schoefs B, Dumas-Gaudot E (2010) Proteomic analysis of Medicago truncatula root plastids. Proteomics 10:2123–2137PubMedCrossRefGoogle Scholar

Daniell H, Lee S-B, Grevich J, Saski C, Quesada-Vargas T, Guda C, Tomkins J, Jansen R (2006) Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes. Theor Appl Genet 112:1503–1518PubMedCrossRefGoogle Scholar

Danon A (1997) Translational regulation in the chloroplast. Plant Physiol 115:1293–1298PubMedCrossRefGoogle Scholar

De Santis-Maciossek G, Kofer W, Bock A, Schoch S, Maier RM, Wanner G, Rüdiger W, Koop HU, Herrmann RG (1999) Targeted disruption of the plastid RNA polymerase genes rpoA, B and C1: molecular biology, biochemistry and ultrastructure. Plant J 18:477–489PubMedCrossRefGoogle Scholar

Demarsy E, Courtois F, Azevedo J, Buhot L, Lerbs-Mache S (2006) Building up of the plastid transcriptional machinery during germination and early plant development. Plant Physiol 142:993–1003PubMedCrossRefGoogle Scholar

Deng XW, Gruissem W (1988) Constitutive transcription and regulation of gene expression in non-photosynthetic plastids of higher plants. EMBO J 7:3301–3308PubMedGoogle Scholar

Dhingra A, Bies DH, Lehner KR, Folta KM (2006) Green light adjusts the plastid transcriptome during early photomorphogenic development. Plant Physiol 142:1256–1266PubMedCrossRefGoogle Scholar

Dix KP, Rawson JRY (1983) In vivo transcriptional products of the chloroplast DNA of Euglena gracilis. Curr Genet 7:265–272CrossRefGoogle Scholar

Dombrowski S, Brennicke A, Binder S (1997) 3′-Inverted repeats in plant mitochondrial mRNAs are processing signals rather than transcription terminators. EMBO J 16:5069–5076PubMedCrossRefGoogle Scholar

Dong FG, Wilson KG, Makaroff CA (1998) The radish (Raphanus sativus L.) mitochondrial cox2 gene contains an ACG at the predicted translation initiation site. Curr Genet 34:79–87PubMedCrossRefGoogle Scholar

Dreyfus M, Régnier P (2002) The poly(A) tail of mRNAs: bodyguard in eukaryotes, scavenger in bacteria. Cell 111:611–613PubMedCrossRefGoogle Scholar

Duchêne AM, Giritch A, Hoffmann B, Cognat V, Lancelin D, Peeters NM, Zaepfel M, Maréchal-Drouard L, Small ID (2005) Dual targeting is the rule for organellar aminoacyl-tRNA synthetases in Arabidopsis thaliana. Proc Natl Acad Sci USA 102:16484–16489PubMedCrossRefGoogle Scholar

Duff RJ, Moore FB (2005) Pervasive RNA editing among hornwort rbcL transcripts except Leiosporoceros. J Mol Evol 61:571–578PubMedCrossRefGoogle Scholar

Eberhard S, Drapier D, Wollman FA (2002) Searching limiting steps in the expression of chloroplast-encoded proteins: relations between gene copy number, transcription, transcript abundance and translation rate in the chloroplast of Chlamydomonas reinhardtii. Plant J 31:149–160PubMedCrossRefGoogle Scholar

Emrich SJ, Barbazuk WB, Li L, Schnable PS (2007) Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res 17:69–73PubMedCrossRefGoogle Scholar

Erickson B, Stern DB, Higgs DC (2005) Microarray analysis confirms the specificity of a Chlamydomonas reinhardtii chloroplast RNA stability mutant. Plant Physiol 137:534–544PubMedCrossRefGoogle Scholar

Fedorova O, Zingler N (2007) Group II introns: structure, folding and splicing mechanism. Biol Chem 388:665–678PubMedCrossRefGoogle Scholar

Fey J, Maréchal-Drouard L (1999) Compilation and analysis of plant mitochondrial promoter sequences: an illustration of a divergent evolution between monocot and dicot mitochondria. Biochem Biophys Res Commun 256:409–414PubMedCrossRefGoogle Scholar

Forner J, Hölzle A, Jonietz C, Thuss S, Schwarzländer M, Weber B, Meyer RC, Binder S (2008) Mitochondrial mRNA polymorphisms in different Arabidopsis accessions. Plant Physiol 148:1106–1116PubMedCrossRefGoogle Scholar

Freyer R, Kiefer-Meyer MC, Kössel H (1997) Occurrence of plastid RNA editing in all major lineages of land plants. Proc Natl Acad Sci USA 94:6285–6290PubMedCrossRefGoogle Scholar

Fujiwara M, Nagashima A, Kanamaru K, Tanaka K, Takahashi H (2000) Three new nuclear genes, sigD, sigE and sigF, encoding putative plastid RNA polymerase sigma factors in Arabidopsis thaliana. FEBS Lett 481:47–52PubMedCrossRefGoogle Scholar

Gagliardi D, Perrin R, Maréchal-Drouard L, Grienenberger JM, Leaver CJ (2001) Plant mitochondrial polyadenylated mRNAs are degraded by a 3′- to 5′- exoribonuclease activity, which proceeds unimpeded by stable secondary structures. J Biol Chem 276:43541–43547PubMedCrossRefGoogle Scholar

Gargano D, Vezzi A, Scotti N, Gray JC, Valle G, Grillo S, Cardi T (2005) The complete nucleotide sequence genome of potato (Solanum tuberosum cv Désirée) chloroplast DNA. In: Proceedings of the 2nd Solanaceae Genome Workshop 2005, Ischia, 25–29 Sept 2005Google Scholar

Geimer S, Belicová A, Legen J, Sláviková S, Herrmann RG, Krajcovic J (2009) Transcriptome analysis of the Euglena gracilis plastid chromosome. Curr Genet 55:425–438PubMedCrossRefGoogle Scholar

Giegé P, Brennicke A (1999) RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs. Proc Natl Acad Sci USA 96:15324–15329PubMedCrossRefGoogle Scholar

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

Giegé P, Rayapuram N, Meyer EH, Grienenberger JM, Bonnard G (2004) CcmF(C) involved in cytochrome c maturation is present in a large sized complex in wheat mitochondria. FEBS Lett 563:165–169PubMedCrossRefGoogle Scholar

Giegé P, Sweetlove LJ, Cognat V, Leaver CJ (2005) Coordination of nuclear and mitochondrial genome expression during mitochondrial biogenesis in Arabidopsis. Plant Cell 17:1497–1512PubMedCrossRefGoogle Scholar

Glanz S, Kück U (2009) Trans-splicing of organelle introns–a detour to continuous RNAs. Bioessays 31:921–934PubMedCrossRefGoogle Scholar

Gobert A, Gutmann B, Taschner A, Gössringer M, Holzmann J, Hartmann RK, Rossmanith W, Giegé P (2010) A single Arabidopsis organellar protein has RNase P activity. Nat Struct Mol Biol 17:740–744PubMedCrossRefGoogle Scholar

Gonzalez DH, Welchen E, Attallah CV, Comelli RN, Mufarrege EF (2007) Transcriptional coordination of the biogenesis of the oxidative phosphorylation machinery in plants. Plant J 51:105–116PubMedCrossRefGoogle 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 37:5093–5104PubMedCrossRefGoogle Scholar

Grewe F, Herres S, Viehover P, Polsakiewicz M, Weisshaar B, Knoop V (2010) A unique transcriptome: 1782 positions of RNA editing alter 1406 codon identities in mitochondrial mRNAs of the lycophyte Isoetes engelmannii. Nucleic Acids Res 39:2890–2902Google Scholar

Grohmann L, Thieck O, Herz U, Schröder W, Brennicke A (1994) Translation of nad9 mRNAs in mitochondria from Solanum tuberosum is restricted to completely edited transcripts. Nucleic Acids Res 22:3304–3311PubMedCrossRefGoogle Scholar

Gualberto JM, Lamattina L, Bonnard G, Weil JH, Grienenberger JM (1989) RNA editing in wheat mitochondria results in the conservation of protein sequences. Nature 341:660–662PubMedCrossRefGoogle Scholar

Hajdukiewicz PT, Allison LA, Maliga P (1997) The two RNA polymerases encoded by the nuclear and the plastid compartments transcribe distinct groups of genes in tobacco plastids. EMBO J 16:4041–4048PubMedCrossRefGoogle Scholar

Hallick RB, Hong L, Drager RG, Favreau MR, Monfort A, Orsat B, Spielmann A, Stutz E (1993) Complete sequence of Euglena gracilis chloroplast DNA. Nucleic Acids Res 21:3537–3544PubMedCrossRefGoogle Scholar

Hammani K, Okuda K, Tanz SK, Chateigner-Boutin AL, Shikanai T, Small I (2009) A study of new Arabidopsis chloroplast RNA editing mutants reveals general features of editing factors and their target sites. Plant Cell 21:3686–3699PubMedCrossRefGoogle Scholar

Han C-d, Patrie W, Polacco M, Coe EHJ (1993) Aberrations in plastid transcripts and deficiency of plastid DNA in striped and albino mutants in maize. Planta 191:552–563CrossRefGoogle 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 31:5907–5916PubMedCrossRefGoogle Scholar

Hayes R, Kudla J, Gruissem W (1999) Degrading chloroplast mRNA: the role of polyadenylation. Trends Biochem Sci 24:199–202PubMedCrossRefGoogle Scholar

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

Hedtke B, Wagner I, Börner T, Hess WR (1999) Inter-organellar crosstalk in higher plants: impaired chloroplast development affects mitochondrial gene and transcript levels. Plant J 19:635–643PubMedCrossRefGoogle Scholar

Hedtke B, Börner T, Weihe A (2000) One RNA polymerase serving two genomes. EMBO Rep 1:435–440PubMedCrossRefGoogle Scholar

Hess WR, Prombona A, Fieder B, Subramanian AR, Börner T (1993) Chloroplast rps15 and the rpoB/C1/C2 gene cluster are strongly transcribed in ribosome-deficient plastids: evidence for a functioning non-chloroplast-encoded RNA polymerase. EMBO J 12:563–571PubMedGoogle Scholar

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

Hildebrand M, Hallick RB, Passavant CW, Bourque DP (1988) Trans-splicing in chloroplasts: the rps12 loci of Nicotiana tabacum. Proc Natl Acad Sci USA 85:372–376PubMedCrossRefGoogle Scholar

Hirose T, Sugiura M (1997) Both RNA editing and RNA cleavage are required for translation of tobacco chloroplast ndhD mRNA: a possible regulatory mechanism for the expression of a chloroplast operon consisting of functionally unrelated genes. EMBO J 16:6804–6811PubMedCrossRefGoogle Scholar

Hirose T, Sugiura M (2001) Involvement of a site-specific trans-acting factor and a common RNA-binding protein in the editing of chloroplast mRNAs: development of a chloroplast in vitro RNA editing system. EMBO J 20:1144–1152PubMedCrossRefGoogle Scholar

Hirose T, Fan H, Suzuki JY, Wakasugi T, Tsudzuki T, Kössel H, Sugiura M (1996) Occurrence of silent RNA editing in chloroplasts: its species specificity and the influence of environmental and developmental conditions. Plant Mol Biol 30:667–672PubMedCrossRefGoogle Scholar

Hirose T, Kusumegi T, Tsudzuki T, Sugiura M (1999) RNA editing sites in tobacco chloroplast transcripts: editing as a possible regulator of chloroplast RNA polymerase activity. Mol Gen Genet 262:462–467PubMedCrossRefGoogle Scholar

Hoch B, Maier RM, Appel K, Igloi GL, Kössel H (1991) Editing of a chloroplast mRNA by creation of an initiation codon. Nature 353:178–180PubMedCrossRefGoogle Scholar

Hoffmann M, Dombrowski S, Guha C, Binder S (1999) Cotranscription of the rpl5-rps14-cob gene cluster in pea mitochondria. Mol Gen Genet 261:537–545PubMedCrossRefGoogle Scholar

Holec S, Lange H, Kühn K, Alioua M, Börner T, Gagliardi D (2006) Relaxed transcription in Arabidopsis mitochondria is counterbalanced by RNA stability control mediated by polyadenylation and polynucleotide phosphorylase. Mol Cell Biol 26:2869–2876PubMedCrossRefGoogle Scholar

Hollingsworth MJ, Johanningmeier U, Karabin GD, Stiegler GL, Hallick RB (1984) Detection of multiple, unspliced precursor mRNA transcripts for the Mr 32,000 thylakoid membrane protein from Euglena gracilis chloroplasts. Nucleic Acids Res 12:2001–2017PubMedCrossRefGoogle Scholar

Howell KA, Millar AH, Whelan J (2006) Ordered assembly of mitochondria during rice germination begins with promitochondrial structures rich in components of the protein import apparatus. Plant Mol Biol 60:201–223PubMedCrossRefGoogle Scholar

Inada M, Sasaki T, Yukawa M, Tsudzuki T, Sugiura M (2004) A systematic search for RNA editing sites in pea chloroplasts: an editing event causes diversification from the evolutionarily conserved amino acid sequence. Plant Cell Physiol 45:1615–1622PubMedCrossRefGoogle Scholar

Isono K, Niwa Y, Satoh K, Kobayashi H (1997a) Evidence for transcriptional regulation of plastid photosynthesis genes in Arabidopsis thaliana roots. Plant Physiol 114:623–630PubMedCrossRefGoogle Scholar

Isono K, Shimizu M, Yoshimoto K, Niwa Y, Satoh K, Yokota A, Kobayashi H (1997b) Leaf-specifically expressed genes for polypeptides destined for chloroplasts with domains of sigma70 factors of bacterial RNA polymerases in Arabidopsis thaliana. Proc Natl Acad Sci USA 94:14948–14953PubMedCrossRefGoogle Scholar

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 9:283–296PubMedGoogle Scholar

Jonietz C, Forner J, Holzle A, Thuss S, Binder S (2010) RNA PROCESSING FACTOR2 is required for 5′ end processing of nad9 and cox3 mRNAs in mitochondria of Arabidopsis thaliana. Plant Cell 22:443–453PubMedCrossRefGoogle Scholar

Kahlau S, Bock R (2008) Plastid transcriptomics and translatomics of tomato fruit development and chloroplast-to-chromoplast differentiation: chromoplast gene expression largely serves the production of a single protein. Plant Cell 20:856–874PubMedCrossRefGoogle Scholar

Kahlau S, Aspinall S, Gray JC, Bock R (2006) Sequence of the tomato chloroplast DNA and evolutionary comparison of solanaceous plastid genomes. J Mol Evol 63:194–207PubMedCrossRefGoogle Scholar

Kanamaru K, Fujiwara M, Seki M, Katagiri T, Nakamura M, Mochizuki N, Nagatani A, Shinozaki K, Tanaka K, Takahashi H (1999) Plastidic RNA polymerase sigma factors in Arabidopsis. Plant Cell Physiol 40:832–842PubMedCrossRefGoogle Scholar

Kanamaru K, Nagashima A, Fujiwara M, Shimada H, Shirano Y, Nakabayashi K, Shibata D, Tanaka K, Takahashi H (2001) An Arabidopsis sigma factor (SIG2)-dependent expression of plastid-encoded tRNAs in chloroplasts. Plant Cell Physiol 42:1034–1043PubMedCrossRefGoogle Scholar

Kaneko T, Sato S, Kotani H, Tanaka A, Asamizu E, Nakamura Y, Miyajima N, Hirosawa M, Sugiura M, Sasamoto S, Kimura T, Hosouchi T, Matsuno A, Muraki A, Nakazaki N, Naruo K, Okumura S, Shimpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Tabata S (1996) Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res 3:109–136PubMedCrossRefGoogle Scholar

Karcher D, Bock R (1998) Site-selective inhibition of plastid RNA editing by heat shock and antibiotics: a role for plastid translation in RNA editing. Nucleic Acids Res 26:1185–1190PubMedCrossRefGoogle Scholar

Karcher D, Bock R (2002a) The amino acid sequence of a plastid protein is developmentally regulated by RNA editing. J Biol Chem 277:5570–5574PubMedCrossRefGoogle Scholar

Karcher D, Bock R (2002b) Temperature sensitivity of RNA editing and intron splicing reactions in the plastid ndhB transcript. Curr Genet 41:48–52PubMedCrossRefGoogle Scholar

Karcher D, Kahlau S, Bock R (2008) Faithful editing of a tomato-specific mRNA editing site in transgenic tobacco chloroplasts. RNA 14:217–224PubMedCrossRefGoogle Scholar

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. J Biol Chem 283:23333–23342PubMedCrossRefGoogle Scholar

Khanam SM, Naydenov NG, Kadowaki K, Nakamura C (2007) Mitochondrial biogenesis as revealed by mitochondrial transcript profiles during germination and early seedling growth in wheat. Genes Genet Syst 82:409–420PubMedCrossRefGoogle Scholar

Kim M, Christopher DA, Mullet JE (1993) Direct evidence for selective modulation of psbA, rpoA, rbcL and 16S RNA stability during barley chloroplast development. Plant Mol Biol 22:447–463PubMedCrossRefGoogle 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 59:738–749PubMedCrossRefGoogle Scholar

Klaff P, Gruissem W (1991) Changes in chloroplast mRNA stability during leaf development. Plant Cell 3:517–529PubMedGoogle Scholar

Klein RR, Mullet JE (1987) Control of gene expression during higher plant chloroplast biogenesis. Protein synthesis and transcript levels of psbA, psaA-psaB, and rbcL in dark-grown and illuminated barley seedlings. J Biol Chem 262:4341–4348PubMedGoogle Scholar

Knoop V (2004) The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective. Curr Genet 46:123–139PubMedCrossRefGoogle Scholar

Knoop V, Schuster W, Wissinger B, Brennicke A (1991) Trans-splicing integrates an exon of 22 nucleotides into the nad5 messenger RNA in higher plant mitochondria. EMBO J 10:3483–3493PubMedGoogle Scholar

Kobayashi Y, Dokiya Y, Sugita M (2001) Dual targeting of phage-type RNA polymerase to both mitochondria and plastids is due to alternative translation initiation in single transcripts. Biochem Biophys Res Commun 289:1106–1113PubMedCrossRefGoogle Scholar

Kode V, Mudd EA, Iamtham S, Day A (2005) The tobacco plastid accD gene is essential and is required for leaf development. Plant J 44:237–244PubMedCrossRefGoogle Scholar

Kotera E, Tasaka M, Shikanai T (2005) A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts. Nature 433:326–330PubMedCrossRefGoogle Scholar

Kozak M (2005) Regulation of translation via mRNA structure in prokaryotes and eukaryotes. Gene 361:13–37PubMedCrossRefGoogle Scholar

Krause K, Maier RM, Kofer W, Krupinska K, Herrmann RG (2000) Disruption of plastid-encoded RNA polymerase genes in tobacco: expression of only a distinct set of genes is not based on selective transcription of the plastid chromosome. Mol Gen Genet 263:1022–1030PubMedCrossRefGoogle Scholar

Krupinska K, Apel K (1989) Light-induced transformation of etioplasts to chloroplasts of barley without transcriptional control of plastid gene expression. Mol Gen Genet 219:467–473CrossRefGoogle Scholar

Kubicki A, Steinmüller K, Westhoff P (1994) Differential transcription of plastome-encoded genes in the mesophyll and bundle-sheath chloroplasts of the monocotyledonous NADP-malic enzyme-type C4 plants maize and sorghum. Plant Mol Biol 25:669–679PubMedCrossRefGoogle Scholar

Kudla J, Hayes R, Gruissem W (1996) Polyadenylation accelerates degradation of chloroplast mRNA. EMBO J 15:7137–7146PubMedGoogle 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 31:2417–2423PubMedCrossRefGoogle Scholar

Kühn K, Weihe A, Börner T (2005) Multiple promoters are a common feature of mitochondrial genes in Arabidopsis. Nucleic Acids Res 33:337–346PubMedCrossRefGoogle Scholar

Kühn K, Bohne AV, Liere K, Weihe A, Börner T (2007) Arabidopsis phage-type RNA polymerases: accurate in vitro transcription of organellar genes. Plant Cell 19:959–971PubMedCrossRefGoogle Scholar

Kühn K, Richter U, Meyer EH, Delannoy E, de Longevialle AF, 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 21:2762–2779PubMedCrossRefGoogle Scholar

Kuntz M, Evrard J-L, d’Harlingue A, Weil JH, Camara B (1989) Expression of plastid and nuclear genes during chromoplast differentiation in bell pepper (Capsicum annuum) and sunflower (Helianthus annuus). Mol Gen Genet 216:156–163CrossRefGoogle Scholar

Kuntz M, Camara B, Weil JH, Schantz R (1992) The psbL gene from bell pepper (Capsicum annuum): plastid RNA editing also occurs in non-photosynthetic chromoplasts. Plant Mol Biol 20:1185–1188PubMedCrossRefGoogle Scholar

Kunzmann A, Brennicke A, Marchfelder A (1998) 5′ end maturation and RNA editing have to precede tRNA 3′ processing in plant mitochondria. Proc Natl Acad Sci USA 95:108–113PubMedCrossRefGoogle Scholar

Kuroda H, Maliga P (2003) The plastid clpP1 protease gene is essential for plant development. Nature 425:86–89PubMedCrossRefGoogle Scholar

Kurth J, Varotto C, Pesaresi P, Biehl A, Richly E, Salamini F, Leister D (2002) Gene-sequence-tag expression analyses of 1,800 genes related to chloroplast functions. Planta 215:101–109PubMedCrossRefGoogle Scholar

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

Legen J, Kemp S, Krause K, Profanter B, Herrmann RG, Maier RM (2002) Comparative analysis of plastid transcription profiles of entire plastid chromosomes from tobacco attributed to wild-type and PEP-deficient transcription machineries. Plant J 31:171–188PubMedCrossRefGoogle Scholar

Leino M, Teixeira R, Landgren M, Glimelius K (2003) Brassica napus lines with rearranged Arabidopsis mitochondria display CMS and a range of developmental aberrations. Theor Appl Genet 106:1156–1163PubMedGoogle Scholar

Leino M, Thyselius S, Landgren M, Glimelius K (2004) Arabidopsis thaliana chromosome III restores fertility in a cytoplasmic male-sterile Brassica napus line with A. thaliana mitochondrial DNA. Theor Appl Genet 109:272–279PubMedCrossRefGoogle Scholar

Leino M, Landgren M, Glimelius K (2005) Alloplasmic effects on mitochondrial transcriptional activity and RNA turnover result in accumulated transcripts of Arabidopsis orfs in cytoplasmic male-sterile Brassica napus. Plant J 42:469–480PubMedCrossRefGoogle Scholar

Lemieux B, Aharoni A, Schena M (1998) Overview of DNA chip technology. Mol Breed 4:277–289CrossRefGoogle 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 USA 90:5509–5513PubMedCrossRefGoogle Scholar

Liere K, Börner T (2007) Transcription and transcriptional regulation in plastids. Top Curr Genet 19:121–174CrossRefGoogle Scholar

Liere K, Link G (1995) RNA-binding activity of the matK protein encoded by the chloroplast trnK intron from mustard (Sinapis alba L.). Nucleic Acids Res 23:917–921PubMedCrossRefGoogle Scholar

Liere K, Maliga P (1999) In vitro characterization of the tobacco rpoB promoter reveals a core sequence motif conserved between phage-type plastid and plant mitochondrial promoters. EMBO J 18:249–257PubMedCrossRefGoogle Scholar

Li-Pook-Than J, Carrillo C, Bonen L (2004) Variation in mitochondrial transcript profiles of protein-coding genes during early germination and seedling development in wheat. Curr Genet 46:374–380PubMedCrossRefGoogle Scholar

Lu B, Hanson MR (1994) A single homogeneous form of ATP6 protein accumulates in petunia mitochondria despite the presence of differentially edited atp6 transcripts. Plant Cell 6:1955–1968PubMedGoogle Scholar

Lupold DS, Caoile AG, Stern DB (1999) Genomic context influences the activity of maize mitochondrial cox2 promoters. Proc Natl Acad Sci USA 96:11670–11675PubMedCrossRefGoogle Scholar

MacLean D, Jerome CA, Brown AP, Gray JC (2008) Co-regulation of nuclear genes encoding plastid ribosomal proteins by light and plastid signals during seedling development in tobacco and Arabidopsis. Plant Mol Biol 66:475–490PubMedCrossRefGoogle Scholar

Magee AM, Kavanagh TA (2002) Plastid genes ­transcribed by the nucleus-encoded plastid RNA polymerase show increased transcript accumulation in transgenic plants expressing a chloroplast-localized phage T7 RNA polymerase. J Exp Bot 53:2341–2349PubMedCrossRefGoogle Scholar

Magee AM, Coyne S, Murphy D, Horvath EM, Medgyesy P, Kavanagh TA (2004) T7 RNA polymerase-directed expression of an antibody fragment transgene in plastids causes a semi-lethal pale-green seedling phenotype. Transgenic Res 13:325–337PubMedCrossRefGoogle Scholar

Magee AM, MacLean D, Gray JC, Kavanagh TA (2007) Disruption of essential plastid gene expression caused by T7 RNA polymerase-mediated transcription of plastid transgenes during early seedling development. Transgenic Res 16:415–428PubMedCrossRefGoogle Scholar

Maier RM, Neckermann K, Igloi GL, Kössel H (1995) Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J Mol Biol 251:614–628PubMedCrossRefGoogle Scholar

Malek O, Lättig K, Hiesel R, Brennicke A, Knoop V (1996) RNA editing in bryophytes and a molecular phylogeny of land plants. EMBO J 15:1403–1411PubMedGoogle Scholar

Marano MR, Carrillo N (1992) Constitutive transcription and stable RNA accumulation in plastids during the conversion of chloroplasts to chromoplasts in ripening tomato fruits. Plant Physiol 100:1103–1113PubMedCrossRefGoogle Scholar

Maréchal-Drouard L, Kumar R, Remacle C, Small I (1996a) RNA editing of larch mitochondrial tRNA(His) precursors is a prerequisite for processing. Nucleic Acids Res 24:3229–3234PubMedCrossRefGoogle Scholar

Maréchal-Drouard L, Cosset A, Remacle C, Ramamonjisoa D, Dietrich A (1996b) A single editing event is a prerequisite for efficient processing of potato mitochondrial phenylalanine tRNA. Mol Cell Biol 16:3504–3510PubMedGoogle Scholar

Mayfield SP, Yohn CB, Cohen A, Danon A (1995) Regulation of chloroplast gene expression. Annu Rev Plant Physiol Plant Mol Biol 46:147–166CrossRefGoogle Scholar

Meng Q, Wang Y, Liu XQ (2005) An intron-encoded protein assists RNA splicing of multiple similar introns of different bacterial genes. J Biol Chem 280:35085–35088PubMedCrossRefGoogle Scholar

Mereschkowsky C (1905) Ueber Natur und Ursprung der Chromatophoren im Pflanzenreiche. Biol Centralbl 25:593–604Google Scholar

Meyers BC, Galbraith DW, Nelson T, Agrawal V (2004) Methods for transcriptional profiling in plants. Be fruitful and replicate. Plant Physiol 135:637–652PubMedCrossRefGoogle Scholar

Miller ME, Jurgenson JE, Reardon EM, Price CA (1983) Plastid translation in organello and in vitro during light-induced development in Euglena. J Biol Chem 258:14478–14484PubMedGoogle Scholar

Minoda A, Nagasawa K, Hanaoka M, Horiuchi M, Takahashi H, Tanaka K (2005) Microarray profiling of plastid gene expression in a unicellular red alga, Cyanidioschyzon merolae. Plant Mol Biol 59:375–385PubMedCrossRefGoogle Scholar

Miyata Y, Sugita M (2004) Tissue- and stage-specific RNA editing of rps14 transcripts in moss (Physcomitrella patens) chloroplasts. J Plant Physiol 161:113–115PubMedCrossRefGoogle Scholar

Mohr G, Lambowitz AM (2003) Putative proteins related to group II intron reverse transcriptase/maturases are encoded by nuclear genes in higher plants. Nucleic Acids Res 31:647–652PubMedCrossRefGoogle Scholar

Mower J, Palmer J (2006) Patterns of partial RNA editing in mitochondrial genes of Beta vulgaris. Mol Genet Genomics 276:285–293PubMedCrossRefGoogle Scholar

Muise RC, Hauswirth WW (1992) Transcription in maize mitochondria: effects of tissue and mitochondrial genotype. Curr Genet 22:235–242PubMedCrossRefGoogle Scholar

Mullet JE (1993) Dynamic regulation of chloroplast transcription. Plant Physiol 103:309–313PubMedCrossRefGoogle Scholar

Nagashima A, Hanaoka M, Motohashi R, Seki M, Shinozaki K, Kanamaru K, Takahashi H, Tanaka K (2004) DNA microarray analysis of plastid gene expression in an Arabidopsis mutant deficient in a plastid transcription factor sigma, SIG2. Biosci Biotechnol Biochem 68:694–704PubMedCrossRefGoogle Scholar

Nakagawa N, Sakurai N (2006) A mutation in At-nMat1a, which encodes a nuclear gene having high similarity to group II intron maturase, causes impaired splicing of mitochondrial NAD4 transcript and altered carbon metabolism in Arabidopsis thaliana. Plant Cell Physiol 47:772–783PubMedCrossRefGoogle Scholar

Nakamura T, Furuhashi Y, Hasegawa K, Hashimoto H, Watanabe K, Obokata J, Sugita M, Sugiura M (2003) Array-based analysis on tobacco plastid transcripts: preparation of a genomic microarray containing all genes and all intergenic regions. Plant Cell Physiol 44:861–867PubMedCrossRefGoogle Scholar

Nakamura T, Sugiura C, Kobayashi Y, Sugita M (2005) Transcript profiling in plastid arginine tRNA-CCG gene knockout moss: construction of Physcomitrella patens plastid DNA microarray. Plant Biol 7:258–265PubMedCrossRefGoogle Scholar

Naydenov NG, Khanam SM, Atanassov A, Nakamura C (2008) Expression profiles of respiratory components associated with mitochondrial biogenesis during germination and seedling growth under normal and restricted conditions in wheat. Genes Genet Syst 83:31–41PubMedCrossRefGoogle Scholar

Naydenov NG, Khanam S, Siniauskaya M, Nakamura C (2010) Profiling of mitochondrial transcriptome in germinating wheat embryos and seedlings subjected to cold, salinity and osmotic stresses. Genes Genet Syst 85:31–42PubMedCrossRefGoogle Scholar

Neckermann K, Zeltz P, Igloi GL, Kössel H, Maier RM (1994) The role of RNA editing in conservation of start codons in chloroplast genomes. Gene 146:177–182PubMedCrossRefGoogle 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 268:434–445PubMedCrossRefGoogle Scholar

Obukosia SD, Richards CM, Boyer CD (2003) Expression of plastid-encoded photosynthetic genes during chloroplast or chromoplast differentiation in Cucurbitae pepo L. fruits. Phytochemistry 64:1213–1221PubMedCrossRefGoogle Scholar

Ohyama K, Fukuzawa H, Kohchi T, Shirai H, Sano T, Sano S, Umesono K, Shiki Y, Takeuchi M, Chang Z, Aota S, Inokuchi H, Ozeki H (1986) Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature 322:572–574CrossRefGoogle Scholar

Okada S, Brennicke A (2006) Transcript levels in plant mitochondria show a tight homeostasis during day and night. Mol Genet Genomics 276:71–78PubMedCrossRefGoogle Scholar

Okuda K, Nakamura T, Sugita M, Shimizu T, Shikanai T (2006) A pentatricopeptide repeat protein is a site recognition factor in chloroplast RNA editing. J Biol Chem 281:37661–37667PubMedCrossRefGoogle Scholar

Okuda K, Myouga F, Motohashi R, Shinozaki K, Shikanai T (2007) Conserved domain structure of pentatricopeptide repeat proteins involved in chloroplast RNA editing. Proc Natl Acad Sci USA 104:8178–8183PubMedCrossRefGoogle Scholar

Peeters NM, Hanson MR (2002) Transcript abundance supercedes editing efficiency as a factor in developmental variation of chloroplast gene expression. RNA 8:497–511PubMedCrossRefGoogle Scholar

Peled-Zehavi H, Danon A (2007) Translation and translational regulation in chloroplasts. Top Curr Genet 19:249–281CrossRefGoogle Scholar

Perrin R, Lange H, Grienenberger JM, Gagliardi D (2004a) AtmtPNPase is required for multiple aspects of the 18S rRNA metabolism in Arabidopsis thaliana mitochondria. Nucleic Acids Res 32:5174–5182PubMedCrossRefGoogle Scholar

Perrin R, Meyer EH, Zaepfel M, Kim YJ, Mache R, Grienenberger JM, Gualberto JM, Gagliardi D (2004b) Two exoribonucleases act sequentially to process mature 3′-ends of atp9 mRNAs in Arabidopsis mitochondria. J Biol Chem 279:25440–25446PubMedCrossRefGoogle Scholar

Pfalz J, Bayraktar OA, Prikryl J, Barkan A (2009) Site-specific binding of a PPR protein defines and stabilizes 5′ and 3′ mRNA termini in chloroplasts. EMBO J 28:2042–2052PubMedCrossRefGoogle Scholar

Phreaner CG, Williams MA, Mulligan RM (1996) Incomplete editing of rps12 transcripts results in the synthesis of polymorphic polypeptides in plant mitochondria. Plant Cell 8:107–117PubMedGoogle Scholar

Piechulla B, Imlay KRC, Gruissem W (1985) Plastid gene expression during fruit ripening in tomato (Lycopersicon esculentum). Plant Mol Biol 5:373–384CrossRefGoogle Scholar

Pring DR, Mullen JA, Kempken F (1992) Conserved sequence blocks 5′ to start codons of plant mitochondrial genes. Plant Mol Biol 19:313–317PubMedCrossRefGoogle Scholar

Pyke KA (2007) Plastid biogenesis and differentiation. Top Curr Genet 19:1–28CrossRefGoogle 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 580:5641–5646PubMedCrossRefGoogle Scholar

Rawson JR, Boerma CL (1976) A measurement of the fraction of chloroplast DNA transcribed during chloroplast development in Euglena gracilis. Biochemistry 15:588–592PubMedCrossRefGoogle Scholar

Remacle C, Maréchal-Drouard L (1996) Charac­terization of the potato mitochondrial transcription unit containing ‘native’ trnS (GCU), trnF (GAA) and trnP (UGG). Plant Mol Biol 30:553–563PubMedCrossRefGoogle Scholar

Ribas-Carbo M, Taylor NL, Giles L, Busquets S, Finnegan PM, Day DA, Lambers H, Medrano H, Berry JA, Flexas J (2005) Effects of water stress on respiration in soybean leaves. Plant Physiol 139:466–473PubMedCrossRefGoogle Scholar

Richly E, Dietzmann A, Biehl A, Kurth J, Laloi C, Apel K, Salamini F, Leister D (2003) Covariations in the nuclear chloroplast transcriptome reveal a regulatory master-switch. EMBO Rep 4:491–498PubMedCrossRefGoogle Scholar

Rüdinger M, Funk HT, Rensing SA, Maier UG, Knoop V (2009) RNA editing: only eleven sites are present in the Physcomitrella patens mitochondrial transcriptome and a universal nomenclature proposal. Mol Genet Genomics 281:473–481PubMedCrossRefGoogle Scholar

Ruf S, Kössel H (1997) Tissue-specific and differential editing of the two ycf3 editing sites in maize plastids. Curr Genet 32:19–23PubMedCrossRefGoogle Scholar

Sakai A, Kawano S, Kuroiwa T (1992) Conversion of proplastids to amyloplasts in tobacco cultured cells is accompanied by changes in the transcriptional activities of plastid genes. Plant Physiol 100:1062–1066PubMedCrossRefGoogle Scholar

Saldanha R, Mohr G, Belfort M, Lambowitz AM (1993) Group I and group II introns. FASEB J 7:15–24PubMedGoogle Scholar

Salinas T, Duchêne AM, Maréchal-Drouard L (2008) Recent advances in tRNA mitochondrial import. Trends Biochem Sci 33:320–329PubMedCrossRefGoogle Scholar

Schmitz-Linneweber C, Barkan A (2007) RNA splicing and RNA editing in chloroplasts. Top Curr Genet 19:213–248CrossRefGoogle Scholar

Schmitz-Linneweber C, Regel R, Du TG, Hupfer H, Herrmann RG, Maier RM (2002) The plastid chromosome of Atropa belladonna and its comparison with that of Nicotiana tabacum: the role of RNA editing in generating divergence in the process of plant speciation. Mol Biol Evol 19:1602–1612PubMedCrossRefGoogle Scholar

Schmitz-Linneweber C, Williams-Carrier R, Barkan A (2005) RNA Immunoprecipitation and microarray analysis show a chloroplast pentatricopeptide repeat protein to be associated with the 5′ region of mRNAs whose translation it activates. Plant Cell 17:2791–2804PubMedCrossRefGoogle Scholar

Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115PubMedCrossRefGoogle Scholar

Schulze A, Downward J (2001) Navigating gene expression using microarrays-a technology review. Nat Cell Biol 3:E190–E195PubMedCrossRefGoogle Scholar

Schuster W (1993) Ribosomal protein gene rpl5 is cotranscribed with the nad3 gene in Oenothera mitochondria. Mol Gen Genet 240:445–449PubMedGoogle Scholar

Schweer J, Loschelder H, Link G (2006) A promoter switch that can rescue a plant sigma factor mutant. FEBS Lett 580:6617–6622PubMedCrossRefGoogle Scholar

Serino G, Maliga P (1998) RNA polymerase subunits encoded by the plastid rpo genes are not shared with the nucleus-encoded plastid enzyme. Plant Physiol 117:1165–1170PubMedCrossRefGoogle Scholar

Shiina T, Tsunoyama Y, Nakahira Y, Khan MS (2005) Plastid RNA polymerases, promoters, and transcription regulators in higher plants. In: Jeon KW (ed) International review of cytology, vol 244. Academic, Amsterdam, pp 1–68Google Scholar

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

Shikanai T, Shimizu K, Ueda K, Nishimura Y, Kuroiwa T, Hashimoto T (2001) The chloroplast clpP gene, encoding a proteolytic subunit of ATP-dependent protease, is indispensable for chloroplast development in tobacco. Plant Cell Physiol 42:264–273PubMedCrossRefGoogle Scholar

Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, Matsubayashi T, Zaita N, Chunwongse J, Obokata J, Yamaguchi-Shinozaki K, Ohto C, Torazawa K, Meng BY, Sugita M, Deno H, Kamogashira T, Yamada K, Kusuda J, Takaiwa F, Kato A, Tohdoh N, Shimida H, Sugiura M (1986) The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J 5:2043–2049PubMedGoogle Scholar

Siddique MA, Grossmann J, Gruissem W, Baginsky S (2006) Proteome analysis of bell pepper (Capsicum annuum L.) chromoplasts. Plant Cell Physiol 47:1663–1673PubMedCrossRefGoogle Scholar

Silhavy D, Maliga P (1998) Mapping of promoters for the nucleus-encoded plastid RNA polymerase (NEP) in the iojap maize mutant. Curr Genet 33:340–344PubMedCrossRefGoogle Scholar

Siniauskaya M, Naydenov N, Davydenko O, Nakamura C (2008) Macroarray for studying chloroplast gene expression profiles associated with the initial development of wheat. In: Proceedings of the 11th International Wheat Genetics Symposium, Sidney University Press, SidneyGoogle Scholar

Small ID, Peeters N (2000) The PPR motif – a TPR-related motif prevalent in plant organellar proteins. Trends Biochem Sci 25:46–47PubMedCrossRefGoogle Scholar

Stears RL, Martinsky T, Schena M (2003) Trends in microarray analysis. Nat Med 9:140–145PubMedCrossRefGoogle Scholar

Stern DB, Kindle KL (1993) 3′end maturation of the Chlamydomonas reinhardtii chloroplast atpB mRNA is a two-step process. Mol Cell Biol 13:2277–2285PubMedGoogle Scholar

Stern DB, Goldschmidt-Clermont M, Hanson MR (2010) Chloroplast RNA metabolism. Annu Rev Plant Biol 61:125–155PubMedCrossRefGoogle Scholar

Sugiura M, Hirose T, Sugita M (1998) Evolution and mechanism of translation in chloroplasts. Annu Rev Genet 32:437–459PubMedCrossRefGoogle Scholar

Svensson AS, Rasmusson AG (2001) Light-dependent gene expression for proteins in the respiratory chain of potato leaves. Plant J 28:73–82PubMedCrossRefGoogle Scholar

Takenaka M, Verbitskiy D, van der Merwe JA, Zehrmann A, Brennicke A (2008) The process of RNA editing in plant mitochondria. Mitochondrion 8:35–46PubMedCrossRefGoogle Scholar

Tanaka K, Tozawa Y, Mochizuki N, Shinozaki K, Nagatani A, Wakasa K, Takahashi H (1997) Characterization of three cDNA species encoding plastid RNA polymerase sigma factors in Arabidopsis thaliana: evidence for the sigma factor heterogeneity in higher plant plastids. FEBS Lett 413:309–313PubMedCrossRefGoogle Scholar

Tasaki E, Hattori M, Sugita M (2010) The moss pentatricopeptide repeat protein with a DYW domain is responsible for RNA editing of mitochondrial ccmFc transcript. Plant J 62:560–570PubMedCrossRefGoogle Scholar

Tavares-Carreón F, Camacho-Villasana Y, Zamudio-Ochoa A, Shingú-Vázquez M, Torres-Larios A, Pérez-Martínez X (2008) The pentatricopeptide repeats present in Pet309 are necessary for translation but not for stability of the mitochondrial cox1 mRNA in yeast. J Biol Chem 283:1472–1479PubMedCrossRefGoogle Scholar

Tillich M, Funk HT, Schmitz-Linneweber C, Poltnigg P, Sabater B, Martin M, Maier RM (2005) Editing of plastid RNA in Arabidopsis thaliana ecotypes. Plant J 43:708–715PubMedCrossRefGoogle Scholar

Tillich M, Lehwark P, Morton BR, Maier UG (2006) The evolution of chloroplast RNA editing. Mol Biol Evol 23:1912–1921PubMedCrossRefGoogle Scholar

Tracy RL, Stern DB (1995) Mitochondrial transcription initiation: promoter structures and RNA polymerases. Curr Genet 28:205–216PubMedCrossRefGoogle Scholar

Tsudzuki T, Wakasugi T, Sugiura M (2001) Comparative analysis of RNA editing sites in higher plant chloroplasts. J Mol Evol 53:327–332PubMedCrossRefGoogle 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 15:57–61PubMedCrossRefGoogle Scholar

Uyttewaal M, Mireau H, Rurek M, Hammani K, Arnal N, Quadrado M, Giegé P (2008) PPR336 is associated with polysomes in plant mitochondria. J Mol Biol 375:626–636PubMedCrossRefGoogle Scholar

Valkov VT, Scotti N, Kahlau S, Maclean D, Grillo S, Gray JC, Bock R, Cardi T (2009) Genome-wide analysis of plastid gene expression in potato leaf chloroplasts and tuber amyloplasts: transcriptional and posttranscriptional control. Plant Physiol 150:2030–2044PubMedCrossRefGoogle Scholar

Vaughn JC, Mason MT, Sper-Whitis GL, Kuhlman P, Palmer JD (1995) Fungal origin by horizontal transfer of a plant mitochondrial group I intron in the chimeric coxI gene of Peperomia. J Mol Evol 41:563–572PubMedCrossRefGoogle Scholar

Verbitskiy D, Zehrmann A, Brennicke A, Takenaka M (2010) A truncated MEF11 protein shows site-specific effects on mitochondrial RNA editing. Plant Signal Behav 5:558–560Google Scholar

Vogel A, Schilling O, Späth B, Marchfelder A (2005) The tRNase Z family of proteins: physiological functions, substrate specificity and structural properties. Biol Chem 386:1253–1264PubMedGoogle Scholar

Wakasugi T, Hirose T, Horihata M, Tsudzuki T, Kössel H, Sugiura M (1996) Creation of a novel protein-coding region at the RNA level in black pine chloroplasts: the pattern of RNA editing in the gymnosperm chloroplast is different from that in angiosperms. Proc Natl Acad Sci USA 93:8766–8770PubMedCrossRefGoogle Scholar

Wang L, Li P, Brutnell TP (2010) Exploring plant transcriptomes using ultra high-throughput sequencing. Brief Funct Genomics 9:118–128PubMedCrossRefGoogle Scholar

Wank H, SanFilippo J, Singh RN, Matsuura M, Lambowitz AM (1999) A reverse transcriptase/maturase promotes splicing by binding at its own coding segment in a group II intron RNA. Mol Cell 4:239–250PubMedCrossRefGoogle Scholar

Weber AP, Weber KL, Carr K, Wilkerson C, Ohlrogge JB (2007) Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiol 144:32–42PubMedCrossRefGoogle Scholar

Welchen E, Gonzalez DH (2006) Overrepresentation of elements recognized by TCP-domain transcription factors in the upstream regions of nuclear genes encoding components of the mitochondrial oxidative phosphorylation machinery. Plant Physiol 141:540–545PubMedCrossRefGoogle Scholar

Wissinger B, Schuster W, Brennicke A (1991) Trans splicing in Oenothera mitochondria: nad1 mRNAs are edited in exon and trans-splicing group-II intron sequences. Cell 65:473–482PubMedCrossRefGoogle Scholar

Wolf PG, Rowe CA, Hasebe M (2004) High levels of RNA editing in a vascular plant chloroplast genome: analysis of transcripts from the fern Adiantum capillus-veneris. Gene 339:89–97PubMedCrossRefGoogle Scholar

Wood CK, Dudley P, Albury MS, Affourtit C, Leach GR, Pratt JR, Whitehouse DG, Moore AL (1996) Developmental regulation of respiratory activity and protein import in plant mitochondria. Biochem Soc Trans 24:746–749PubMedGoogle Scholar

Yamaguchi K, Subramanian AR (2000) The plastid ribosomal proteins. Identification of all the proteins in the 50 S subunit of an organelle ribosome (chloroplast). J Biol Chem 275:28466–28482PubMedCrossRefGoogle Scholar

Yamaguchi K, Subramanian AR (2003) Proteomic identification of all plastid-specific ribosomal proteins in higher plant chloroplast 30S ribosomal subunit. Eur J Biochem 270:190–205PubMedCrossRefGoogle Scholar

Yamaguchi K, von Knoblauch K, Subramanian AR (2000) The plastid ribosomal proteins. Identification of all the proteins in the 30 S subunit of an organelle ribosome (chloroplast). J Biol Chem 275:28455–28465PubMedCrossRefGoogle Scholar

Yamaguchi K, Prieto S, Beligni MV, Haynes PA, McDonald WH, Yates JR 3rd, Mayfield SP (2002) Proteomic characterization of the small subunit of Chlamydomonas reinhardtii chloroplast ribosome: identification of a novel S1 domain-containing protein and unusually large orthologs of bacterial S2, S3, and S5. Plant Cell 14:2957–2974PubMedCrossRefGoogle Scholar

Yamaguchi K, Beligni MV, Prieto S, Haynes PA, McDonald WH, Yates JR 3rd, Mayfield SP (2003) Proteomic characterization of the Chlamydomonas reinhardtii chloroplast ribosome. Identification of proteins unique to the 70S ribosome. J Biol Chem 278:33774–33785PubMedCrossRefGoogle Scholar

Yukawa M, Tsudzuki T, Sugiura M (2005) The 2005 version of the chloroplast DNA sequence from tobacco (Nicotiana tabacum). Plant Mol Biol Rep 23:359–365CrossRefGoogle Scholar

Zandueta-Criado A, Bock R (2004) Surprising features of plastid ndhD transcripts: addition of non-encoded nucleotides and polysome association of mRNAs with an unedited start codon. Nucleic Acids Res 32:542–550PubMedCrossRefGoogle Scholar

Zehrmann A, van der Merwe JA, Verbitskiy D, Brennicke A, Takenaka M (2008) Seven large variations in the extent of RNA editing in plant mitochondria between three ecotypes of Arabidopsis thaliana. Mitochondrion 8:319–327PubMedCrossRefGoogle 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 21:558–567PubMedCrossRefGoogle Scholar

Zerges W (2000) Translation in chloroplasts. Biochimie 82:583–601PubMedCrossRefGoogle Scholar

Zybailov B, Friso G, Kim J, Rudella A, Rodriguez VR, Asakura Y, Sun Q, van Wijk KJ (2009) Large scale comparative proteomics of a chloroplast Clp protease mutant reveals folding stress, altered protein homeostasis, and feedback regulation of metabolism. Mol Cell Proteomics 8:1789–1810PubMedCrossRefGoogle Scholar