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  • Alonso, J.M., Stepanova, A.N., Leisse, T.J. et al. (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science, 301, 653657.
  • Arsova, B., Hoja, U., Wimmelbacher, M., Greiner, E., Ustun, S., Melzer, M., Petersen, K., Lein, W. and Bornke, F. (2010) Plastidial thioredoxin z interacts with two fructokinase-like proteins in a thiol-dependent manner: evidence for an essential role in chloroplast development in Arabidopsis and Nicotiana benthamiana. Plant Cell, 22, 14981515.
  • Barbrook, A.C., Howe, C.J. and Purton, S. (2006) Why are plastid genomes retained in non-photosynthetic organisms? Trends Plant Sci. 11, 101108.
  • Beator, J. and Kloppstech, K. (1993) The circadian oscillator coordinates the synthesis of apoproteins and their pigments during chloroplast development. Plant Physiol. 103, 191196.
  • Chi, W., Mao, J., Li, Q., Ji, D., Zou, M., Lu, C. and Zhang, L. (2010) Interaction of the pentatricopeptide-repeat protein DELAYED GREENING 1 with sigma factor SIG6 in the regulation of chloroplast gene expression in Arabidopsis cotyledons. Plant J. 64, 1425.
  • Chory, J., Nagpal, P. and Peto, C.A. (1991) Phenotypic and genetic analysis of det2, a new mutant that affects light-regulated seedling development in Arabidopsis. Plant Cell, 3, 445459.
  • Coll, N.S., Danon, A., Meurer, J., Cho, W.K. and Apel, K. (2009) Characterization of soldat8, a suppressor of singlet oxygen-induced cell death in Arabidopsis seedlings. Plant Cell Physiol. 50, 707718.
  • Conradt, B. (2009) Genetic control of programmed cell death during animal development. Annu. Rev. Genet. 43, 493523.
  • Czarnecki, O., Hedtke, B., Melzer, M., Rothbart, M., Richter, A., Schroter, Y., Pfannschmidt, T. and Grimm, B. (2011) An Arabidopsis GluTR binding protein mediates spatial separation of 5-aminolevulinic acid synthesis in chloroplasts. Plant Cell, 23, 44764491.
  • Delannoy, E., Stanley, W.A., Bond, C.S. and Small, I.D. (2007) Pentatricopeptide repeat (PPR) proteins as sequence-specificity factors in post-transcriptional processes in organelles. Biochem. Soc. Trans. 35, 16431647.
  • Demarsy, E., Courtois, F., Azevedo, J., Buhot, L. and Lerbs-Mache, S. (2006) Building up of the plastid transcriptional machinery during germination and early plant development. Plant Physiol. 142, 9931003.
  • Estavillo, G.M., Crisp, P.A., Pornsiriwong, W. et al. (2011) Evidence for a SAL1-PAP chloroplast retrograde pathway that functions in drought and high light signaling in Arabidopsis. Plant Cell, 23, 39924012.
  • Favory, J.J., Kobayshi, M., Tanaka, K., Peltier, G., Kreis, M., Valay, J.G. and Lerbs-Mache, S. (2005) Specific function of a plastid sigma factor for ndhF gene transcription. Nucleic Acids Res. 33, 59915999.
  • Fernandez, A.P. and Strand, A. (2008) Retrograde signaling and plant stress: plastid signals initiate cellular stress responses. Curr. Opin. Plant Biol. 11, 509513.
  • Gray, J.C., Sullivan, J.A., Wang, J.H., Jerome, C.A. and MacLean, D. (2003) Coordination of plastid and nuclear gene expression. Philos. Trans. R. Soc. Lond. B Biol. Sci. 358, 135145.
  • Hanaoka, M., Kanamaru, K., Takahashi, H. and Tanaka, K. (2003) Molecular genetic analysis of chloroplast gene promoters dependent on SIG2, a nucleus-encoded sigma factor for the plastid-encoded RNA polymerase, in Arabidopsis thaliana. Nucleic Acids Res. 31, 70907098.
  • Harel, E. and Klein, S. (1972) Light dependent formation of -aminolevulinic acid in etiolated leaves of higher plants. Biochem. Biophys. Res. Commun. 49, 364370.
  • Hendry, G. and Price, A.H. (1993) Stress indicators: chlorophylls and carotenoids. In: Methods in Comparative Plant Ecology – A Laboratory Manual (Hendry, G. and Grime, J.P. (eds)). London: Chapman and Hall, pp. 148152.
  • Ishizaki, Y., Tsunoyama, Y., Hatano, K., Ando, K., Kato, K., Shinmyo, A., Kobori, M., Takeba, G., Nakahira, Y. and Shiina, T. (2005) A nuclear-encoded sigma factor, Arabidopsis SIG6, recognizes sigma-70 type chloroplast promoters and regulates early chloroplast development in cotyledons. Plant J. 42, 133144.
  • Kanamaru, K., Nagashima, A., Fujiwara, M., Shimada, H., Shirano, Y., Nakabayashi, K., Shibata, D., Tanaka, K. and Takahashi, H. (2001) An Arabidopsis sigma factor (SIG2)-dependent expression of plastid-encoded tRNAs in chloroplasts. Plant Cell Physiol. 42, 10341043.
  • Kindgren, P., Kremnev, D., Blanco, N.E., de Dios Barajas Lopez, J., Fernandez, A.P., Tellgren-Roth, C., Small, I. and Strand, A. (2012) The plastid redox insensitive 2 mutant of Arabidopsis is impaired in PEP activity and high light-dependent plastid redox signalling to the nucleus. Plant J. 70, 279291.
  • Kobayashi, Y., Kanesaki, Y., Tanaka, A., Kuroiwa, H., Kuroiwa, T. and Tanaka, K. (2009) Tetrapyrrole signal as a cell-cycle coordinator from organelle to nuclear DNA replication in plant cells. Proc. Natl Acad. Sci. USA, 106, 803807.
  • Kohrer, C. and Rajbhandary, U.L. (2008) The many applications of acid urea polyacrylamide gel electrophoresis to studies of tRNAs and aminoacyl-tRNA synthetases. Methods, 44, 129138.
  • Koussevitzky, S., Nott, A., Mockler, T.C., Hong, F., Sachetto-Martins, G., Surpin, M., Lim, J., Mittler, R. and Chory, J. (2007) Signals from chloroplasts converge to regulate nuclear gene expression. Science, 316, 715719.
  • Lai, Z., Li, Y., Wang, F., Cheng, Y., Fan, B., Yu, J.Q. and Chen, Z. (2011) Arabid-opsis sigma factor binding proteins are activators of the WRKY33 transcription factor in plant defense. Plant Cell. 23, 38243841.
  • Laloi, C., Przybyla, D. and Apel, K. (2006) A genetic approach towards elucidating the biological activity of different reactive oxygen species in Arabidopsis thaliana. J. Exp. Bot. 57, 17191724.
  • Langmead, B., Schatz, M.C., Lin, J., Pop, M. and Salzberg, S.L. (2009) Searching for SNPs with cloud computing. Genome Biol. 10, R134.
  • Larkin, R.M., Alonso, J.M., Ecker, J.R. and Chory, J. (2003) GUN4, a regulator of chlorophyll synthesis and intracellular signaling. Science, 299, 902906.
  • Liu, Z. and Butow, R.A. (2006) Mitochondrial retrograde signaling. Annu. Rev. Genet. 40, 159185.
  • Loschelder, H., Schweer, J., Link, B. and Link, G. (2006) Dual temporal role of plastid sigma factor 6 in Arabidopsis development. Plant Physiol. 142, 642650.
  • Lukens, J.H., Mathews, D.E. and Durbin, R.D. (1987) Effect of tagetitoxin on the levels of ribulose 1,5-bisphosphate carboxylase, ribosomes, and RNA in plastids of wheat leaves. Plant Physiol. 84, 808813.
  • Lysenko, E.A. (2007) Plant sigma factors and their role in plastid transcription. Plant Cell Rep. 26, 845859.
  • Martin, W., Rujan, T., Richly, E., Hansen, A., Cornelsen, S., Lins, T., Leister, D., Stoebe, B., Hasegawa, M. and Penny, D. (2002) Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc. Natl Acad. Sci. USA, 99, 1224612251.
  • Masuda, T. and Takahashi, S. (2006) Chemiluminescent-based method for heme determination by reconstitution with horseradish peroxidase apo-enzyme. Anal. Biochem. 355, 307309.
  • Mochizuki, N., Brusslan, J.A., Larkin, R., Nagatani, A. and 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. USA, 98, 20532058.
  • Mochizuki, N., Tanaka, R., Tanaka, A., Masuda, T. and Nagatani, A. (2008) The steady-state level of Mg-protoporphyrin IX is not a determinant of plastid-to-nucleus signaling in Arabidopsis. Proc. Natl Acad. Sci. USA, 105, 1518415189.
  • Nagashima, A., Hanaoka, M., Motohashi, R., Seki, M., Shinozaki, K., Kanamaru, K., Takahashi, H. and Tanaka, K. (2004a) DNA microarray analysis of plastid gene expression in an Arabidopsis mutant deficient in a plastid transcription factor sigma, SIG2. Biosci. Biotechnol. Biochem. 68, 694704.
  • Nagashima, A., Hanaoka, M., Shikanai, T., Fujiwara, M., Kanamaru, K., Takahashi, H. and Tanaka, K. (2004b) The multiple-stress responsive plastid sigma factor, SIG5, directs activation of the psbD blue light-responsive promoter (BLRP) in Arabidopsis thaliana. Plant Cell Physiol. 45, 357368.
  • Nott, A., Jung, H.S., Koussevitzky, S. and Chory, J. (2006) Plastid-to-nucleus retrograde signaling. Annu. Rev. Plant Biol. 57, 739759.
  • Pfannschmidt, T. (2010) Plastidial retrograde signalling–a true “plastid factor” or just metabolite signatures? Trends Plant Sci. 15, 427435.
  • Pfannschmidt, T. and Link, G. (1997) The A and B forms of plastid DNA-dependent RNA polymerase from mustard (Sinapis alba L.) transcribe the same genes in a different developmental context. Mol. Gen. Genet. 257, 3544.
  • Pfannschmidt, T., Schutze, K., Fey, V., Sherameti, I. and Oelmuller, R. (2003) Chloroplast redox control of nuclear gene expression – a new class of plastid signals in interorganellar communication. Antioxid. Redox Signal. 5, 95101.
  • Pogson, B.J., Woo, N.S., Forster, B. and Small, I.D. (2008) Plastid signalling to the nucleus and beyond. Trends Plant Sci. 13, 602609.
  • Privat, I., Hakimi, M.A., Buhot, L., Favory, J.J. and Mache-Lerbs, S. (2003) Characterization of Arabidopsis plastid sigma-like transcription factors SIG1, SIG2 and SIG3. Plant Mol. Biol. 51, 385399.
  • Rapp, J.C. and Mullet, J.E. (1991) Chloroplast transcription is required to express the nuclear genes rbcS and cab. Plastid DNA copy number is regulated independently. Plant Mol. Biol. 17, 813823.
  • Ruckle, M.E., DeMarco, S.M. and Larkin, R.M. (2007) Plastid signals remodel light signaling networks and are essential for efficient chloroplast biogenesis in Arabidopsis. Plant Cell, 19, 39443960.
  • Saini, G., Meskauskiene, R., Pijacka, W., Roszak, P., Sjogren, L.L., Clarke, A.K., Straus, M. and Apel, K. (2011) ‘Happy on norflurazon’ (hon) mutations implicate perturbance of plastid homeostasis with activating stress acclimatization and changing nuclear gene expression in norflurazon-treated seedlings. Plant J. 65, 690702.
  • Schmitz-Linneweber, C. and Small, I. (2008) Pentatricopeptide repeat proteins: a socket set for organelle gene expression. Trends Plant Sci. 13, 663670.
  • Schon, A., Krupp, G., Gough, S., Berry-Lowe, S., Kannangara, C.G. and Soll, D. (1986) The RNA required in the first step of chlorophyll biosynthesis is a chloroplast glutamate tRNA. Nature, 322, 281284.
  • Schweer, J., Turkeri, H., Kolpack, A. and Link, G. (2010) Role and regulation of plastid sigma factors and their functional interactors during chloroplast transcription – recent lessons from Arabidopsis thaliana. Eur. J. Cell Biol. 89, 940946.
  • Shimizu, M., Kato, H., Ogawa, T., Kurachi, A., Nakagawa, Y. and Kobayashi, H. (2010) Sigma factor phosphorylation in the photosynthetic control of photosystem stoichiometry. Proc. Natl Acad. Sci. USA, 107, 1076010764.
  • Shin, J., Kim, K., Kang, H., Zulfugarov, I.S., Bae, G., Lee, C.H., Lee, D. and Choi, G. (2009) Phytochromes promote seedling light responses by inhibiting four negatively-acting phytochrome-interacting factors. Proc. Natl Acad. Sci. USA, 106, 76607665.
  • Shirano, Y., Shimada, H., Kanamaru, K. et al. (2000) Chloroplast development in Arabidopsis thaliana requires the nuclear-encoded transcription factor sigma B. FEBS Lett. 485, 178182.
  • Su, T.T. (2006) Cellular responses to DNA damage: one signal, multiple choices. Annu. Rev. Genet. 40, 187208.
  • Susek, R.E., Ausubel, F.M. and Chory, J. (1993) Signal transduction mutants of Arabidopsis uncouple nuclear CAB and RBCS gene expression from chloroplast development. Cell, 74, 787799.
  • Trapnell, C., Pachter, L. and Salzberg, S.L. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 11051111.
  • Trapnell, C., Williams, B.A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M.J., Salzberg, S.L., Wold, B.J. and Pachter, L. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511515.
  • Turkeri, H., Schweer, J. and Link, G. (2012) Phylogenetic and functional features of the plastid transcription kinase cpCK2 from Arabidopsis signify a role of cysteinyl SH-groups in regulatory phosphorylation of plastid sigma factors. FEBS J. 279, 395409.
  • Vasileuskaya, Z., Oster, U. and Beck, C.F. (2005) Mg-protoporphyrin IX and heme control HEMA, the gene encoding the first specific step of tetrapyrrole biosynthesis, in Chlamydomonas reinhardtii. Eukaryot. Cell, 4, 16201628.
  • Vinti, G., Hills, A., Campbell, S., Bowyer, J.R., Mochizuki, N., Chory, J. and Lopez-Juez, E. (2000) Interactions between hy1 and gun mutants of Arabidopsis, and their implications for plastid/nuclear signalling. Plant J. 24, 883894.
  • Wagner, D., Przybyla, D., Op den Camp, R. et al. (2004) The genetic basis of singlet oxygen-induced stress responses of Arabidopsis thaliana. Science, 306, 11831185.
  • Woodson, J.D. and Chory, J. (2008) Coordination of gene expression between organellar and nuclear genomes. Nat. Rev. Genet. 9, 383395.
  • Woodson, J.D., Perez-Ruiz, J.M. and Chory, J. (2011) Heme synthesis by plastid ferrochelatase I regulates nuclear gene expression in plants. Curr. Biol. 21, 897903.
  • Yin, L., Wu, N., Curtin, J.C. et al. (2007) Rev-erbalpha, a heme sensor that coordinates metabolic and circadian pathways. Science, 318, 17861789.
  • Zghidi, W., Merendino, L., Cottet, A., Mache, R. and Lerbs-Mache, S. (2007) Nucleus-encoded plastid sigma factor SIG3 transcribes specifically the psbN gene in plastids. Nucleic Acids Res. 35, 455464.
  • Zhang, L. and Hach, A. (1999) Molecular mechanism of heme signaling in yeast: the transcriptional activator Hap1 serves as the key mediator. Cell. Mol. Life Sci. 56, 415426.