H. Aach, H. Bode, D. G. Robinson, and J. E. Graebe, ent -Kaurene synthase is located in proplastids of meristematic shoot tissues, Planta, vol.202, issue.2, pp.211-219, 1997.
DOI : 10.1007/s004250050121

L. A. Allison, The role of sigma factors in plastid transcription, Biochimie, vol.82, issue.6-7, pp.6-7, 2000.
DOI : 10.1016/S0300-9084(00)00611-8

L. A. Allison, L. D. Simon, and P. Maliga, Deletion of rpoB reveals a second distinct transcription system in plastids of higher plants, Embo Journal, issue.11, pp.15-2802, 1996.

S. G. Andersson, O. Karlberg, B. Canback, and C. G. Kurland, On the origin of mitochondria: a genomics perspective, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.358, issue.1429, pp.358-165, 1429.
DOI : 10.1098/rstb.2002.1193

J. Azevedo, F. Courtois, M. A. Hakimi, E. Demarsy, T. Lagrange et al., Intraplastidial trafficking of a phage-type RNA polymerase is mediated by a thylakoid RING-H2 protein, Proceedings of the National Academy of Sciences of the United States of America, pp.105-9123, 2008.
DOI : 10.1073/pnas.0800909105
URL : https://hal.archives-ouvertes.fr/hal-00310388

S. Baginsky, K. Tiller, and G. Link, Transcription factor phosphorylation by a protein kinase associated with chloroplast RNA polymerase from mustard, 1997.

J. M. Bain, A Crystalline Inclusion In the Chloroplates of the Outer Hyphoderminal Cells of the Banana Fruit, Australian Journal of Biological Sciences, vol.21, issue.3, p.421, 1968.
DOI : 10.1071/BI9680421

N. R. Baker and W. L. Butler, Development of the Primary Photochemical Apparatus of Photosynthesis during Greening of Etiolated Bean Leaves, PLANT PHYSIOLOGY, vol.58, issue.4, pp.526-529, 1976.
DOI : 10.1104/pp.58.4.526

S. Beick, C. Schmitz-linneweber, R. Williams-carrier, B. Jensen, and A. Barkan, The Pentatricopeptide Repeat Protein PPR5 Stabilizes a Specific tRNA Precursor in Maize Chloroplasts, Molecular and Cellular Biology, vol.28, issue.17, pp.28-5337, 2008.
DOI : 10.1128/MCB.00563-08

A. Ben-shem, F. Frolow, and N. Nelson, Crystal structure of plant photosystem I, Nature, vol.426, issue.6967, pp.426-630, 2003.
DOI : 10.1038/nature02200

M. Bligny, F. Courtois, S. Thaminy, C. C. Chang, T. Lagrange et al., Regulation of plastid rDNA transcription by interaction of CDF2 with two different RNA polymerases, The EMBO Journal, vol.19, issue.8, pp.19-1851, 2000.
DOI : 10.1093/emboj/19.8.1851

R. Bock, M. Hermann, and H. Kossel, In vivo dissection of cis-acting determinants for plastid RNA editing, Embo Journal, vol.15, issue.18, pp.5052-5059, 1996.

A. V. Bohne, V. Irihimovitch, A. Weihe, and D. B. Stern, Chlamydomonas reinhardtii encodes a single sigma(70)-like factor which likely functions in chloroplast transcription, Current Genetics, issue.5, pp.49-333, 2006.

C. Bolle, V. V. Kusnetsov, R. G. Herrmann, and R. Oelmuller, The spinach AtpC and AtpD genes contain elements for light-regulated, plastid-dependent and organ-specific expression in the vicinity of the transcription start sites, The Plant Journal, vol.9, issue.1, pp.21-30, 1996.
DOI : 10.1046/j.1365-313X.1996.09010021.x

T. J. Bollenbach, G. Schuster, V. Portnoy, and D. B. Stern, Processing, degradation, and polyadenylation of chloroplast transcripts, Topics in Current Genetics Cell and Molecular Biology of Plastids, 2008.
DOI : 10.1007/4735_2007_0235

T. M. Bourett, K. J. Czymmek, and R. J. Howard, Ultrastructure of chloroplast protuberances in rice leaves preserved by high-pressure freezing, Planta, vol.208, issue.4, pp.472-479, 1999.
DOI : 10.1007/s004250050584

F. Bouvier, R. A. Backhaus, and B. Camara, Induction and control of chromoplastspecific carotenoid genes by oxidative stress, Journal of Biological Chemistry, issue.46, pp.273-30651, 1998.

E. A. Campbell, O. Muzzin, M. Chlenov, J. L. Sun, C. A. Olson et al., Structure of the Bacterial RNA Polymerase Promoter Specificity ?? Subunit, Molecular Cell, vol.9, issue.3, pp.527-539, 2002.
DOI : 10.1016/S1097-2765(02)00470-7

G. Canino, E. Bocian, N. Barbezier, M. Echeverria, J. Forner et al., Arabidopsis Encodes Four tRNase Z Enzymes, PLANT PHYSIOLOGY, vol.150, issue.3, pp.1494-1502, 2009.
DOI : 10.1104/pp.109.137950
URL : https://hal.archives-ouvertes.fr/hal-00697567

M. L. Carter, A. C. Smith, H. Kobayashi, S. Purton, and D. L. Herrin, Structure, circadian regulation and bioinformatic analysis of the unique sigma factor gene in Chlamydomonas reinhardtii, Photosynthesis Research, vol.97, issue.1, pp.339-349, 2004.
DOI : 10.1007/s11120-004-4213-6

H. C. Chen and D. B. Stern, Specific ribonuclease-activities in spinach-chloroplasts promote messenger-RNA maturation and degradation, Journal of Biological Chemistry, issue.35, pp.266-24205, 1991.

L. J. Chen, S. A. Rogers, D. C. Bennett, M. C. Hu, and E. M. Orozco, An in vitro transcription termination system to analyze chloroplast promoters: identification of multiple promoters for the spinach atpB gene, Current Genetics, vol.79, issue.1, pp.55-64, 1990.
DOI : 10.1007/BF00313249

Y. Choquet and O. Vallon, Synthesis, assembly and degradation of thylakoid membrane proteins, Biochimie, vol.82, issue.6-7, pp.6-7, 2000.
DOI : 10.1016/S0300-9084(00)00609-X

Y. Choquet and F. A. Wollman, Translational regulations as specific traits of chloroplast gene expression, FEBS Letters, vol.15, issue.1, pp.39-42, 2002.
DOI : 10.1016/S0014-5793(02)03260-X

F. Courtois, L. Merendino, E. Demarsy, R. Mache, and S. Lerbs-mache, Phage-Type RNA Polymerase RPOTmp Transcribes the rrn Operon from the PC Promoter at Early Developmental Stages in Arabidopsis, PLANT PHYSIOLOGY, vol.145, issue.3, pp.145-712, 2007.
DOI : 10.1104/pp.107.103846
URL : https://hal.archives-ouvertes.fr/hal-00268364

A. L. Cozens, J. E. Walker, A. L. Phillips, A. K. Huttly, and J. C. Gray, A 6th subunit of atp synthase, an f0 component, is encoded in the pea chloroplast genome, Embo Journal, vol.5, issue.2, pp.217-222, 1986.

D. L. Daniels, W. J. Michels, and A. M. Pyle, Two Competing Pathways for Self-splicing by Group II Introns: A Quantitative Analysis ofin VitroReaction Rates and Products, Journal of Molecular Biology, vol.256, issue.1, pp.31-49, 1996.
DOI : 10.1006/jmbi.1996.0066

B. Daum, D. Nicastro, I. Austin, J. Mcintosh, R. J. Ku¨hlbrandtaku¨hlbrandta et al., Arrangement of Photosystem II and ATP Synthase in Chloroplast Membranes of Spinach and Pea, The Plant Cell, vol.22, issue.4, pp.1299-1312, 2010.
DOI : 10.1105/tpc.109.071431

I. L. De-la-sierra-gallay, L. Zig, A. Jamalli, and H. Putzer, Structural insights into the dual activity of RNase J, Nature Structural & Molecular Biology, vol.60, issue.2, pp.206-212, 2008.
DOI : 10.1038/nsmb.1376

D. Santis-maciossek, G. Kofer, W. Bock, A. Schoch, S. Maier et al., Targeted disruption of the plastid RNA polymerase genes rpoA, B and C1: molecular biology, biochemistry and ultrastructure, The Plant Journal, vol.27, issue.5, pp.477-489, 1999.
DOI : 10.1093/nar/26.2.415

J. P. Dekker and E. J. Boekema, Supramolecular organization of thylakoid membrane proteins in green plants, Biochimica et Biophysica Acta (BBA) - Bioenergetics, vol.1706, issue.1-2, pp.12-39, 2005.
DOI : 10.1016/j.bbabio.2004.09.009

E. Demarsy, F. Courtois, J. Azevedo, L. Buhot, and S. Lerbs-mache, Building Up of the Plastid Transcriptional Machinery during Germination and Early Plant Development, PLANT PHYSIOLOGY, vol.142, issue.3, pp.993-1003, 2006.
DOI : 10.1104/pp.106.085043
URL : https://hal.archives-ouvertes.fr/hal-00264129

J. Deruere, S. Romer, A. Dharlingue, R. A. Backhaus, M. Kuntz et al., Fibril Assembly and Carotenoid Overaccumulation in Chromoplasts: A Model for Supramolecular Lipoprotein Structures, THE PLANT CELL ONLINE, vol.6, issue.1, pp.119-133, 1994.
DOI : 10.1105/tpc.6.1.119

D. Drapier, B. Rimbault, O. Vallon, F. A. Wollman, and Y. Choquet, Intertwined translational regulations set uneven stoichiometry of chloroplast ATP synthase subunits, The EMBO Journal, vol.23, issue.15, pp.26-3581, 2007.
DOI : 10.1038/sj.emboj.7601802

S. D. Dyall, M. T. Brown, and P. J. Johnson, Ancient Invasions: From Endosymbionts to Organelles, Science, vol.304, issue.5668, pp.304-253, 2004.
DOI : 10.1126/science.1094884

K. Esau, Anatomical and cytological studies on beet mosaic, Journal of Agricultural Research, vol.69, pp.95-0117, 1944.

A. Esen, A simple method for quantitative, semiquantitative, and qualitative assay of protein, Analytical Biochemistry, vol.89, issue.1, pp.264-273, 1978.
DOI : 10.1016/0003-2697(78)90749-2

J. J. Favory, M. Kobayshi, K. Tanaka, G. Peltier, M. Kreis et al., Specific function of a plastid sigma factor for ndhF gene transcription, Nucleic Acids Research, vol.33, issue.18, pp.33-5991, 2005.
DOI : 10.1093/nar/gki908
URL : https://hal.archives-ouvertes.fr/hal-00021708

O. Fedorova and N. Zingler, Group II introns: structure, folding and splicing mechanism, Biological Chemistry, vol.388, issue.7, pp.665-678, 2007.
DOI : 10.1515/BC.2007.090

M. Ferro, D. Salvi, H. Riviere-rolland, T. Vermat, D. Seigneurin-berny et al., Integral membrane proteins of the chloroplast envelope: Identification and subcellular localization of new transporters, Proceedings of the National Academy of Sciences of the United States of America, pp.99-11487, 2002.
DOI : 10.1073/pnas.172390399

N. Fischer, O. Stampacchia, K. Redding, and J. D. Rochaix, Selectable marker recycling in the chloroplast, MGG Molecular & General Genetics, vol.14, issue.Suppl, pp.373-380, 1996.
DOI : 10.1007/BF02172529

A. A. Gatenby, S. J. Rothstein, and M. Nomura, Translational coupling of the maize chloroplast atpB and atpE genes, Proceedings of the National Academy of Sciences, vol.86, issue.11, pp.86-4066, 1989.
DOI : 10.1073/pnas.86.11.4066

J. Georg, A. Honsel, B. Voss, H. Rennenberg, and W. R. Hess, A long antisense RNA in plant chloroplasts, New Phytologist, vol.34, issue.3, pp.615-622, 2010.
DOI : 10.1111/j.1469-8137.2010.03203.x

M. Goldschmidt-clermont, Transgenic expression of aminoglycoside adenine transferase in the chloroplast: a selectable marker for site-directed transformation of chlamydomonas, Nucleic Acids Research, vol.19, issue.15, pp.4083-4089, 1991.
DOI : 10.1093/nar/19.15.4083

M. Goldschmidt-clermont, Chloroplast splicing, The Chlamydomonas Sourcebook. Organellar and Metabolic Processes, pp.915-936, 2008.
URL : https://hal.archives-ouvertes.fr/hal-01086068

M. Goldschmidt-clermont, Y. Choquet, J. Girardbascou, F. Michel, M. Schirmerrahire et al., A small chloroplast RNA may be required for trans-splicing in chlamydomonas reinhardtii, Cell, vol.65, issue.1, pp.135-143, 1991.
DOI : 10.1016/0092-8674(91)90415-U

M. Goldschmidt-clermont, J. Girard-bascou, Y. , C. , &. D. et al., Trans-splicing mutants of Chlamydomonas reinhardtii, MGG Molecular & General Genetics, vol.223, issue.3, pp.417-425, 1990.
DOI : 10.1007/BF00264448

M. W. Gray, G. Burger, and B. F. Lang, Mitochondrial evolution, Science, issue.5407, pp.283-1476, 1999.

G. Groth and H. Strotmann, New results about structure, function and regulation of the chloroplast ATP synthase (CF0CF1), Physiologia Plantarum, vol.244, issue.1, pp.142-148, 1999.
DOI : 10.1073/pnas.94.20.10583

M. Guertin and G. Bellemare, Synthesis of Chloroplast Ribonucleic Acid in Chlamydomonas reinhardtii Toluene-Treated Cells, European Journal of Biochemistry, vol.68, issue.1, pp.125-129, 1979.
DOI : 10.1016/0005-2787(74)90315-3

B. E. Gunning, Membrane geometry of ?open? prolamellar bodies, Protoplasma, vol.422, issue.1-4, pp.4-15, 2001.
DOI : 10.1007/BF01280299

F. Haddad, A. Q. Qin, J. M. Giger, H. Y. Guo, and K. M. Baldwin, Potential pitfalls in the accuracy of analysis of natural sense-antisense RNA pairs by reverse transcription-PCR, BMC Biotechnology, vol.7, issue.1, 2007.
DOI : 10.1186/1472-6750-7-21

P. T. Hajdukiewicz, L. A. Allison, and P. Maliga, The two RNA polymerases encoded by the nuclear and the plastid compartments transcribe distinct groups of genes in tobacco plastids, The EMBO Journal, vol.16, issue.13, pp.16-4041, 1997.
DOI : 10.1093/emboj/16.13.4041

M. A. Hakimi, I. Privat, J. G. Valay, and S. Lerbs-mache, Evolutionary conservation of C-terminal domains of primary Sigma(70)-type transcription factors between plants and bacteria, Journal of Biological Chemistry, issue.13, pp.275-9215, 2000.

K. Hammani, K. Okuda, S. K. Tanz, A. L. Chateigner-boutin, T. Shikanai et al., A Study of New Arabidopsis Chloroplast RNA Editing Mutants Reveals General Features of Editing Factors and Their Target Sites, The Plant Cell, vol.21, issue.11, pp.3686-3699, 2009.
DOI : 10.1105/tpc.109.071472

C. D. Han, E. H. Coe, and R. A. Martienssen, Molecular-cloning and characterization of iojap (ij), a pattern striping gene of maize, Embo Journal, issue.11, pp.11-4037, 1992.

M. Hanaoka, K. Kanamaru, M. Fujiwara, H. Takahashi, and K. Tanaka, Glutamyl-tRNA mediates a switch in RNA polymerase use during chloroplast biogenesis, EMBO reports, vol.272, issue.6, pp.545-550, 2005.
DOI : 10.1073/pnas.95.9.5021

J. B. Harris and H. J. Arnott, Effects of senescence on chloroplasts of the tobacco leaf, Tissue and Cell, vol.5, issue.4, pp.527-544, 1973.
DOI : 10.1016/S0040-8166(73)80043-6

J. B. Harris and V. G. Schaefer, Some Correlated Events in Aging Leaf Tissues of Tree Tomato and Tobacco, Botanical Gazette, vol.142, issue.1, pp.43-54, 1981.
DOI : 10.1086/337195

R. Hayes, M. L. Hegeman, C. E. Hanson, and M. R. , Sequence elements critical for efficient RNA editing of a tobacco chloroplast transcript in vivo and in vitro, Nucleic Acids Research, vol.34, issue.13, pp.34-3742, 2006.
DOI : 10.1093/nar/gkl490

R. Hayes, J. Kudla, G. Schuster, L. Gabay, P. Maliga et al., Chloroplast mRNA 3'-end processing by a high molecular weight protein complex is regulated by nuclear encoded RNA binding proteins, Embo Journal, vol.15, issue.5, pp.1132-1141, 1996.

B. Hedtke, T. Borner, and A. Weihe, Mitochondrial and Chloroplast Phage-Type RNA Polymerases in Arabidopsis, Science, vol.277, issue.5327, pp.277-809, 1997.
DOI : 10.1126/science.277.5327.809

B. Hedtke, T. Borner, and A. Weihe, One RNA polymerase serving two genomes, EMBO reports, vol.19, issue.5, pp.435-440, 2000.
DOI : 10.1093/embo-reports/kvd086

B. Hedtke, J. Legen, A. Weihe, R. G. Herrmann, and T. Borner, Six active phage-type RNA polymerase genes in Nicotiana tabacum, The Plant Journal, vol.88, issue.6, pp.625-637, 2002.
DOI : 10.1023/A:1006392424384

B. Hedtke, M. Meixner, S. Gillandt, E. Richter, T. Borner et al., Green fluorescent protein as a marker to investigate targeting of organellar RNA polymerases of higher plantsin vivo, The Plant Journal, vol.28, issue.5, pp.557-561, 1999.
DOI : 10.1093/nar/25.12.2319

I. Hernandez-pinzon, J. H. Ross, K. A. Barnes, A. P. Damant, and D. J. Murphy, Composition and role of tapetal lipid bodies in the biogenesis of the pollen coat of Brassica napus, Planta, vol.208, issue.4, pp.588-598, 1999.
DOI : 10.1007/s004250050597

L. H. Herrin, T. C. Kuo, and M. Goldschmidt-clermont, The molecular biology of chloroplasts and mitochondria inChlamydomonas (RNA splicing in the chloroplast), pp.451-458, 1998.

R. G. Herrmann, H. J. Bohnert, K. V. Kowallik, and J. M. Schmitt, Size, conformation and purity of chloroplast DNA of some higher plants, Biochimica et Biophysica Acta (BBA) - Nucleic Acids and Protein Synthesis, vol.378, issue.2, pp.305-317, 1975.
DOI : 10.1016/0005-2787(75)90118-5

W. R. Hess, A. Prombona, B. Fieder, A. R. Subramanian, and T. Borner, 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 Journal, vol.12, issue.2, pp.563-571, 1993.

A. Hicks, R. G. Drager, D. C. Higgs, and D. B. Stern, An mRNA 3' Processing Site Targets Downstream Sequences for Rapid Degradation in Chlamydomonas Chloroplasts, Journal of Biological Chemistry, vol.277, issue.5, pp.3325-3333, 2002.
DOI : 10.1074/jbc.M108979200

T. Hirose and M. Sugiura, Multiple elements required for translation of plastid atpB mRNA lacking the Shine-Dalgarno sequence, Nucleic Acids Research, vol.32, issue.11, pp.3503-3510, 2004.
DOI : 10.1093/nar/gkh682

A. Homann and G. Link, DNA-binding and transcription characteristics of three cloned sigma factors from mustard (Sinapis alba L.) suggest overlapping and distinct roles in plastid gene expression, European Journal of Biochemistry, vol.206, issue.6, pp.1288-1300, 2003.
DOI : 10.1016/S0092-8674(00)81329-X

C. F. Hongay, P. L. Grisafi, T. Galitski, and G. R. Fink, Antisense Transcription Controls Cell Fate in Saccharomyces cerevisiae, Cell, vol.127, issue.4, pp.735-745, 2006.
DOI : 10.1016/j.cell.2006.09.038

J. K. Hoober, C. O. Boyd, and L. G. Paavola, Origin of Thylakoid Membranes in Chlamydomonas reinhardtii y-1 at 38??C, PLANT PHYSIOLOGY, vol.96, issue.4, pp.1321-1328, 1991.
DOI : 10.1104/pp.96.4.1321

C. J. Howe, A. C. Barbrook, R. E. Nisbet, P. J. Lockhart, and A. W. Larkum, The origin of plastids, Philosophical Transactions of the Royal Society B-Biological Sciences, pp.363-2675, 1504.

K. Hsieh and A. H. Huang, Endoplasmic Reticulum, Oleosins, and Oils in Seeds and Tapetum Cells, PLANT PHYSIOLOGY, vol.136, issue.3, pp.3427-3434, 2004.
DOI : 10.1104/pp.104.051060

G. S. Hudson, J. G. Mason, T. A. Holton, B. Koller, G. B. Cox et al., A gene cluster in the spinach and pea chloroplast genomes encoding one CF1 and three CF0 subunits of the H+-ATP synthase complex and the ribosomal protein S2, Journal of Molecular Biology, vol.196, issue.2, pp.283-298, 1987.
DOI : 10.1016/0022-2836(87)90690-5

W. J. Hurkman and G. S. Kennedy, Fine structure and development of proteoplasts in primary leaves of mung bean, Protoplasma, vol.73, issue.1-2, pp.171-184, 1976.
DOI : 10.1007/BF01279337

M. Ikeuchi, Y. Inoue, and W. Vermaas, Characterization of photosystem II subunits from the cyanobacterium Synechocystis sp. PCC6803. In Phototsynthesis: from light to biospere, pp.297-300, 1995.

M. Inada, T. Sasaki, M. Yukawa, T. Tsudzuki, and M. Sugiura, A Systematic Search for RNA Editing Sites in Pea Chloroplasts: an Editing Event Causes Diversification from the Evolutionarily Conserved Amino Acid Sequence, Plant and Cell Physiology, vol.45, issue.11, pp.45-1615, 2004.
DOI : 10.1093/pcp/pch191

Y. Ishizaki, Y. Tsunoyama, K. Hatano, K. Ando, K. Kato et al., A nuclear-encoded sigma factor, Arabidopsis SIG6, recognizes sigma-70 type chloroplast promoters and regulates early chloroplast development in cotyledons, The Plant Journal, vol.22, issue.2, pp.133-144, 2005.
DOI : 10.1111/j.1365-313X.2005.02362.x

K. A. Jarrel, R. C. Dietrich, and P. S. Perlman, Group II intron domain 5 facilitates a trans-splicing reaction., Molecular and Cellular Biology, vol.8, issue.6, pp.2361-2366, 1988.
DOI : 10.1128/MCB.8.6.2361

K. A. Jarrell, C. L. Peebles, R. C. Dietrich, S. L. Romiti, and P. S. Perlman, Group-II intron self-splicing -alternative reaction conditions yield novel products, Journal of Biological Chemistry, issue.7, pp.263-3432, 1988.

B. D. Jenkins, D. J. Kulhanek, and A. Barkan, Nuclear Mutations That Block Group II RNA Splicing in Maize Chloroplasts Reveal Several Intron Classes with Distinct Requirements for Splicing Factors, THE PLANT CELL ONLINE, vol.9, issue.3, pp.283-296, 1997.
DOI : 10.1105/tpc.9.3.283

P. E. Jensen, R. Bassi, E. J. Boekema, J. P. Dekker, S. Jansson et al., Structure, function and regulation of plant photosystem I, Biochimica et Biophysica Acta (BBA) - Bioenergetics, vol.1767, issue.5, pp.1767-335, 2007.
DOI : 10.1016/j.bbabio.2007.03.004

P. Juneau, L. Lay, P. Boddi, A. Samson, G. Popovic et al., Relationship Between the Structural and Functional Changes of the Photosynthetic Apparatus During Chloroplast???Chromoplast Transition in Flower Bud of Lilium longiflorum??, Photochemistry and Photobiology, vol.128, issue.4, pp.377-381, 2002.
DOI : 10.1562/0031-8655(2002)075<0377:RBTSAF>2.0.CO;2

K. Kanamaru, A. Nagashima, M. Fujiwara, H. Shimada, Y. Shirano et al., An Arabidopsis sigma factor (SIG2)-dependent expression of plastidencoded tRNAs in chloroplasts, Plant and Cell Physiology, issue.10, pp.42-1034, 2001.

S. Kapoor, J. Y. Suzuki, and M. Sugiura, Identification and functional significance of a new class of non-consensus-type plastid promoters, The Plant Journal, vol.11, issue.2, pp.327-337, 1997.
DOI : 10.1046/j.1365-313X.1997.11020327.x

S. Kapoor, T. Wakasugi, H. Deno, and M. Sugiura, An atpE-specific promoter within the coding region of the atpB gene in tobacco chloroplast DNA, Current Genetics, vol.79, issue.3, pp.263-268, 1994.
DOI : 10.1007/BF00309558

Y. Kashino, H. Koike, M. Yoshio, H. Egashira, M. Ikeuchi et al., Low-Molecular-Mass Polypeptide Components of a Photosystem II Preparation from the Thermophilic Cyanobacterium Thermosynechococcus vulcanus, Plant and Cell Physiology, vol.43, issue.11, pp.43-1366, 2002.
DOI : 10.1093/pcp/pcf168

J. Kern and G. Renger, Photosystem II: Structure and mechanism of the water:plastoquinone oxidoreductase, Photosynthesis Research, vol.409, issue.2-3, pp.183-202, 2007.
DOI : 10.1007/s11120-007-9201-1

M. Kim, K. E. Thum, D. T. Morishige, and J. E. Mullet, Detailed architecture of the barley chloroplast psbD-psbC blue light-responsive promoter, Journal of Biological Chemistry, issue.8, pp.274-4684, 1999.

J. T. Kirk and R. A. Tilney-bassett, kirk,jto -plastids -their chemistry structure growth and inheritance, Scientific American, vol.217, issue.3, p.302, 1967.

Y. Kobayashi, Y. Dokiya, Y. Kumazawa, and M. Sugita, Non-AUG translation initiation of mRNA encoding plastid-targeted phage-type RNA polymerase in Nicotiana sylvestris, Biochemical and Biophysical Research Communications, vol.299, issue.1, pp.57-61, 2002.
DOI : 10.1016/S0006-291X(02)02579-2

Y. Kobayashi, Y. Dokiya, and M. Sugita, Dual Targeting of Phage-Type RNA Polymerase to both Mitochondria and Plastids Is Due to Alternative Translation Initiation in Single Transcripts, Biochemical and Biophysical Research Communications, vol.289, issue.5, pp.1106-1113, 2001.
DOI : 10.1006/bbrc.2001.6130

Y. Kobayashi, Y. Dokiya, M. Sugiura, Y. Niwa, and M. Sugita, Genomic organization and organ-specific expression of a nuclear gene encoding phage-type RNA polymerase in Nicotiana sylvestris, Gene, vol.279, issue.1, pp.33-40, 2001.
DOI : 10.1016/S0378-1119(01)00729-6

R. Kolodner and K. K. Tewari, Molecular-size and conformation of chloroplast deoxyribonucleic acid from pea leaves, Journal of Biological Chemistry, vol.247, issue.19, p.6355, 1972.

E. Kotera, M. Tasaka, and T. Shikanai, A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts, Nature, vol.101, issue.7023, pp.326-330, 2005.
DOI : 10.1073/pnas.96.26.15324

K. Krause, R. M. Maier, W. Kofer, K. Krupinska, and R. G. Herrmann, 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, MGG - Molecular and General Genetics, vol.263, issue.6, pp.1022-1030, 2000.
DOI : 10.1007/PL00008690

K. B. Krishna, M. K. Joshi, B. Vani, and P. Mohanty, Structure-function correlation during the etioplast-chloroplast transition in cucumber cotyledonary leaves, Photosynthetica, vol.36, issue.1/2, pp.199-212, 1999.
DOI : 10.1023/A:1007043409538

T. S. Kroeger, K. P. Watkins, G. Friso, K. J. Van-wijk, and A. Barkan, A plantspecific RNA-binding domain revealed through analysis of chloroplast group II intron splicing, Proceedings of the National Academy of Sciences of the United States of America, pp.4537-4542, 2009.

H. A. Lancer, C. E. Cohen, and J. A. Schiff, Changing Ratios of Phototransformable Protochlorophyll and Protochlorophyllide of Bean Seedlings Developing in the Dark, PLANT PHYSIOLOGY, vol.57, issue.3, pp.369-374, 1976.
DOI : 10.1104/pp.57.3.369

M. Lapidot and Y. Pilpel, Genome-wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms, EMBO reports, vol.266, issue.12, pp.1216-1222, 2006.
DOI : 10.1016/S0092-8674(01)00466-4

A. Larkum, P. Lockhart, and C. Howe, The origin of plastids: A shopping bag model, Photosynthesis Research, vol.91, issue.2-3, p.1815, 2007.

A. Larkum, P. J. Lockhart, and C. J. Howe, Shopping for plastids, Trends in Plant Science, vol.12, issue.5, pp.189-195, 2007.
DOI : 10.1016/j.tplants.2007.03.011

J. G. Lebkuecher, K. A. Haldeman, C. E. Harris, S. L. Holz, S. A. Joudah et al., Development of Photosystem-II Activity during Irradiance of Etiolated Helianthus (Asteraceae) Seedlings, American Journal of Botany, vol.86, issue.8, pp.86-1087, 1999.
DOI : 10.2307/2656970

R. M. Leech, Chloroplast development in angiosperms: current knowledge and future prospects, Chloroplast Biogenesis, vol.5, pp.1-21, 1984.

J. Legen, S. Kemp, K. Krause, B. Profanter, R. G. Herrmann et al., Comparative analysis of plastid transcription profiles of entire plastid chromosomes from tobacco attributed to wild-type and PEP-deficient transcription machineries, The Plant Journal, vol.31, issue.2, pp.31-171, 2002.
DOI : 10.1046/j.1365-313X.2002.01349.x

S. Lerbs-mache, The 110-KDa polypeptide of spinach plastid DNA-dependent RNApolymerase -single-subunit enzyme or catalytic core of multimeric enzyme complexes, Proceedings of the National Academy of Sciences of the United States of America, issue.12, pp.90-5509, 1993.

S. Lerbs-mache, Function of plastid sigma factors in higher plants: regulation of gene expression or just preservation of constitutive transcription?, Plant Molecular Biology, vol.35, issue.3-5, 2011.
DOI : 10.1007/s11103-010-9714-4
URL : https://hal.archives-ouvertes.fr/hal-00586781

J. W. Lilly, J. E. Maul, and D. B. Stern, The Chlamydomonas reinhardtti organellar genomes respond transcriptionally and post-transcriptionally to abiotic stimuli, Plant Cell, issue.11, pp.14-2681, 2002.

B. Liu and R. F. Troxler, Molecular characterization of a positively photoregulated nuclear gene for a chloroplast RNA polymerase sigma factor in Cyanidium caldarium., Proceedings of the National Academy of Sciences, vol.93, issue.8, pp.93-3313, 1996.
DOI : 10.1073/pnas.93.8.3313

N. Ljubesic, Ultrastructural changes of plastids during the yellowing of the fruit of Cucurbita pepo var pyriformis, Acta Bot Croatia, vol.31, pp.47-53, 1972.

M. Lonetto, M. Gribskov, and C. A. Gross, The sigma 70 family: sequence conservation and evolutionary relationships., Journal of Bacteriology, vol.174, issue.12, pp.3843-3849, 1992.
DOI : 10.1128/jb.174.12.3843-3849.1992

H. Loschelder, J. Schweer, B. Link, and G. Link, Dual Temporal Role of Plastid Sigma Factor 6 in Arabidopsis Development, PLANT PHYSIOLOGY, vol.142, issue.2, pp.642-650, 2006.
DOI : 10.1104/pp.106.085878

B. Lung, A. Zemann, M. J. Madej, M. Schuelke, S. Techritz et al., Identification of small non-coding RNAs from mitochondria and chloroplasts, Nucleic Acids Research, vol.34, issue.14, pp.34-3842, 2006.
DOI : 10.1093/nar/gkl448

W. Martin, M. Hoffmeister, C. Rotte, and K. Henze, An Overview of Endosymbiotic Models for the Origins of Eukaryotes, Their ATP-Producing Organelles (Mitochondria and Hydrogenosomes), and Their Heterotrophic Lifestyle, Biological Chemistry, vol.382, issue.11, pp.382-1521, 2001.
DOI : 10.1515/BC.2001.187

W. Martin and M. Muller, The hydrogen hypothesis for the first eukaryote, Nature, vol.392, issue.6671, pp.37-41, 1998.
DOI : 10.1038/32096

W. Martin and M. J. Russell, On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.358, issue.1429, pp.358-59, 1429.
DOI : 10.1098/rstb.2002.1183

K. Meierhoff, S. Felder, T. Nakamura, N. Bechtold, and G. Schuster, HCF152, an Arabidopsis RNA Binding Pentatricopeptide Repeat Protein Involved in the Processing of Chloroplast psbB-psbT-psbH-petB-petD RNAs, THE PLANT CELL ONLINE, vol.15, issue.>6, pp.15-1480, 2003.
DOI : 10.1105/tpc.010397

W. Z. Meng, R. H. Nicholson, L. Nathania, A. V. Pertzev, and A. W. Nicholson, New approaches to understanding double-stranded RNA processing by ribonuclease III: Purification and assays of homodimeric and heterodimeric forms of RNAse III from bacterial extremophiles and mesophiles, Rna Turnover in Bacteria, pp.119-129, 2008.

C. Mereschkowsky, Uber natur und ursprung der chromatophoren im pflanzenreiche, biol. centrabl, vol.25, pp.593-604, 1905.

F. Michel, K. Umesono, and H. Ozeki, Comparative and functional anatomy of group II catalytic introns ??? a review, Gene, vol.82, issue.1, pp.5-30, 1989.
DOI : 10.1016/0378-1119(89)90026-7

T. Miyagi, S. Kapoor, M. Sugita, and M. Sugiura, Transcript analysis of the tobacco plastid operon rps2/atpI/H/F/A reveals the existence of a non-consensus type II (NCII) promoter upstream of the atpI coding sequence, Molecular and General Genetics MGG, vol.257, issue.3, pp.299-307, 1998.
DOI : 10.1007/s004380050651

T. Mochizuki, Y. Onda, E. Fujiwara, M. Wada, and Y. Toyoshima, Two independent light signals cooperate in the activation of the plastid psbD blue light-responsive promoter in Arabidopsis, Febs Letters, vol.571, pp.1-3, 2004.

R. A. Monde, G. Schuster, and D. B. Stern, Processing and degradation of chloroplast mRNA, Biochimie, vol.82, issue.6-7, pp.6-7, 2000.
DOI : 10.1016/S0300-9084(00)00606-4

C. W. Morden, K. H. Wolfe, C. W. Depamphilis, and J. D. Palmer, Plastid translation and transcription genes in a nonphotosynthetic plant -intact, missing and pseudo genes, Embo Journal, issue.11, pp.10-3281, 1991.

D. Moreira and P. Lopez-garcia, Symbiosis Between Methanogenic Archaea and ??-Proteobacteria as the Origin of Eukaryotes: The Syntrophic Hypothesis, Journal of Molecular Evolution, vol.47, issue.5, pp.517-530, 1998.
DOI : 10.1007/PL00006408

E. A. Mudd, S. Sullivan, M. F. Gisby, A. Mironov, C. S. Kwon et al., A 125 kDa RNase E/G-like protein is present in plastids and is essential for chloroplast development and autotrophic growth in Arabidopsis, Journal of Experimental Botany, vol.59, issue.10, pp.59-2597, 2008.
DOI : 10.1093/jxb/ern126

J. E. Mullet, Chloroplast Development and Gene Expression, Annual Review of Plant Physiology and Plant Molecular Biology, vol.39, issue.1, pp.475-502, 1988.
DOI : 10.1146/annurev.pp.39.060188.002355

J. E. Mullet, Dynamic Regulation of Chloroplast Transcription, Plant Physiology, vol.103, issue.2, pp.309-313, 1993.
DOI : 10.1104/pp.103.2.309

J. E. Mullet, E. M. Orozco, and N. H. Chua, Multiple transcripts for higher plantrbcL andatpB genes and localization of the transcription initiation site of therbcL gene, Plant Molecular Biology, vol.106, issue.1, pp.39-54, 1985.
DOI : 10.1007/BF02498714

A. Nagashima, M. Hanaoka, R. Motohashi, M. Seki, K. Shinozaki et al., Mutant Deficient in a Plastid Transcription Factor Sigma, SIG2, Bioscience, Biotechnology, and Biochemistry, vol.44, issue.8, pp.694-704, 2004.
DOI : 10.1105/tpc.005595

A. Nagashima, M. Hanaoka, T. Shikanai, M. Fujiwara, K. Kanamaru et al., The Multiple-Stress Responsive Plastid Sigma Factor, SIG5, Directs Activation of the psbD Blue Light-Responsive Promoter (BLRP) in Arabidopsis thaliana, Plant and Cell Physiology, vol.45, issue.4, pp.357-368, 2004.
DOI : 10.1093/pcp/pch050

D. Neff, S. Tripathi, K. Middendorf, H. Stahlberg, H. J. Butt et al., Chloroplast F0F1ATP Synthase Imaged by Atomic Force Microscopy, Journal of Structural Biology, vol.119, issue.2, pp.139-148, 1997.
DOI : 10.1006/jsbi.1997.3891

E. H. Newcomb, FINE STRUCTURE OF PROTEIN-STORING PLASTIDS IN BEAN ROOT TIPS, The Journal of Cell Biology, vol.33, issue.1, p.143, 1967.
DOI : 10.1083/jcb.33.1.143

N. Nishizawa and S. Mori, Ultrastructure of the Thylakoid Membrane in Tomato Leaf Chloroplast Revealed by Liquid Helium Rapid-Freezing and Substitution-Fixation Method, Plant and Cell Physiology, vol.30, issue.1, pp.1-7, 1989.
DOI : 10.1093/oxfordjournals.pcp.a077703

H. Noji and M. Yoshida, The Rotary Machine in the Cell, ATP Synthase, Journal of Biological Chemistry, vol.276, issue.3, pp.1665-1668, 2001.
DOI : 10.1074/jbc.R000021200

W. L. Ogren, Photorespiration: Pathways, Regulation, and Modification, Annual Review of Plant Physiology, vol.35, issue.1, pp.415-442, 1984.
DOI : 10.1146/annurev.pp.35.060184.002215

N. Ohnishi, Y. Kashino, K. Satoh, S. Ozawa, and Y. Takahashi, Chloroplast-encoded Polypeptide PsbT Is Involved in the Repair of Primary Electron Acceptor QA of Photosystem II during Photoinhibition in Chlamydomonas reinhardtii, Journal of Biological Chemistry, vol.282, issue.10, pp.282-7107, 2007.
DOI : 10.1074/jbc.M606763200

N. Ohnishi and Y. Takahashi, Chloroplast-encoded PsbT is required for efficient biogenesis of photosystem??II complex in the green alga Chlamydomonas reinhardtii, Photosynthesis Research, vol.17, issue.1-3, pp.1-3, 2008.
DOI : 10.1007/s11120-008-9344-8

K. Okuda, A. L. Chateigner-boutin, T. Nakamura, E. Delannoy, M. Sugita et al., Pentatricopeptide Repeat Proteins with the DYW Motif Have Distinct Molecular Functions in RNA Editing and RNA Cleavage in Arabidopsis Chloroplasts, THE PLANT CELL ONLINE, vol.21, issue.1, pp.146-156, 2009.
DOI : 10.1105/tpc.108.064667

K. Okuda, F. Myouga, R. Motohashi, K. Shinozaki, and T. Shikanai, Conserved domain structure of pentatricopeptide repeat proteins involved in chloroplast RNA editing, Proceedings of the National Academy of Sciences, vol.104, issue.19, pp.8178-8183, 2007.
DOI : 10.1073/pnas.0700865104

K. Okuda, T. Nakamura, M. Sugita, T. Shimizu, and T. Shikanai, A Pentatricopeptide Repeat Protein Is a Site Recognition Factor in Chloroplast RNA Editing, Journal of Biological Chemistry, vol.281, issue.49, pp.281-37661, 2006.
DOI : 10.1074/jbc.M608184200

D. J. Oldenburg and A. J. Bendich, Changes in the Structure of DNA Molecules and the Amount of DNA Per Plastid During Chloroplast Development in Maize, Journal of Molecular Biology, vol.344, issue.5, pp.1311-1330, 2004.
DOI : 10.1016/j.jmb.2004.10.001

Y. Onda, Y. Yagi, Y. Saito, N. Takenaka, and Y. Toyoshima, Light induction of Arabidopsis SIG1 and SIG5 transcripts in mature leaves: differential roles of cryptochrome 1 and cryptochrome 2 and dual function of SIG5 in the recognition of plastid promoters, Plant Journal, issue.6, pp.55-968, 2008.

E. M. Orozco, L. J. Chen, and R. J. Eilers, The divergently transcribed rbcL and atpB genes of tobacco plastid DNA are separated by nineteen base pairs, Current Genetics, vol.79, issue.1, pp.65-71, 1990.
DOI : 10.1007/BF00313250

K. W. Osteryoung and J. Nunnari, The Division of Endosymbiotic Organelles, Science, vol.302, issue.5651, pp.1698-1704, 2003.
DOI : 10.1126/science.1082192

G. J. Ostheimer, R. Williams-carrier, S. Belcher, E. Osborne, J. Gierke et al., Group II intron splicing factors derived by diversification of an ancient RNAbinding domain, Embo Journal, issue.15, pp.22-3919, 2003.

E. Pacini, P. E. Taylor, M. B. Singh, and R. B. Knox, Development of Plastids in Pollen and Tapetum of Rye-grass, Lolium perenne L, Annals of Botany, vol.70, issue.2, pp.179-188, 1992.
DOI : 10.1093/oxfordjournals.aob.a088455

J. D. Palmer, THE SYMBIOTIC BIRTH AND SPREAD OF PLASTIDS: HOW MANY TIMES AND WHODUNIT?, Journal of Phycology, vol.51, issue.1, pp.4-11, 2003.
DOI : 10.1046/j.1529-8817.2003.02185.x

H. Park, L. L. Eggink, R. W. Roberson, and J. K. Hoober, TRANSFER OF PROTEINS FROM THE CHLOROPLAST TO VACUOLES IN CHLAMYDOMONAS REINHARDTII (CHLOROPHYTA): A PATHWAY FOR DEGRADATION, Journal of Phycology, vol.35, issue.3, pp.528-538, 1999.
DOI : 10.1046/j.1529-8817.1999.3530528.x

H. Park, S. S. Kreunen, A. J. Cuttriss, D. Dellapenna, and B. J. Pogson, Identification of the Carotenoid Isomerase Provides Insight into Carotenoid Biosynthesis, Prolamellar Body Formation, and Photomorphogenesis, THE PLANT CELL ONLINE, vol.14, issue.2, pp.321-332, 2002.
DOI : 10.1105/tpc.010302

B. Parthier, Gerontoplasts -the yellow end in the ontogenesis of chloroplasts, Endocytobiosis and Cell Research, vol.5, issue.2, pp.163-190, 1988.

C. L. Peebles, E. J. Benatan, K. A. Jarrell, and P. S. Perlman, Group II Intron Self-splicing: Development of Alternative Reaction Conditions and Identification of a Predicted Intermediate, Cold Spring Harbor Symposia on Quantitative Biology, vol.52, issue.0, pp.223-232, 1987.
DOI : 10.1101/SQB.1987.052.01.027

R. Perrin, H. Lange, J. M. Grienenberger, and D. Gagliardi, AtmtPNPase is required for multiple aspects of the 18S rRNA metabolism in Arabidopsis thaliana mitochondria, Nucleic Acids Research, vol.32, issue.17, pp.32-5174, 2004.
DOI : 10.1093/nar/gkh852

A. V. Pertzev and A. W. Nicholson, Characterization of RNA sequence determinants and antideterminants of processing reactivity for a minimal substrate of Escherichia coli ribonuclease III, Nucleic Acids Research, vol.34, issue.13, pp.3708-3721, 2006.
DOI : 10.1093/nar/gkl459

J. Pfalz, O. A. Bayraktar, J. Prikryl, and A. Barkan, Site-specific binding of a PPR protein defines and stabilizes 5??? and 3??? mRNA termini in chloroplasts, The EMBO Journal, vol.85, issue.14, pp.28-2042, 2009.
DOI : 10.1111/j.1365-313X.2004.02035.x

I. Privat, M. A. Hakimi, L. Buhot, J. J. Favory, and S. Lerbs-mache, Characterization of Arabidopsis plastid sigma-like transcription factors SIG1, SIG2 and SIG3, Plant Molecular Biology, issue.3, pp.51-385, 2003.

K. A. Pyke, Plastid Division and Development, THE PLANT CELL ONLINE, vol.11, issue.4, pp.549-556, 1999.
DOI : 10.1105/tpc.11.4.549

K. A. Pyke and R. M. Leech, Chloroplast Division and Expansion Is Radically Altered by Nuclear Mutations in Arabidopsis thaliana, PLANT PHYSIOLOGY, vol.99, issue.3, pp.1005-1008, 1992.
DOI : 10.1104/pp.99.3.1005

F. Repoila and F. Darfeuille, Small regulatory non-coding RNAs in bacteria: physiology and mechanistic aspects, Biology of the Cell, vol.17, issue.2, pp.117-131, 2009.
DOI : 10.1042/BC20070137

M. L. Richter, R. Hein, and B. Huchzermeyer, Important subunit interactions in the chloroplast ATP synthase, Biochimica et Biophysica Acta (BBA) - Bioenergetics, vol.1458, issue.2-3, pp.326-342, 2000.
DOI : 10.1016/S0005-2728(00)00084-0

H. Ris and W. Plaut, Ultra structure of DNA containing areas in the chloroplast of chlamydomonas, Cell Biology, vol.13, pp.593-604, 1962.

R. W. Robert and J. H. Kenneth, Advances in photosynthesis and respiration. 'The Structure and Function of Plastids, 2007.

E. J. Robertson and R. M. Leech, Significant Changes in Cell and Chloroplast Development in Young Wheat Leaves (Triticum aestivum cv Hereward) Grown in Elevated CO2, Plant Physiology, vol.107, issue.1, pp.63-71, 1995.
DOI : 10.1104/pp.107.1.63

J. H. Ross, C. Milanesi, D. J. Murphy, and R. Cresti, Rapid-freeze fixation and substitution improves tissue preservation of microspores and tapetum in Brassica napus, Sexual Plant Reproduction, vol.12, issue.4, pp.237-240, 2000.
DOI : 10.1007/s004970050007

A. Sakai, C. Saito, N. Inada, and T. Kuroiwa, Transcriptional Activities of the Chloroplast-Nuclei and Proplastid-Nuclei Isolated from Tobacco Exhibit Different Sensitivities to Tagetitoxin: Implication of the Presence of Distinct RNA Polymerases, Plant and Cell Physiology, vol.39, issue.9, pp.928-934, 1998.
DOI : 10.1093/oxfordjournals.pcp.a029456

R. Saldanha, G. Mohr, M. Belfort, and A. M. Lambowitz, Group-I and group-II introns, Faseb Journal, vol.7, issue.1, pp.15-24, 1993.

. Sambrook, Northern blotting: transfer of denatured RNA to membranes, Nature Methods, vol.2, issue.12, pp.997-998, 2005.

Y. Sasaki, A. Kozaki, A. Ohmori, H. Iguchi, and Y. Nagano, Chloroplast RNA Editing Required for Functional Acetyl-CoA Carboxylase in Plants, Journal of Biological Chemistry, vol.276, issue.6, pp.276-3937, 2001.
DOI : 10.1074/jbc.M008166200

S. Sato, Y. Nakamura, T. Kaneko, E. Asamizu, and S. Tabata, Complete Structure of the Chloroplast Genome of Arabidopsis thaliana, DNA Research, vol.6, issue.5, pp.283-290, 1999.
DOI : 10.1093/dnares/6.5.283

H. Schagger, Tricine???SDS-PAGE, Nature Protocols, vol.39, issue.1, pp.16-22, 2006.
DOI : 10.1038/nprot.2006.4

A. Schein, S. Sheffy-levin, F. Glaser, and G. Schuster, The RNase E/G-type endoribonuclease of higher plants is located in the chloroplast and cleaves RNA similarly to the E. coli enzyme, RNA, vol.14, issue.6, pp.14-1057, 2008.
DOI : 10.1261/rna.907608

A. F. Schimper, Ueber die entwickelung der chlorophyllkoerner und farbkoerper, Botanische Zeitung, vol.41, pp.105-113, 1883.

C. Schmitz-linneweber and A. Barkan, RNA splicing and RNA editing in chloroplasts, Cell and Molecular Biology of Plastids, pp.213-248, 2007.
DOI : 10.1007/4735_2007_0233

C. Schmitz-linneweber, R. E. Williams-carrier, P. M. Williams-voelker, T. S. Kroeger, A. Vichas et al., A Pentatricopeptide Repeat Protein Facilitates the trans-Splicing of the Maize Chloroplast rps12 Pre-mRNA, THE PLANT CELL ONLINE, vol.18, issue.10, pp.18-2650, 2006.
DOI : 10.1105/tpc.106.046110

J. Schweer, H. Loschelder, and G. Link, A promoter switch that can rescue a plant sigma factor mutant, FEBS Letters, vol.223, issue.28-29, pp.28-29, 2006.
DOI : 10.1016/j.febslet.2006.11.010

J. Schweer, H. Turkeri, B. Link, and G. Link, AtSIG6, a plastid sigma factor from Arabidopsis, reveals functional impact of cpCK2 phosphorylation, The Plant Journal, vol.26, issue.4, pp.192-202, 2010.
DOI : 10.1111/j.1365-313X.2010.04138.x

G. Serino and P. Maliga, Genes Are Not Shared with the Nucleus-Encoded Plastid Enzyme, Plant Physiology, vol.117, issue.4, pp.1165-1170, 1998.
DOI : 10.1104/pp.117.4.1165

T. Shikanai, Cyclic Electron Transport Around Photosystem I: Genetic Approaches, Annual Review of Plant Biology, vol.58, issue.1, pp.199-217, 2007.
DOI : 10.1146/annurev.arplant.58.091406.110525

M. Shimizu, H. Kato, T. Ogawa, A. Kurachi, Y. Nakagawa et al., Sigma factor phosphorylation in the photosynthetic control of photosystem stoichiometry, Proceedings of the National Academy of Sciences of the United States of America, pp.10760-10764, 2010.
DOI : 10.1073/pnas.0911692107

K. Shinozaki, H. Deno, A. Kato, and M. Sugiura, Overlap and cotranscription of the genes for the beta-subunit and epsilon-subunit of tobacco chloroplast ATPase, Gene, vol.24, issue.2-3, pp.147-155, 1983.

K. Shinozaki and M. Sugiura, The nucleotide sequence of the tobacco chloroplast gene for the large subunit of ribulose-l,5-bisphosphate carboxylase/oxygenase, Gene, vol.20, issue.1, pp.91-102, 1982.
DOI : 10.1016/0378-1119(82)90090-7

H. J. Sluiman and G. M. Lokhorst, The ultrastructure of cellular division (autosporogenesis) in the coccoid green alga, Trebouxia aggregate, revealed by rapid freeze fixation and freeze substitution, Protoplasma, pp.144149-159, 1988.

J. Soll and E. Schleiff, Protein import into chloroplasts, Current Opinion in Plant Biology, vol.5, issue.6, pp.198-208, 2004.
DOI : 10.1016/S1369-5266(02)00296-0

L. A. Staehelin, Chloroplast structure: from chlorophyll granules to supra-molecular architecture of thylakoid membranes, Photosynthesis Research, vol.76, pp.1-3, 2003.
DOI : 10.1007/1-4020-3324-9_64

D. J. Stahl, S. R. Rodermel, L. Bogorad, and A. R. Subramanian, Co-transcription pattern of an introgressed operon in the maize chloroplast genome comprising four ATP synthase subunit genes and the ribosomal rps2, Plant Molecular Biology, vol.16, issue.6, pp.1069-1076, 1993.
DOI : 10.1007/BF00023603

D. B. Stern, M. Goldschmidt-clermont, and R. H. Maureen, Chloroplast RNA Metabolism, Annual Review of Plant Biology, vol.61, issue.1, pp.125-155, 2010.
DOI : 10.1146/annurev-arplant-042809-112242

D. B. Stern and K. L. Kindle, 3'end maturation of the Chlamydomonas reinhardtii chloroplast atpB mRNA is a two-step process., Molecular and Cellular Biology, vol.13, issue.4, pp.2277-2285, 1993.
DOI : 10.1128/MCB.13.4.2277

N. E. Stollar and M. J. Hollingsworth, Expression of the Large ATP Synthase Gene Cluster from Spinach Chloroplasts, Journal of Plant Physiology, vol.144, issue.2, pp.141-149, 1994.
DOI : 10.1016/S0176-1617(11)80535-3

M. Sugiura, RNA Editing in Chloroplasts, In RNA Editing. Nucleic Acids and Molecular Biology, pp.123-142, 2008.
DOI : 10.1007/978-3-540-73787-2_6

S. J. Surzycki and D. L. Shellenbarger, Purification and characterization of a putative sigma factor from chlamydomonas-reinhardi, Proceedings of the National Academy of Sciences of the United States of America, issue.11, pp.73-3961, 1976.

M. Swiatecka-hagenbruch, K. Liere, and T. Börner, High diversity of plastidial promoters in Arabidopsis thaliana, Molecular Genetics and Genomics, vol.15, issue.6, pp.725-734, 2007.
DOI : 10.1007/s00438-007-0222-4

K. Tanaka, K. Oikawa, N. Ohta, H. Kuroiwa, T. Kuroiwa et al., Nuclear Encoding of a Chloroplast RNA Polymerase Sigma Subunit in a Red Alga, Science, vol.272, issue.5270, pp.272-1932, 1996.
DOI : 10.1126/science.272.5270.1932

B. C. Thomas, X. Q. Li, and P. Gegenheimer, Chloroplast ribonuclease P does not utilize the ribozyme-type pre-tRNA cleavage mechanism, RNA, vol.6, issue.4, pp.545-553, 2000.
DOI : 10.1017/S1355838200991465

W. W. Thomson and J. M. Whatley, Development of Nongreen Plastids, Annual Review of Plant Physiology, vol.31, issue.1, pp.375-394, 1980.
DOI : 10.1146/annurev.pp.31.060180.002111

K. Tiller and G. Link, Phosphorylation and dephosphorylation affect functionalcharacteristics of chloroplast and etioplast transcription systems from mustard (sinapis-alba l), Embo Journal, vol.12, issue.5, pp.1745-1753, 1993.

J. T. Ting, S. S. Wu, C. Ratnayake, and A. H. Huang, Constituents of the tapetosomes and elaioplasts inBrassica campestristapetum and their degradation and retention during microsporogenesis, The Plant Journal, vol.262, issue.5, pp.541-551, 1998.
DOI : 10.1073/pnas.94.23.12711

Y. Tozawa, M. Teraishi, T. Sasaki, K. Sonoike, Y. Nishiyama et al., The plastid sigma factor SIG1 maintains photosystem I activity via regulated expression of the psaA operon in rice chloroplasts, The Plant Journal, vol.35, issue.1, pp.124-132, 2007.
DOI : 10.1111/j.1365-313X.2007.03216.x

G. B. Trepp, D. W. Plank, J. S. Gantt, and C. P. Vance, NADH-Glutamate Synthase in Alfalfa Root Nodules. Immunocytochemical Localization, Plant Physiology, vol.119, issue.3, pp.829-837, 1999.
DOI : 10.1104/pp.119.3.829

R. F. Troxler, F. Zhang, J. Hu, and L. Bogorad, Evidence That [sigma] Factors Are Components of Chloroplast RNA Polymerase, Plant Physiology, vol.104, issue.2, pp.753-759, 1994.
DOI : 10.1104/pp.104.2.753

Y. Tsunoyama, Y. Ishizaki, K. Morikawa, M. Kobori, Y. Nakahira et al., Blue light-induced transcription of plastid-encoded psbD gene is mediated by a nuclear-encoded transcription initiation factor, AtSig5, Proceedings of the National Academy of Sciences of the United States of America, pp.3304-3309, 2004.
DOI : 10.1073/pnas.0308362101

M. Turmel, R. R. Gutell, J. P. Mercier, C. Otis, and C. Lemieux, Analysis of the Chloroplast Large Subunit Ribosomal RNA Gene from 17 Chlamydomonas Taxa, Journal of Molecular Biology, vol.232, issue.2, pp.446-467, 1993.
DOI : 10.1006/jmbi.1993.1402

P. Umate, S. Schwenkert, I. Karbat, C. Dal-bosco, L. Mlcochova et al., Deletion of PsbM in Tobacco Alters the QB Site Properties and the Electron Flow within Photosystem II, Journal of Biological Chemistry, vol.282, issue.13, pp.282-9758, 2007.
DOI : 10.1074/jbc.M608117200

R. Vanderveen, J. Kwakman, and L. A. Grivell, Mutations at the lariat acceptor site allow self-splicing of a group-II intron without lariat formation, Embo Journal, vol.6, issue.12, pp.3827-3831, 1987.

J. Vogel, T. Borner, and W. R. Hess, Comparative analysis of splicing of the complete set of chloroplast group II introns in three higher plant mutants, Nucleic Acids Research, vol.27, issue.19, pp.3866-3874, 1999.
DOI : 10.1093/nar/27.19.3866

D. Von-wettstein, Discovery of a protein required for photosynthetic membrane assembly, Proceedings of the National Academy of Sciences of the United States of America, pp.3633-3635, 2001.
DOI : 10.1073/pnas.071056598

A. R. Wellburn and R. Hampp, Appearance of photochemical function in prothylakoids during plastid development, Biochimica et Biophysica Acta (BBA) - Bioenergetics, vol.547, issue.2, pp.380-397, 1979.
DOI : 10.1016/0005-2728(79)90019-7

A. Werner and D. Swan, What are natural antisense transcripts good for? Biochemical Society Transactions, pp.1144-1149, 2010.

P. Westhoff and R. G. Herrmann, Complex RNA maturation in chloroplasts. The psbB operon from spinach, European Journal of Biochemistry, vol.12, issue.3, pp.551-564, 1988.
DOI : 10.1038/322572a0

J. M. Whatley, VARIATIONS IN THE BASIC PATHWAY OF CHLOROPLAST DEVELOPMENT, New Phytologist, vol.52, issue.2, p.407, 1977.
DOI : 10.1083/jcb.45.1.158

J. P. Woessner, N. W. Gillham, and J. E. Boynton, Chloroplast genes encoding subunits of the H+-ATPase complex of Chlamydomonas reinhardtii are rearranged compared to higher plants: sequence of the atpE gene and location of the atpF and atpI genes, Plant Molecular Biology, vol.79, issue.2, pp.151-158, 1987.
DOI : 10.1007/BF00025326

F. A. Wollman, L. Minai, and R. Nechushtai, The biogenesis and assembly of photosynthetic proteins in thylakoid membranes, Biochimica Et Biophysica Acta- Bioenergetics, issue.1, pp.1411-1432, 1999.

M. Wosten, Eubacterial sigma-factors, FEMS Microbiology Reviews, vol.22, issue.3, pp.127-150, 1998.
DOI : 10.1111/j.1574-6976.1998.tb00364.x

S. S. Wu, K. A. Platt, C. Ratnayake, T. W. Wang, J. T. Ting et al., Isolation and characterization of neutral-lipid-containing organelles and globuli-filled plastids from Brassica napus tapetum, Proceedings of the National Academy of Sciences of the United States of America, pp.94-12711, 1997.
DOI : 10.1073/pnas.94.23.12711

J. J. Yang and D. B. Stern, The Spinach Chloroplast Endoribonuclease CSP41 Cleaves the 3'-Untranslated Region of petD mRNA Primarily within Its Terminal Stem-Loop Structure, Journal of Biological Chemistry, vol.272, issue.19, pp.272-12874, 1997.
DOI : 10.1074/jbc.272.19.12874

J. L. Yao, S. Roy-chowdhury, and L. A. Allison, AtSig5 Is an Essential Nucleus-Encoded Arabidopsis ??-Like Factor, PLANT PHYSIOLOGY, vol.132, issue.2, pp.739-747, 2003.
DOI : 10.1104/pp.102.017913

O. Yazgan and J. E. Krebs, Noncoding but nonexpendable: transcriptional regulation by large noncoding RNA in eukaryotesThis paper is one of a selection of papers published in this Special Issue, entitled 28th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process., Biochemistry and Cell Biology, vol.85, issue.4, pp.484-496, 2007.
DOI : 10.1139/O07-061

S. Yehudai-resheff, S. L. Zimmer, Y. Komine, and D. B. Stern, Integration of Chloroplast Nucleic Acid Metabolism into the Phosphate Deprivation Response in Chlamydomonas reinhardtii, THE PLANT CELL ONLINE, vol.19, issue.3, pp.1023-1038, 2007.
DOI : 10.1105/tpc.106.045427

M. Yukawa and M. Sugiura, Termination codon-dependent translation of partially overlapping ndhC-ndhK transcripts in chloroplasts, Proceedings of the National Academy of Sciences, vol.105, issue.49, pp.19550-19554, 2008.
DOI : 10.1073/pnas.0809240105

W. Zghidi, L. Merendino, A. Cottet, R. Mache, and S. Lerbs-mache, Nucleus-encoded plastid sigma factor SIG3 transcribes specifically the psbN gene in plastids, Nucleic Acids Research, vol.35, issue.2, pp.455-464, 2007.
DOI : 10.1093/nar/gkl1067

F. Zito, R. Kuras, Y. Choquet, H. Kossel, and F. A. Wollman, Mutations of cytochrome b(6) in Chlamydomonas reinhardtii disclose the functional significance for a proline to leucine conversion by petB editing in maize and tobacco, Plant Molecular Biology, vol.33, issue.1, pp.79-86, 1997.
DOI : 10.1023/A:1005734809834

R. Zoschke, M. Nakamura, K. Liere, M. Sugiura, T. Borner et al., An organellar maturase associates with multiple group II introns, Proceedings of the National Academy of Sciences, vol.107, issue.7, pp.3245-3250, 2010.
DOI : 10.1073/pnas.0909400107