The dynamics of photosynthesis

Annual Review of Genetics

Volumn 42, Issue , 2008, Pages 463-515

  Eberhard, Stephan ^a   Finazzi, Giovanni ^a   Wollman, Francis André ^a  

^a INST DE BIOLOGIE PHYSICO CHIMIQUE   (France)

Author keywords

Acclimation; Electron transfer; Functional genomics; Intracellular signaling; Light harvesting; Photosynthesis; Proteomics

Indexed keywords

ACCLIMATIZATION; CELL NUCLEUS; CHLOROPLAST; CYTOSOL; ELECTRON TRANSPORT; ENVIRONMENTAL FACTOR; LIGHT ADAPTATION; LIGHT HARVESTING SYSTEM; NONHUMAN; NONPHOTOCHEMICAL QUENCHING; PHOTOSYNTHESIS; PRIORITY JOURNAL; REVIEW; SIGNAL TRANSDUCTION;

ANIMALS; ARABIDOPSIS; BIOPHYSICS; CHLAMYDOMONAS; ELECTRON TRANSPORT; GENE EXPRESSION; MODELS, BIOLOGICAL; PHOTOSYNTHESIS; PHOTOSYNTHETIC REACTION CENTER COMPLEX PROTEINS; REGULON; SIGNAL TRANSDUCTION;

EID: 58749116610     PISSN: 00664197     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.genet.42.110807.091452     Document Type: Review

References (332)

1. Adam Z, Ostersetzer O. 2001. Degradation of unassembled and damaged thylakoid proteins. Biochem. Soc. Trans. 29:427-30
2. Adam Z, Rudella A, van Wijk KJ. 2006. Recent advances in the study of Clp, FtsH and other proteases located in chloroplasts. Curr. Opin. Plant Biol. 9:234-40
3. Albertsson P. 2001. A quantitative model of the domain structure of the photosynthetic membrane. Trends Plant Sci. 6:349-58
4. Allen JF. 1992. Protein phosphorylation in regulation of photosynthesis. Biochim. Biophys. Acta 1098:275-335
5. Allen JF. 2002. Photosynthesis of ATP-electrons, proton pumps, rotors and poise. Cell 110:273-76
6. Aluru MR, Yu F, Fu A, Rodermel S. 2006. Arabidopsis variegation mutants: new insights into chloroplast biogenesis. J. Exp. Bot. 57:1871-81
7. Amme S, Matros A, Schlesier B, Mock HP. 2006. Proteome analysis of cold stress response in Arabidopsis thaliana using DIGE-technology. J. Exp. Bot. 57:1537-46
8. Anderson JM, Chow WS, Park YI. 1995. The grand design of photosynthesis: acclimation of the photosynthetic apparatus to environmental clues. Photosynth. Res. 46:129-39
9. Ang LH, Chattopadhyay S, Wei N, Oyama T, Okada K, et al. 1998. Molecular interaction between COP1 and HY5 defines a regulatory switch for light control of Arabidopsis development. Mol. Cell 1:213-22
10. Antao CM, Malcata FX. 2005. Plant serine proteases: biochemical, physiological and molecular features. Plant Physiol. Biochem. 43:637-50
11. Apel K, Hirt H. 2004. Reactive oxygen species: metabolism, oxidative stress, and signal transduction. Annu. Rev. Plant Biol. 55:373-99
12. Arkin AP, Goldman ER, Robles SJ, Goddard CA, Coleman WJ, et al. 1990. Applications of imaging spectroscopy in molecular biology. II. Colony screening based on absorption spectra. Biotechnology 8:746-49
13. Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, et al. 2004. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science 306:79-86
14. Arnon DI. 1959. Conversion of light into chemical energy in photosynthesis. Nature 184:10-21
15. Aro EM, Suorsa M, Rokka A, Allahverdiyeva Y, Paakkarinen V, et al. 2005. Dynamics of photosystem II: a proteomic approach to thylakoid protein complexes. J. Exp. Bot. 56:347-56
16. Aro EM, Virgin I, Andersson B. 1993. Photoinhibition of Photosystem II. Inactivation, protein damage and turnover. Biochim. Biophys. Acta 1143:113-34
17. Asada K. 1999. The water-water cycle in chloroplasts: scavenging of active oxygens and dissipation of excess photons. Annu. Rev. Plant Physiol. Plant Mol. Biol. 50:601-39
18. Atienza SG, Faccioli P, Perrotta G, Dalfino G, Zschiesche W, et al. 2004. Large scale analysis of transcripts abundance in barley subjected to several single and combined abiotic stress conditions. Plant Sci. 167:1359-65
19. Avenson TJ, Cruz JA, Kanazawa A, Kramer DM. 2005. Regulating the proton budget of higher plant photosynthesis. Proc. Natl. Acad. Sci. USA 102:9709-13
20. Badger M, von Caemmerer S, Ruuska S, Nakano H. 2000. Electron flow to oxygen in higher plants and algae: rates and control of direct photoreduction (Mehler reaction) and rubisco oxygenase. Philos. Trans. R. Soc. London Ser. B 355:1433-46
21. Bailey S, Melis A, Mackey KR, Cardol P, Finazzi G, et al. 2008. Alternative photosynthetic electron flow to oxygen in marine Synechococcus. Biochim. Biophys. Acta. In press
22. Ballottari M, Dall'Osto L, Morosinotto T, Bassi R. 2007. Contrasting behavior of higher plant photosystem I and II antenna systems during acclimation. J. Biol. Chem. 282:8947-58
23. Barber J, Andersson B. 1992. Too much of a good thing: Light can be bad for photosynthesis. Trends Biochem. Sci. 17:61-66
24. Barkan A, Goldschmidt-Clermont M. 2000. Participation of nuclear genes in chloroplast gene expression. Biochimie 82:559-72
25. Barneche F, Winter V, Crevecoeur M, Rochaix JD. 2006. ATAB2 is a novel factor in the signalling pathway of light-controlled synthesis of photosystem proteins. EMBO J. 25:5907-18
26. Barnes D, Mayfield SP. 2003. Redox control of posttranscriptional processes in the chloroplast. Antioxid. Redox Signal. 5:89-94
27. Bar-Nun S, Schantz R, Ohad I. 1977. Appearance and composition of chlorophyll-protein complexes I and II during chloroplast membrane biogenesis in Chlamydomonas reinhardtii y-1. Biochim. Biophys. Acta 459:451-67
28. Beck CF. 2005. Signaling pathways from the chloroplast to the nucleus. Planta 222:743-56
29. Becker B, Holtgrefe S, Jung S, Wunrau C, Kandlbinder A, et al. 2006. Influence of the photoperiod on redox regulation and stress responses in Arabidopsis thaliana L. (Heynh.) plants under long- and short-day conditions. Planta 224:380-93
30. Beligni MV, Yamaguchi K, Mayfield SP. 2004. The translational apparatus of Chlamydomonas reinhardtii chloroplast. Photosynth. Res. 82:315-25
31. Bellafiore S, Barneche F, Peltier G, Rochaix JD. 2005. State transitions and light adaptation require chloroplast thylakoid protein kinase STN7. Nature 433:892-95
32. Bendall DS, Manasse RS. 1995. Cyclic photophosphorylation and electron transport. Biochim. Biophys. Acta 1229:23-38
33. Bennoun P, Delepelaire P. 1982. Isolation of photosynthesis mutants in Chlamydomonas. In Methods in Chloroplast Molecular Biology, ed. M Edelman, N-H Chua, RB Hallick, pp. 25-38. Amsterdam: Elsevier Biomed. Press
34. Bennoun P, Levine RP. 1967. Detecting mutants that have impaired photosynthesis by their increased level of fluorescence. Plant Physiol. 42:1284-87
35. Ben-Shem A, Frolow F, Nelson N. 2004. Evolution of photosystem I - from symmetry through pseudosymmetry to asymmetry. FEBS Lett. 564:274-80
36. Ben-Shem A, Frolow F, Nelson N. 2004. Light-harvesting features revealed by the structure of plant photosystem I. Photosynth. Res. 81:239-50
37. Bergantino E, Dainese P, Cerovic Z, Sechi S, Bassi R. 1995. A post-translational modification of the photosystem II subunit CP29 protects maize from cold stress. J. Biol. Chem. 270:8474-81
38. Bibby TS, Nield J, Barber J. 2001. Iron deficiency induces the formation of an antenna ring around trimeric photosystem I in cyanobacteria. Nature 412:743-45
39. 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 344:33-41
40. Bilger W, Björkman Ö. 1990. Role of the xanthophyll cycle in photoprotection elucidated by measurments of light-induced absorbance changes, fluorescence and photosynthesis in leaves of Hedera canariensis. Photosynth. Res. 25:173-86
41. Blasing OE, Gibon Y, Gunther M, Hohne M, Morcuende R, et al. 2005. Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis. Plant Cell 17:3257-81
42. Boekema EJ, Hifney A, Yakushevska AE, Piotrowski M, Keegstra W, et al. 2001. A giant chlorophyllprotein complex induced by iron deficiency in cyanobacteria. Nature 412:745-48
43. Bollenbach TJ, Schuster G, Stern DB. 2004. Cooperation of endo- and exoribonucleases in chloroplast mRNA turnover. Prog. Nucleic Acid Res. Mol. Biol. 78:305-37
44. Bonardi V, Pesaresi P, Becker T, Schleiff E, Wagner R, et al. 2005. Photosystem II core phosphorylation and photosynthetic acclimation require two different protein kinases. Nature 437:1179-82
45. Bonaventura C, Myers J. 1969. Fluorescence and oxygen evolution from Chlorella pyrenoidosa. Biochim. Biophys. Acta 189:366-83
46. Boyer PD. 1997. The ATP synthase - a splendid molecular machine. Annu. Rev. Biochem. 66:717-49
47. Breyton C, Nandha B, Johnson GN, Joliot P, Finazzi G. 2006. Redox modulation of cyclic electron flow around photosystem I in C3 plants. Biochemistry 45:13465-75
48. Briantais JM, Vernotte C, Picaud M, Krause GH. 1979. A quantitative study of the slow decline of chlorophyll a fluorescence in isolated chloroplasts. Biochim. Biophys. Acta 548:128-38
49. Briat JF, Curie C, Gaymard F. 2007. Iron utilization and metabolism in plants. Curr. Opin. Plant Biol. 10:276-82
50. Buchanan BB, Balmer Y. 2005. Redox regulation: a broadening horizon. Annu. Rev. Plant Biol. 56:187-220
51. Bulte L, Gans P, Rebeille F, Wollman FA. 1990. ATP control on state transitions in vivo in Chlamydomonas reinhardtii. Biochim. Biophys. Acta 1020:72-80
52. Cardol P, Bailleul B, Rappaport F, Derelle E, Béal D, et al. 2008. An original adaptation of photosynthesis in the marine green alga Ostreococcus. Proc. Natl. Acad. Sci. USA 105:7881-86
53. Cardol P, Gloire G, Havaux M, Remacle C, Matagne R, Franck F. 2003. Photosynthesis and state transitions in mitochondrial mutants of Chlamydomonas reinhardtii affected in respiration. Plant Physiol. 133:2010-20
54. Chao DY, Luo YH, Shi M, Luo D, Lin HX. 2005. Salt-responsive genes in rice revealed by cDNA microarray analysis. Cell Res. 15:796-810
55. Chattopadhyay S, Ang LH, Puente P, Deng XW, Wei N. 1998. Arabidopsis bZIP protein HY5 directly interacts with light-responsive promoters in mediating light control of gene expression. Plant Cell 10:673-83
56. Chekounova E, Voronetskaya V, Papenbrock J, Grimm B, Beck CF. 2001. Characterization of Chlamydomonas mutants defective in the H subunit of Mg-chelatase. Mol. Genet. Genomics 266:363-73
57. Chen M, Bibby TS, Nield J, Larkum A, Barber J. 2005. Iron deficiency induces a chlorophyll D-binding Pcb antenna system around Photosystem I in Acaryochloris marina. Biochim. Biophys. Acta 1708:367-74
58. Chen YB, Durnford DG, Koblizek M, Falkowski PG. 2004. Plastid regulation of Lhcb1 transcription in the chlorophyte alga Dunaliella tertiolecta. Plant Physiol. 136:3737-50
59. Choquet Y, Wollman FA. 2002. Translational regulations as specific traits of chloroplast gene expression. FEBS Lett. 529:39-42
60. Christie JM. 2007. Phototropin blue-light receptors. Annu. Rev. Plant Biol. 58:21-45
61. Cohen I, Sapir Y, Shapira M. 2006. A conserved mechanism controls translation of Rubisco large subunit in different photosynthetic organisms. Plant Physiol. 141:1089-97
62. Cramer WA, Zhang H. 2006. Consequences of the structure of the cytochrome b6f complex for its charge transfer pathways. Biochim. Biophys. Acta 1757:339-45
63. Cramer WA, Zhang H, Yan J, Kurisu G, Smith JL. 2006. Transmembrane traffic in the cytochrome b6f complex. Annu. Rev. Biochem. 75:769-90
64. Cruz JA, Avenson TJ, Kanazawa A, Takizawa K, Edwards GE, Kramer DM. 2005. Plasticity in light reactions of photosynthesis for energy production and photoprotection. J. Exp. Bot. 56:395-406
65. Curie C, Briat JF. 2003. Iron transport and signaling in plants. Annu. Rev. Plant Biol. 54:183-206
66. DalCorso G, Pesaresi P, Masiero S, Aseeva E, Schunemann D, et al. 2008. A complex containing PGRL1 and PGR5 is involved in the switch between linear and cyclic electron flow in Arabidopsis. Cell 132:273-85
67. Deisenhofer J, Epp O, Miki K, Huber R, Michel H. 1984. X-ray structure analysis of a membrane protein complex. Electron density map at 3 Å resolution and a model of the chromophores of the photosynthetic reaction center from Rhodopseudomonas viridis. J. Mol. Biol. 180:385-98
68. Depege N, Bellafiore S, Rochaix JD. 2003. Role of chloroplast protein kinase Stt7 in LHCII phosphorylation and state transition in Chlamydomonas. Science 299:1572-75
69. Desikan R, S AH-M, Hancock JT, Neill SJ. 2001. Regulation of the Arabidopsis transcriptome by oxidative stress. Plant Physiol. 127:159-72
70. Drozak A, Romanowska E. 2006. Acclimation of mesophyll and bundle sheath chloroplasts of maize to different irradiances during growth. Biochim. Biophys. Acta 1757:1539-46
71. Duhring U, Irrgang KD, Lunser K, Kehr J, Wilde A. 2006. Analysis of photosynthetic complexes from a cyanobacterial ycf37 mutant. Biochim. Biophys. Acta 1757:3-11
72. Durnford DG, Price JA, McKim SM, Sarchfield ML. 2003. Light-harvesting complex gene expression is controlled by both transcriptional and post-transcriptionalPosttranscriptional mechanisms during photoacclimation in Chlamydomonas reinhardtii. Physiol. Plant 118:193-205
73. Dutilleul C, Driscoll S, Cornic G, De Paepe R, Foyer CH, Noctor G. 2003. Functional mitochondrial complex I is required by tobacco leaves for optimal photosynthetic performance in photorespiratory conditions and during transients. Plant Physiol. 131:264-75
74. Edwards GE, Walker DA. 1983. C3, C4: Mechanisms, and Cellular and Environmental Regulation of Photosynthesis. Textbook on C3, C4 Photosynthesis. Oxford: Blackwell Sci.
75. Escoubas JM, Lomas M, LaRoche J, Falkowski PG. 1995. Light intensity regulation of cab gene transcription is signaled by the redox state of the plastoquinone pool. Proc. Natl. Acad. Sci. USA 92:10237-41
76. Faccioli P, Provero P, Herrmann C, Stanca AM, Morcia C, Terzi V. 2005. From single genes to coexpression networks: extracting knowledge from barley functional genomics. Plant Mol. Biol. 58:739-50
77. Falkowski PG, Owens TG. 1980. Light-shade adaptation: two strategies in marine phytoplankton. Plant Physiol. 66:592-95
78. Ferreira S, Hjerno K, Larsen M, Wingsle G, Larsen P, et al. 2006. Proteome profiling of Populus euphratica Oliv. upon heat stress. Ann. Bot. 98:361-77
79. Fey V, Wagner R, Brautigam K, Pfannschmidt T. 2005. Photosynthetic redox control of nuclear gene expression. J. Exp. Bot. 56:1491-98
80. Finazzi G, Forti G. 2004. Metabolic flexibility of the green alga Chlamydomonas reinhardtii as revealed by the link between state transitions and cyclic electron flow. Photosynth. Res. 82:327-38
81. Fischer BB, Wiesendanger M, Eggen RI. 2006. Growth condition-dependent sensitivity, photodamage and stress response of Chlamydomonas reinhardtii exposed to high light conditions. Plant Cell Physiol. 47:1135-45
82. Forti G, Caldiroli G. 2005. State transitions in Chlamydomonas reinhardtii. The role of the Mehler reaction in state 2-to-state 1 transition. Plant Physiol. 137:492-99
83. Forti G, Elli G. 1995. The function of ascorbic acid in photosynthetic phosphorylation. Plant Physiol. 109:1207-11
84. Frank HA, Cogdell RJ. 1996. Carotenoids in photosynthesis. Photochem. Photobiol. 63:257-64
85. Frenkel M, Bellafiore S, Rochaix JD, Jansson S. 2007. Hierarchy amongst photosynthetic acclimation responses for plant fitness. Physiol. Plant 129:455-59
86. Frigerio S, Campoli C, Zorzan S, Fantoni LI, Crosatti C, et al. 2007. Photosynthetic antenna size in higher plants is controlled by the plastoquinone redox state at the post-transcriptionalPosttranscriptional rather than transcriptional level. J. Biol. Chem. 282:29457-69
87. Gadjev I, Vanderauwera S, Gechev TS, Laloi C, Minkov IN, et al. 2006. Transcriptomic footprints disclose specificity of reactive oxygen species signaling in Arabidopsis. Plant Physiol. 141:436-45
88. Geigenberger P, Kolbe A, Tiessen A. 2005. Redox regulation of carbon storage and partitioning in response to light and sugars. J. Exp. Bot. 56:1469-79
89. Genoud T, Millar AJ, Nishizawa N, Kay SA, Schafer E, et al. 1998. An Arabidopsis mutant hypersensitive to red and far-red light signals. Plant Cell 10:889-904
90. Genty B, Harbinson J, Briantais JM, Baker NR. 1990. The relationship between nonphotochemical quenching of chlorophyll fluorescence and the rates of photosystem 2 photochemistry in leaves. Photosynth. Res. 25:249-57
91. Ghassemian M, Lutes J, Tepperman JM, Chang HS, Zhu T, et al. 2006. Integrative analysis of transcript and metabolite profiling data sets to evaluate the regulation of biochemical pathways during photomorphogenesis. Arch. Biochem. Biophys. 448:45-59
92. Giacomelli L, Rudella A, van Wijk KJ. 2006. High light response of the thylakoid proteome in Arabidopsis wild type and the ascorbate-deficient mutant vtc2-2. A comparative proteomics study. Plant Physiol. 141:685-701
93. Gilmore AM, Hazlett TL, Govindjee. 1995. Xanthophyll cycle-dependent quenching of photosystem II chlorophyll a fluorescence: formation of a quenching complex with a short fluorescence lifetime. Proc. Natl. Acad. Sci. USA 92:2273-77
94. Golding AJ, Finazzi G, Johnson GN. 2004. Reduction of the thylakoid electron transport chain by stromal reductants - evidence for activation of cyclic electron transport upon dark adaptation or under drought. Planta 220:356-63
95. Goulas E, Schubert M, Kieselbach T, Kleczkowski LA, Gardestrom P, et al. 2006. The chloroplast lumen and stromal proteomes of Arabidopsis thaliana show differential sensitivity to short- and long-term exposure to low temperature. Plant J. 47:720-34
96. Gray JC, Sullivan JA, Wang JH, Jerome CA, MacLean D. 2003. Coordination of plastid and nuclear gene expression. Philos. Trans. R. Soc. London Ser. B 358:135-44; discussion 144-45
97. Guikema JA, Sherman LA. 1983. Chlorophyll-protein organization of membranes from the cyanobacterium Anacystis nidulans. Arch. Biochem. Biophys. 220:155-66
98. Guikema JA, Sherman LA. 1984. Influence of iron deprivation on the membrane composition of Anacystis nidulans. Plant Physiol. 74:90-95
99. Hajheidari M, Abdollahian-Noghabi M, Askari H, Heidari M, Sadeghian SY, et al. 2005. Proteome analysis of sugar beet leaves under drought stress. Proteomics 5:950-60
100. +-dependent ferredoxin oxidoreductase lead to impaired plant growth and restrict photosynthetic activity of transgenic tobacco plants. Plant J. 29:281-93
101. Hald S, Nandha B, Gallois P, Johnson GN. 2008. Feedback regulation of photosynthetic electron transport by NADP(H) redox poise. Biochim. Biophys. Acta. In press
102. Harmer SL, Hogenesch JB, Straume M, Chang HS, Han B, et al. 2000. Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290:2110-13
103. Hassidim M, Yakir E, Fradkin D, Hilman D, Kron I, et al. 2007. Mutations in chloroplast RNA binding provide evidence for the involvement of the chloroplast in the regulation of the circadian clock in Arabidopsis. Plant J. 51:551-62
104. Hayes R, Kudla J, Gruissem W. 1999. Degrading chloroplast mRNA: the role of polyadenylation. Trends Biochem. Sci. 24:199-202
105. Heber U, Walker D. 1992. Concerning a dual function of coupled cyclic electron transport in leaves. Plant Physiol. 100:1621-26
106. Hill R, Bendall F. 1960. Function of the two cytochrome components in chloroplasts: a working hypothesis. Nature 186:136-37
107. Holm M, Ma LG, Qu LJ, Deng XW. 2002. Two interacting bZIP proteins are direct targets of COP1-mediated control of light-dependent gene expression in Arabidopsis. Genes Dev. 16:1247-59
108. Holt NE, Fleming GR, Niyogi KK. 2004. Toward an understanding of the mechanism of nonphotochemical quenching in green plants. Biochemistry 43:8281-89
109. Holt NE, Zigmantas D, Valkunas L, Li XP, Niyogi KK, Fleming GR. 2005. Carotenoid cation formation and the regulation of photosynthetic light harvesting. Science 307:433-36
110. Hope AB. 1993. The chloroplast cytochrome bf complex: a critical focus on function. Biochim. Biophys. Acta 1143:1-22
111. Horton P, Ruban A. 2005. Molecular design of the photosystem II light-harvesting antenna: photosynthesis and photoprotection. J. Exp. Bot. 56:365-73
112. Horton P, Ruban AV, Walters RG. 1996. Regulation of light harvesting in green plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 47:655-84
113. Ihalainen JA, D'Haene S, Yeremenko N, van Roon H, Arteni AA, et al. 2005. Aggregates of the chlorophyll-binding protein IsiA (CP43′) dissipate energy in cyanobacteria. Biochemistry 44:10846-53
114. Im CS, Eberhard S, Huang K, Beck CF, Grossman AR. 2006. Phototropin involvement in the expression of genes encoding chlorophyll and carotenoid biosynthesis enzymes and LHC apoproteins in Chlamydomonas reinhardtii. Plant J. 48:1-16
115. Im CS, Grossman AR. 2001. Identification and regulation of high light-induced genes in Chlamydomonas reinhardtii. Plant J. 30:301-13
116. 2 regulation in Chlamydomonas reinhardtii using genome-wide approaches. Photosynth. Res. 75:111-25
117. Ingle RA, Schmidt UG, Farrant JM, Thomson JA, Mundree SG. 2007. Proteomic analysis of leaf proteins during dehydration of the resurrection plant Xerophyta viscosa. Plant Cell Environ. 30:435-46
118. Irihimovitch V, Shapira M. 2000. Glutathione redox potential modulated by reactive oxygen species regulates translation of Rubisco large subunit in the chloroplast. J. Biol. Chem. 275:16289-95
119. Ivanov AG, Krol M, Sveshnikov D, Selstam E, Sandstrom S, et al. 2006. Iron deficiency in cyanobacteria causes monomerization of photosystem I trimers and reduces the capacity for state transitions and the effective absorption cross section of photosystem I in vivo. Plant Physiol. 141:1436-45
120. Jackowski G, Olkiewicz P, Zelisko A. 2003. The acclimative response of the main light-harvesting chlorophyll a/b-protein complex of photosystem II (LHCII) to elevated irradiances at the level of trimeric subunits. J. Photochem. Photobiol. B 70:163-70
121. Jansson S. 1999. A guide to the Lhc genes and their relatives in Arabidopsis/IT. Trends Plant Sci. 4:236-40
122. Jiao Y, Lau OS, Deng XW. 2007. Light-regulated transcriptional networks in higher plants. Nat. Rev. Genet. 8:217-30
123. Jiao Y, Ma L, Strickland E, Deng XW. 2005. Conservation and divergence of light-regulated genome expression patterns during seedling development in rice and Arabidopsis. Plant Cell 17:3239-56
124. Jiao Y, Yang H, Ma L, Sun N, Yu H, et al. 2003. A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development. Plant Physiol. 133:1480-93
125. Johanningmeier U. 1988. Possible control of transcript levels by chlorophyll precursors in Chlamydomonas. Eur. J. Biochem. 177:417-24
126. Johanningmeier U, Howell SH. 1984. Regulation of light-harvesting chlorophyll-binding protein mRNA accumulation in Chlamydomonas reinhardtii. Possible involvement of chlorophyll synthesis precursors. J. Biol. Chem. 259:13541-49
127. John Andrews T, Whitney SM. 2003. Manipulating ribulose bisphosphate carboxylase/oxygenase in the chloroplasts of higher plants. Arch. Biochem. Biophys. 414:159-69
128. Johnson GN. 2003. Thiol regulation of the thylakoid electron transport chain - a missing link in the regulation of photosynthesis? Biochemistry 42:3040-44
129. Johnson GN. 2005. Cyclic electron transport in C3 plants: fact or artefact? J. Exp. Bot. 56:407-16
130. Joliot P, Beal D, Joliot A. 2004. Cyclic electron flow under saturating excitation of dark-adapted Arabidopsis leaves. Biochim. Biophys. Acta 1656:166-76
131. Joliot P, Joliot A. 2002. Cyclic electron transfer in plant leaf. Proc. Natl. Acad. Sci. USA 99:10209-14
132. Joliot P, Joliot A. 2006. Cyclic electron flow in C3 plants. Biochim. Biophys. Acta 1757:362-68
133. Kawasaki S, Borchert C, Deyholos M, Wang H, Brazille S, et al. 2001. Gene expression profiles during the initial phase of salt stress in rice. Plant Cell 13:889-905
134. Keren N, Berg A, van Kan PJ, Levanon H, Ohad II. 1997. Mechanism of photosystem II photoinactivation and D1 protein degradation at low light: the role of back electron flow. Proc. Natl. Acad. Sci. USA 94:1579-84
135. Kern J, Biesiadka J, Loll B, Saenger W, Zouni A. 2007. Structure of the Mn4-Ca cluster as derived from X-ray diffraction. Photosynth. Res. 92:389-405
136. Khan MS. 2007. Engineering photorespiration in chloroplasts: a novel strategy for increasing biomass production. Trends Biotechnol. 25:437-40
137. Kim J, Mayfield SP. 2002. The active site of the thioredoxin-like domain of chloroplast protein disulfide isomerase, RB60, catalyzes the redox-regulated binding of chloroplast poly(A)-binding protein, RB47, to the 5′ untranslated region of psbA mRNA. Plant Cell Physiol. 43:1238-43
138. Kimura M, Yamamoto YY, Seki M, Sakurai T, Sato M, et al. 2003. Identification of Arabidopsis genes regulated by high light-stress using cDNA microarray. Photochem. Photobiol. 77:226-33
139. Kiss AZ, Ruban AV, Horton P. 2008. The PsbS protein controls the organization of the photosystem II antenna in higher plant thylakoid membranes. J. Biol. Chem. 283:3972-78
140. Klaff P, Gruissem W. 1991. Changes in chloroplast mRNA stability during leaf development. Plant Cell 3:517-29
141. Kleffmann T, von Zychlinski A, Russenberger D, Hirsch-Hoffmann M, Gehrig P, et al. 2007. Proteome dynamics during plastid differentiation in rice. Plant Physiol. 143:912-23
142. Klimmek F, Sjodin A, Noutsos C, Leister D, Jansson S. 2006. Abundantly and rarely expressed Lhc protein genes exhibit distinct regulation patterns in plants. Plant Physiol. 140:793-804
143. Koornneef M, Rolff E, Spruit CJP. 1980. Genetic control of light inhibited hypocotyl elongation in Arabidopsis thaliana (L.). Planzenphysiologie 100:147-60
144. Kotera E, Tasaka M, Shikanai T. 2005. A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts. Nature 433:326-30
145. Koussevitzky S, Nott A, Mockler TC, Hong F, Sachetto-Martins G, et al. 2007. Signals from chloroplasts converge to regulate nuclear gene expression. Science 316:715-19
146. Kramer DM, Avenson TJ, Edwards GE. 2004. Dynamic flexibility in the light reactions of photosynthesis governed by both electron and proton transfer reactions. Trends Plant Sci. 9:349-57
147. Kropat J, Oster U, Rudiger W, Beck CF. 1997. Chlorophyll precursors are signals of chloroplast origin involved in light induction of nuclear heat-shock genes. Proc. Natl. Acad. Sci. USA 94:14168-72
148. Kropat J, Oster U, Rudiger W, Beck CF. 2000. Chloroplast signalling in the light induction of nuclear HSP70 genes requires the accumulation of chlorophyll precursors and their accessibility to cytoplasm/nucleus. Plant J. 24:523-31
149. Kulheim C, Agren J, Jansson S. 2002. Rapid regulation of light harvesting and plant fitness in the field. Science 297:91-93
150. Kurisu G, Zhang H, Smith JL, Cramer WA. 2003. Structure of the cytochrome b6f complex of oxygenic photosynthesis: tuning the cavity. Science 302:1009-14
151. Kurth J, Varotto C, Pesaresi P, Biehl A, Richly E, et al. 2002. Gene-sequence-tag expression analyses of 1,800 genes related to chloroplast functions. Planta 215:101-9
152. Laisk A, Eichelmann H, Oja V, Peterson RB. 2005. Control of cytochrome b6f at low and high light intensity and cyclic electron transport in leaves. Biochim. Biophys. Acta 1708:79-90
153. Laisk A, Eichelmann H, Oja V, Talts E, Scheibe R. 2007. Rates and roles of cyclic and alternative electron flow in potato leaves. Plant Cell Physiol. 48:1575-88
154. Laisk A, Oja V. 2000. Alteration of photosystem II properties with nonphotochemical excitation quenching. Philos. Trans. R. Soc. London Ser. B 355:1405-18
155. Laloi C, Przybyla D, Apel K. 2006. A genetic approach toward elucidating the biological activity of different reactive oxygen species in Arabidopsis thaliana. J. Exp. Bot. 57:1719-24
156. Larbi A, Abadia A, Abadia J, Morales F. 2006. Down coregulation of light absorption, photochemistry, and carboxylation in Fe-deficient plants growing in different environments. Photosynth. Res. 89:113-26
157. Lavergne J, Joliot P. 1991. Restricted diffusion in photosynthetic membranes. Trends Biochem. Sci. 16:129-34
158. Lax JE, Arteni AA, Boekema EJ, Pistorius EK, Michel KP, Rogner M. 2007. Structural response of Photosystem 2 to iron deficiency: characterization of a new photosystem 2-IdiA complex from the cyanobacterium Thermosynechococcus elongatus BP-1. Biochim. Biophys. Acta 1767:528-34
159. Lee J, He K, Stolc V, Lee H, Figueroa P, et al. 2007. Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development. Plant Cell 19:731-49
160. Lee KP, Kim C, Landgraf F, Apel K. 2007. EXECUTER1- and EXECUTER2-dependent transfer of stress-related signals from the plastid to the nucleus of Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 104:10270-75
161. Leister D. 2005. Genomics-based dissection of the cross-talk of chloroplasts with the nucleus and mitochondria in Arabidopsis. Gene 354:110-16
162. Lemaire C, Wollman FA, Bennoun P. 1988. Restoration of phototrophic growth in a mutant of Chlamydomonas reinhardtii in which the chloroplast atpB gene of the ATP synthase has a deletion: an example of mitochondria- dependent photosynthesis. Proc. Natl. Acad. Sci. USA 85:1344-48
163. Leonhardt K, Straus NA. 1992. An iron stress operon involved in photosynthetic electron transport in the marine cyanobacterium Synechococcus sp. PCC 7002. J. Gen. Microbiol. 138:1613-21
164. Li XP, Björkman O, Shih C, Grossman AR, Rosenquist M, et al. 2000. A pigment-binding protein essential for regulation of photosynthetic light harvesting. Nature 403:391-95
165. Li XP, Gilmore AM, Caffarri S, Bassi R, Golan T, et al. 2004. Regulation of photosynthetic light harvesting involves intrathylakoid lumen pH sensing by the PsbS protein. J. Biol. Chem. 279:22866-74
166. Li XP, Muller-Moule P, Gilmore AM, Niyogi KK. 2002. PsbS-dependent enhancement of feedback de-excitation protects photosystem II from photoinhibition. Proc. Natl. Acad. Sci. USA 99:15222-27
167. Lian X, Wang S, Zhang J, Feng Q, Zhang L, et al. 2006. Expression profiles of 10,422 genes at early stage of low nitrogen stress in rice assayed using a cDNA microarray. Plant Mol. Biol. 60:617-31
168. Lin C, Shalitin D. 2003. Cryptochrome structure and signal transduction. Annu. Rev. Plant Biol. 54:469-96
169. Lohr M, Im CS, Grossman AR. 2005. Genome-based examination of chlorophyll and carotenoid biosynthesis in Chlamydomonas reinhardtii. Plant Physiol. 138:490-515
170. Loza-Tavera H, Vargas-Suarez M, Diaz-Mireles E, Torres-Marquez ME, Gonzalez de la Vara LE, et al. 2006. Phosphorylation of the spinach chloroplast 24 kDa RNA-binding protein (24RNP) increases its binding to petD and psbA 3′ untranslated regions. Biochimie 88:1217-28
171. Lunde C, Jensen PE, Haldrup A, Knoetzel J, Scheller HV. 2000. The PSI-H subunit of photosystem I is essential for state transitions in plant photosynthesis. Nature 408:613-15
172. Lunde C, Jensen PE, Rosgaard L, Haldrup A, Gilpin MJ, Scheller HV. 2003. Plants impaired in state transitions can to a large degree compensate for their defect. Plant Cell Physiol. 44:44-54
173. Ma L, Chen C, Liu X, Jiao Y, Su N, et al. 2005. A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Res. 15:1274-83
174. Ma L, Gao Y, Qu L, Chen Z, Li J, et al. 2002. Genomic evidence for COP1 as a repressor of light-regulated gene expression and development in Arabidopsis. Plant Cell 14:2383-98
175. Ma L, Li J, Qu L, Hager J, Chen Z, et al. 2001. Light control of Arabidopsis development entails coordinated regulation of genome expression and cellular pathways. Plant Cell 13:2589-607
176. Manuell A, Beligni MV, Yamaguchi K, Mayfield SP. 2004. Regulation of chloroplast translation: interactions of RNA elements, RNA-binding proteins and the plastid ribosome. Biochem. Soc. Trans. 32:601-5
177. Masuda T, Tanaka A, Melis A. 2003. Chlorophyll antenna size adjustments by irradiance in Dunaliella salina involve coordinate regulation of chlorophyll a oxygenase (CAO) and Lhcb gene expression. Plant Mol. Biol. 51:757-71
178. 2-insensitive mutants of the green alga Chlorella ellipsoidea). Plant Physiol. 110:1283-91
179. McKim SM, Durnford DG. 2006. Translational regulation of light-harvesting complex expression during photoacclimation to high-light in Chlamydomonas reinhardtii. Plant Physiol. Biochem. 44:857-65
180. Melis A. 1991. Dynamics of photosynthetic membrane composition and function. Biochim. Biophys. Acta 1058:87-106
181. Merchant SS, Allen MD, Kropat J, Moseley JL, Long JC, et al. 2006. Between a rock and a hard place: trace element nutrition in Chlamydomonas. Biochim. Biophys. Acta 1763:578-94
182. Meskauskiene R, Nater M, Goslings D, Kessler F, op den Camp R, Apel K. 2001. FLU: a negative regulator of chlorophyll biosynthesis in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 98:12826-31
183. Meyer Zu Tittingdorf JM, Rexroth S, Schafer E, Schlichting R, Giersch C, et al. 2004. The stoichiometry of the chloroplast ATP synthase oligomer III in Chlamydomonas reinhardtii is not affected by the metabolic state. Biochim. Biophys. Acta 1659:92-99
184. Michel KP, Pistorius EK. 2004. Adaptation of the photosynthetic electron transport chain in cyanobacteria to iron deficiency: the function of IdiA and IsiA. Physiol. Plant 120:36-50
185. Miles D. 1979. Mutants of higher plants: maize. Methods Enzymol. 69:3-23
186. Miqyass M, van Gorkom HJ, Yocum CF. 2007. The PSII calcium site revisited. Photosynth. Res. 92:275-87
187. Mittler R, Vanderauwera S, Gollery M, Van Breusegem F. 2004. Reactive oxygen gene network of plants. Trends Plant Sci. 9:490-98
188. Miyake C, Asada K. 1992. Thylakoid-bound ascorbate peroxidase in spinach chloroplasts and photoreduction of its primary oxidation product monodehydroascorbate radical in thylakoids. Plant Cell Physiol. 33:541-53
189. 2 in the water-water cycle in watermelon leaves and enhancement of the rate by limitation of photosynthesis. Plant Cell Physiol. 41:335-43
190. Moller IM, Jensen PE, Hansson A. 2007. Oxidative modifications to cellular components in plants. Annu. Rev. Plant Biol. 58:459-81
191. Mori H, Cline K. 2002. A twin arginine signal peptide and the pH gradient trigger reversible assembly of the thylakoid [Delta]pH/Tat translocase. J. Cell Biol. 157:205-10
192. Moseley JL, Allinger T, Herzog S, Hoerth P, Wehinger E, et al. 2002. Adaptation to Fe-deficiency requires remodeling of the photosynthetic apparatus. EMBO J. 21:6709-20
193. Moseley JL, Chang CW, Grossman AR. 2006. Genome-based approaches to understanding phosphorus deprivation responses and PSR1 control in Chlamydomonas reinhardtii. Eukaryot. Cell 5:26-44
194. Moseley JL, Page MD, Alder NP, Eriksson M, Quinn J, et al. 2002. Reciprocal expression of two candidate di-iron enzymes affecting photosystem I and light-harvesting complex accumulation. Plant Cell 14:673-88
195. Müller R, Morant M, Jarmer H, Nilsson L, Nielsen TH. 2007. Genome-wide analysis of the Arabidopsis leaf transcriptome reveals interaction of phosphate and sugar metabolism. Plant Physiol. 143:156-71
196. Munekage Y, Hashimoto M, Miyake C, Tomizawa K, Endo T, et al. 2004. Cyclic electron flow around photosystem I is essential for photosynthesis. Nature 429:579-82
197. Munekage Y, Hojo M, Meurer J, Endo T, Tasaka M, Shikanai T. 2002. PGR5 is involved in cyclic electron flow around photosystem I and is essential for photoprotection in Arabidopsis. Cell 110:361-71
198. Murata N. 1969. Control of excitation transfer in photosynthesis. I. Light-induced change of chlorophyll a fluorescence in Porphyridium cruentum. Biochim. Biophys. Acta 172:242-51
199. Murchie EH, Hubbart S, Peng S, Horton P. 2005. Acclimation of photosynthesis to high irradiance in rice: gene expression and interactions with leaf development. J. Exp. Bot. 56:449-60
200. Mussgnug JH, Wobbe L, Elles I, Claus C, Hamilton M, et al. 2005. NAB1 is an RNA binding protein involved in the light-regulated differential expression of the light-harvesting antenna of Chlamydomonas reinhardtii. Plant Cell 17:3409-21
201. Nagy F, Schafer E. 2002. Phytochromes control photomorphogenesis by differentially regulated, interacting signaling pathways in higher plants. Annu. Rev. Plant Biol. 53:329-55
202. Nandha B, Finazzi G, Joliot P, Hald S, Johnson GN. 2007. The role of PGR5 in the redox poising of photosynthetic electron transport. Biochim. Biophys. Acta 1767:1252-59
203. Naumann B, Busch A, Allmer J, Ostendorf E, Zeller M, et al. 2007. Comparative quantitative proteomics to investigate the remodeling of bioenergetic pathways under iron deficiency in Chlamydomonas reinhardtii. Proteomics 7:3964-79
204. Naumann B, Stauber EJ, Busch A, Sommer F, Hippler M. 2005. N-terminal processing of Lhca3 Is a key step in remodeling of the photosystem I-light-harvesting complex under iron deficiency in Chlamydomonas reinhardtii. J. Biol. Chem. 280:20431-41
205. Nelson N, Ben-Shem A. 2004. The complex architecture of oxygenic photosynthesis. Nat. Rev. Mol. Cell Biol. 5:971-82
206. Nevo R, Charuvi D, Shimoni E, Schwarz R, Kaplan A, et al. 2007. Thylakoid membrane perforations and connectivity enable intracellular traffic in cyanobacteria. EMBO J. 26:1467-73
207. Nilsson A, Stys D, Drakenberg T, Spangfort MD, Forsen S, Allen JF. 1997. Phosphorylation controls the three-dimensional structure of plant light-harvesting complex II. J. Biol. Chem. 272:18350-57
208. Niyogi KK. 1999. Photoprotection revisited: genetic and molecular approaches. Annu. Rev. Plant Physiol. Plant Mol. Biol. 50:333-59
209. Niyogi KK, Björkman O, Grossman AR. 1997. Chlamydomonas xanthophyll cycle mutants identified by video imaging of chlorophyll fluorescence quenching. Plant Cell 9:1369-80
210. Niyogi KK, Li XP, Rosenberg V, Jung HS. 2005. Is PsbS the site of nonphotochemical quenching in photosynthesis? J. Exp. Bot. 56:375-82
211. Noctor G, De Paepe R, Foyer CH. 2007. Mitochondrial redox biology and homeostasis in plants. Trends Plant Sci. 12:125-34
212. Noctor G, Dutilleul C, De Paepe R, Foyer CH. 2004. Use of mitochondrial electron transport mutants to evaluate the effects of redox state on photosynthesis, stress tolerance and the integration of carbon/nitrogen metabolism. J. Exp. Bot. 55:49-57
213. Nott A, Jung HS, Koussevitzky S, Chory J. 2006. Plastid-to-nucleus retrograde signaling. Annu. Rev. Plant Biol. 57:739-59
214. Oelmuller R, Kendrick RE, Briggs WR. 1989. Blue-light mediated accumulation of nuclear-encoded transcripts coding for proteins of the thylakoid membrane is absent in the phytochrome-deficient aurea mutant of tomato. Plant Mol. Biol. 13:223-32
215. Ohgishi M, Saji K, Okada K, Sakai T. 2004. Functional analysis of each blue light receptor, cry1, cry2, phot1, and phot2, by using combinatorial multiple mutants in Arabidopsis. Proc. Natl. Acad. Sci. USA 101:2223-28
216. Oikawa K, Kasahara M, Kiyosue T, Kagawa T, Suetsugu N, et al. 2003. Chloroplast unusual positioning1 is essential for proper chloroplast positioning. Plant Cell 15:2805-15
217. Oono Y, Seki M, Nanjo T, Narusaka M, Fujita M, et al. 2003. Monitoring expression profiles of Arabidopsis gene expression during rehydration process after dehydration using ca 7000 full-length cDNA microarray. Plant J. 34:868-87
218. Oquist G, Huner NP. 2003. Photosynthesis of overwintering evergreen plants. Annu. Rev. Plant Biol. 54:329-55
219. 2 as an alternative electron sink in photosynthesis? Curr. Opin. Plant Biol. 5:193-98
220. Osmond CB, Forster B. 2006. Photoinhibition: then and now. In Photoprotection, Photoinhibition, Gene Regulation and Environment, ed. B Demmig-Adams, W Adams, AK Mattoo, pp. 11-22. Dordrecht, Neth.: Springer
221. Osterlund MT, Hardtke CS, Wei N, Deng XW. 2000. Targeted destabilization of HY5 during light-regulated development of Arabidopsis. Nature 405:462-66
222. Osterlund MT, Wei N, Deng XW. 2000. The roles of photoreceptor systems and the COP1-targeted destabilization of HY5 in light control of Arabidopsis seedling development. Plant Physiol. 124:1520-24
223. Osuna D, Usadel B, Morcuende R, Gibon Y, Blasing OE, et al. 2007. Temporal responses of transcripts, enzyme activities and metabolites after adding sucrose to carbon-deprived Arabidopsis seedlings. Plant J. 49:463-91
224. Oyama T, Shimura Y, Okada K. 1997. The Arabidopsis HY5 gene encodes a bZIP protein that regulates stimulus-induced development of root and hypocotyl. Genes Dev. 11:2983-95
225. Ozturk NZ, Talame V, Deyholos M, Michalowski CB, Galbraith DW, et al. 2002. Monitoring large-scale changes in transcript abundance in drought- and salt-stressed barley. Plant Mol. Biol. 48:551-73
226. Pascal AA, Liu Z, Broess K, van Oort B, van Amerongen H, et al. 2005. Molecular basis of photoprotection and control of photosynthetic light-harvesting. Nature 436:134-37
227. Peltier G, Cournac L. 2002. Chlororespiration. Annu. Rev. Plant Biol. 53:523-50
228. Pesaresi P, Masiero S, Eubel H, Braun HP, Bhushan S, et al. 2006. Nuclear photosynthetic gene expression is synergistically modulated by rates of protein synthesis in chloroplasts and mitochondria. Plant Cell 18:970-91
229. Pesaresi P, Schneider A, Kleine T, Leister D. 2007. Interorganellar communication. Curr. Opin. Plant Biol. 10:600-6
230. Petracek ME, Dickey LF, Huber SC, Thompson WF. 1997. Light-regulated changes in abundance and polyribosome association of ferredoxin mRNA are dependent on photosynthesis. Plant Cell 9:2291-300
231. Petrouleas V, Koulougliotis D, Ioannidis N. 2005. Trapping of metalloradical intermediates of the Sstates at liquid helium temperatures. Overview of the phenomenology and mechanistic implications. Biochemistry 44:6723-28
232. Pfannschmidt T. 2003. Chloroplast redox signals: How photosynthesis controls its own genes. Trends Plant Sci. 8:33-41
233. Pfundel EE, Dilley RA. 1993. The pH dependence of violaxanthin deepoxidation in isolated pea chloroplasts. Plant Physiol. 101:65-71
234. Piippo M, Allahverdiyeva Y, Paakkarinen V, Suoranta UM, Battchikova N, Aro EM. 2006. Chloroplast-mediated regulation of nuclear genes in Arabidopsis thaliana in the absence of light stress. Physiol. Genomics 25:142-52
235. Plucken H, Muller B, Grohmann D, Westhoff P, Eichacker LA. 2002. The HCF136 protein is essential for assembly of the photosystem II reaction center in Arabidopsis thaliana. FEBS Lett. 532:85-90
236. Pogson BJ, Rissler HM. 2000. Genetic manipulation of carotenoid biosynthesis and photoprotection. Philos. Trans. R. Soc. London Ser. B 355:1395-403
237. Polivka T, Herek JL, Zigmantas D, Akerlund HE, Sundstrom V. 1999. Direct observation of the (forbidden) S1 state in carotenoids. Proc. Natl. Acad. Sci. USA 96:4914-17
238. Raines CA. 2006. Transgenic approaches to manipulate the environmental responses of the C3 carbon fixation cycle. Plant Cell Environ. 29:331-39
239. Rappaport F, Diner BA, Redding K. 2006. Optical measurments of secondary electron transfer in photosystem I. In Photosystem I: The Light-Driven Plastocyanin: Ferredoxin Oxydoreductase. Advances in Photosynthesis and Respiration, ed. JH Goldbeck, pp. 223-44. Dordrecht: Springer
240. Raynaud C, Loiselay C, Wostrikoff K, Kuras R, Girard-Bascou J, et al. 2007. Evidence for regulatory function of nucleus-encoded factors on mRNA stabilization and translation in the chloroplast. Proc. Natl. Acad. Sci. USA 104:9093-98
241. Rebeille F, Gans P. 1988. Interaction between chloroplasts and mitochondria in microalgae: role of glycolysis. Plant Physiol. 88:973-75
242. Redding K, vand der Est A. 2006. The directionality of electron transport in photosystem I. In Photosystem I: The Light-Driven Plastocyanin: Ferredoxin Oxidoreductase. Advances in Photosynthesis and Respiration, ed. JH Goldbeck, pp. 413-37. Dordrecht: Springer
243. Reed JW, Nagpal P, Poole DS, Furuya M, Chory J. 1993. Mutations in the gene for the red/far-red light receptor phytochrome B alter cell elongation and physiological responses throughout Arabidopsis development. Plant Cell 5:147-57
244. Remacle C, Matagne RF. 1993. Transmission, recombination and conversion of mitochondrial markers in relation to the mobility of a group I intron in Chlamydomonas. Curr. Genet. 23:518-25
245. Richly E, Dietzmann A, Biehl A, Kurth J, Laloi C, et al. 2003. Covariations in the nuclear chloroplast transcriptome reveal a regulatory master-switch. EMBO Rep. 4:491-98
246. Rintamaki E, Martinsuo P, Pursiheimo S, Aro EM. 2000. Cooperative regulation of light-harvesting complex II phosphorylation via the plastoquinol and ferredoxin-thioredoxin system in chloroplasts. Proc. Natl. Acad. Sci. USA 97:11644-49
247. Rizhsky L, Liang H, Mittler R. 2003. The water-water cycle is essential for chloroplast protection in the absence of stress. J. Biol. Chem. 278:38921-25
248. Rochaix J, Fischer N, Hippler M. 2000. Chloroplast site-directed mutagenesis of photosystem I in Chlamydomonas: electron transfer reactions and light sensitivity. Biochimie 82:635-45
249. Rochaix JD. 2004. Genetics of the biogenesis and dynamics of the photosynthetic machinery in eukaryotes. Plant Cell 16:1650-60
250. Rochaix JD. 2007. Role of thylakoid protein kinases in photosynthetic acclimation. FEBS Lett. 581:2768-75
251. Rockwell NC, Su YS, Lagarias JC. 2006. Phytochrome structure and signaling mechanisms. Annu. Rev. Plant Biol. 57:837-58
252. Rolland F, Baena-Gonzalez E, Sheen J. 2006. Sugar sensing and signaling in plants: conserved and novel mechanisms. Annu. Rev. Plant Biol. 57:675-709
253. Rolland F, Moore B, Sheen J. 2002. Sugar sensing and signaling in plants. Plant Cell 14(Suppl.):S185-205
254. Ruban AV, Berera R, Ilioaia C, van Stokkum IH, Kennis JT, et al. 2007. Identification of a mechanism of photoprotective energy dissipation in higher plants. Nature 450:575-78
255. Rumeau D, Becuwe-Linka N, Beyly A, Louwagie M, Garin J, Peltier G. 2005. New subunits NDH-M, -N, and -O, encoded by nuclear genes, are essential for plastid Ndh complex functioning in higher plants. Plant Cell 17:219-32
256. Rumeau D, Peltier G, Cournac L. 2007. Chlororespiration and cyclic electron flow around PSI during photosynthesis and plant stress response. Plant Cell Environ. 30:1041-51
257. Runge S, van Cleve B, Lebedev N, Armstrong G, Apel K. 1995. Isolation and classification of chlorophyll-deficient xantha mutants of Arabidopsis thaliana. Planta 197:490-500
258. Salekdeh GH, Siopongco J, Wade LJ, Ghareyazie B, Bennett J. 2002. Proteomic analysis of rice leaves during drought stress and recovery. Proteomics 2:1131-45
259. Sandstrom S, Ivanov AG, Park YI, Oquist G, Gustafsson P. 2002. Iron stress responses in the cyanobacterium Synechococcus sp. PCC7942. Physiol. Plant 116:255-63
260. Santabarbara S, Heathcote P, Evans MC. 2005. Modelling of the electron transfer reactions in Photosystem I by electron tunnelling theory: the phylloquinones bound to the PsaA and the PsaB reaction centre subunits of PS I are almost isoenergetic to the iron-sulfur cluster F(X). Biochim. Biophys. Acta 1708:283-310
261. Sarvikas P, Hakala M, Patsikka E, Tyystjarvi T, Tyystjarvi E. 2006. Action spectrum of photoinhibition in leaves of wild type and npq1-2 and npq4-1 mutants of Arabidopsis thaliana. Plant Cell Physiol. 47:391-400
262. Schachtman DP, Shin R. 2007. Nutrient sensing and signaling: NPKS. Annu. Rev. Plant Biol. 58:47-69
263. Schaffer R, Landgraf J, Accerbi M, Simon V, Larson M, Wisman E. 2001. Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis. Plant Cell 13:113-23
264. Scheibe R. 1987. NADP-malate dehydrogenase in C3-plants: regulation and role of a light-activated enzyme. Physiol. Plant 71:393-400
265. Scheible WR, Morcuende R, Czechowski T, Fritz C, Osuna D, et al. 2004. Genome-wide reprogramming of primary and secondary metabolism, protein synthesis, cellular growth processes, and the regulatory infrastructure of Arabidopsis in response to nitrogen. Plant Physiol. 136:2483-99
266. Schottler MA, Kirchhoff H, Weis E. 2004. The role of plastocyanin in the adjustment of the photosynthetic electron transport to the carbon metabolism in tobacco. Plant Physiol. 136:4265-74
267. Schwarz C, Elles I, Kortmann J, Piotrowski M, Nickelsen J. 2007. Synthesis of the D2 protein of photosystem II in Chlamydomonas is controlled by a high molecular mass complex containing the RNA stabilization factor Nac2 and the translational activator RBP40. Plant Cell 19:3627-39
268. Seelert H, Poetsch A, Dencher NA, Engel A, Stahlberg H, Muller DJ. 2000. Structural biology. Proton-powered turbine of a plant motor. Nature 405:418-19
269. Shao N, Vallon O, Dent R, Niyogi KK, Beck CF. 2006. Defects in the cytochrome b6/f complex prevent light-induced expression of nuclear genes involved in chlorophyll biosynthesis. Plant Physiol. 141:1128-37
270. Sharma S. 2007. Adaptation of photosynthesis under iron deficiency in maize. J. Plant Physiol. 164:1261-67
271. Shikanai T. 2007. Cyclic electron transport around photosystem I: genetic approaches. Annu. Rev. Plant Biol. 58:199-217
272. Shikanai T, Munekage Y, Shimizu K, Endo T, Hashimoto T. 1999. Identification and characterization of Arabidopsis mutants with reduced quenching of chlorophyll fluorescence. Plant Cell Physiol. 40:1134-42
273. Shimizu H, Shikanai T. 2007. Dihydrodipicolinate reductase-like protein, CRR1, is essential for chloroplast NAD(P)H dehydrogenase in Arabidopsis. Plant J. 52:539-47
274. Shimoni E, Rav-Hon O, Ohad I, Brumfeld V, Reich Z. 2005. Three-dimensional organization of higher-plant chloroplast thylakoid membranes revealed by electron tomography. Plant Cell 17:2580-86
275. Shutova T, Klimov VV, Andersson B, Samuelsson G. 2007. A cluster of carboxylic groups in PsbO protein is involved in proton transfer from the water oxidizing complex of Photosystem II. Biochim. Biophys. Acta 1767:434-40
276. Singh AK, Sherman LA. 2007. Reflections on the function of IsiA, a cyanobacterial stress-inducible, Chl-binding protein. Photosynth. Res. 93:17-25
277. Sonoike K. 1996. Photoinhibition of photosystem I in Chlamydomonas: electron transfer reactions and light sensitivity of plants. Plant Cell Physiol. 37:239-47
278. Sproviero EM, Gascon JA, McEvoy JP, Brudvig GW, Batista VS. 2007. Quantum mechanics/molecular mechanics structural models of the oxygen-evolving complex of photosystem II. Curr. Opin. Struct. Biol. 17:173-80
279. Stauber EJ, Fink A, Markert C, Kruse O, Johanningmeier U, Hippler M. 2003. Proteomics of Chlamydomonas reinhardtii light-harvesting proteins. Eukaryot. Cell 2:978-94
280. Stern DB, Higgs DC, Yang J. 1997. Transcription and translation in chloroplasts. Trends Plant Sci. 2:308-15
281. Streb P, Aubert S, Gout E, Bligny R. 2003. Reversibility of cold- and light-stress tolerance and accompanying changes of metabolite and antioxidant levels in the two high mountain plant species Soldanella alpina and Ranunculus glacialis. J. Exp. Bot. 54:405-18
282. Stroebel D, Choquet Y, Popot JL, Picot D. 2003. An atypical haem in the cytochrome b6f complex. Nature 426:413-18
283. Strzepek RF, Harrison PJ. 2004. Photosynthetic architecture differs in coastal and oceanic diatoms. Nature 431:689-92
284. Su N, He K, Jiao Y, Chen C, Zhou J, et al. 2007. Distinct reorganization of the genome transcription associates with organogenesis of somatic embryo, shoots, and roots in rice. Plant Mol. Biol. 63:337-49
285. Susek RE, Ausubel FM, Chory J. 1993. Signal transduction mutants of Arabidopsis uncouple nuclear CAB and RBCS gene expression from chloroplast development. Cell 74:787-99
286. Svensson JT, Crosatti C, Campoli C, Bassi R, Stanca AM, et al. 2006. Transcriptome analysis of cold acclimation in barley albina and xantha mutants. Plant Physiol. 141:257-70
287. Szabo I, Bergantino E, Giacometti GM. 2005. Light and oxygenic photosynthesis: energy dissipation as a protection mechanism against photo-oxidation. EMBO Rep. 6:629-34
288. Taji T, Seki M, Satou M, Sakurai T, Kobayashi M, et al. 2004. Comparative genomics in salt tolerance between Arabidopsis and Arabidopsis-related halophyte salt cress using Arabidopsis microarray. Plant Physiol. 135:1697-709
289. Talame V, Ozturk NZ, Bohnert HJ, Tuberosa R. 2007. Barley transcript profiles under dehydration shock and drought stress treatments: a comparative analysis. J. Exp. Bot. 58:229-40
290. Tarantino D, Vannini C, Bracale M, Campa M, Soave C, Murgia I. 2005. Antisense reduction of thylakoidal ascorbate peroxidase in Arabidopsis enhances paraquat-induced photooxidative stress and nitric oxide-induced cell death. Planta 221:757-65
291. Tepperman JM, Zhu T, Chang HS, Wang X, Quail PH. 2001. Multiple transcription-factor genes are early targets of phytochrome A signaling. Proc. Natl. Acad. Sci. USA 98:9437-42
292. Tikkanen M, Piippo M, Suorsa M, Sirpio S, Mulo P, et al. 2006. State transitions revisited-a buffering system for dynamic low light acclimation of Arabidopsis. Plant Mol. Biol. 62:779-93
293. Timperio AM, D'Amici GM, Barta C, Loreto F, Zolla L. 2007. Proteomics, pigment composition, and organization of thylakoid membranes in iron-deficient spinach leaves. J. Exp. Bot. 58:3695-710
294. Tognetti VB, Palatnik JF, Fillat MF, Melzer M, Hajirezaei MR, et al. 2006. Functional replacement of ferredoxin by a cyanobacterial flavodoxin in tobacco confers broad-range stress tolerance. Plant Cell 18:2035-50
295. Tognetti VB, Zurbriggen MD, Morandi EN, Fillat MF, Valle EM, et al. 2007. Enhanced plant tolerance to iron starvation by functional substitution of chloroplast ferredoxin with a bacterial flavodoxin. Proc. Natl. Acad. Sci. USA 104:11495-500
296. +/ATP ratio of proton transport-coupled ATP synthesis and hydrolysis catalysed by CF0F1-liposomes. EMBO J. 22:418-26
297. Turkina MV, Kargul J, Blanco-Rivero A, Villarejo A, Barber J, Vener AV. 2006. Environmentally modulated phosphoproteome of photosynthetic membranes in the green alga Chlamydomonas reinhardtii. Mol. Cell Proteomics 5:1412-25
298. Ulm R, Baumann A, Oravecz A, Mate Z, Adam E, et al. 2004. Genome-wide analysis of gene expression reveals function of the bZIP transcription factor HY5 in the UV-B response of Arabidopsis. Proc. Natl. Acad. Sci. USA 101:1397-402
299. Vainonen JP, Hansson M, Vener AV. 2005. STN8 protein kinase in Arabidopsis thaliana is specific in phosphorylation of photosystem II core proteins. J. Biol. Chem. 280:33679-86
300. van de Meene AM, Hohmann-Marriott MF, Vermaas WF, Roberson RW. 2006. The three-dimensional structure of the cyanobacterium Synechocystis sp. PCC 6803. Arch. Microbiol. 184:259-70
301. Vandepoele K, Casneuf T, Van de Peer Y. 2006. Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics. Genome Biol. 7:R103
302. Varotto C, Pesaresi P, Meurer J, Oelmuller R, Steiner-Lange S, et al. 2000. Disruption of the Arabidopsis photosystem I gene psaE1 affects photosynthesis and impairs growth. Plant J. 22:115-24
303. Varsano T, Wolf SG, Pick U. 2006. A chlorophyll a/b-binding protein homolog that is induced by iron deficiency is associated with enlarged photosystem I units in the eucaryotic alga Dunaliella salina. J. Biol. Chem. 281:10305-15
304. Vener AV. 2007. Environmentally modulated phosphorylation and dynamics of proteins in photosynthetic membranes. Biochim. Biophys. Acta 1767:449-57
305. Vener AV, Van Kan PJ, Gal A, Andersson B, Ohad I. 1995. Activation/deactivation cycle of redox-controlled thylakoid protein phosphorylation. Role of plastoquinol bound to the reduced cytochrome bf complex. J. Biol. Chem. 270:25225-32
306. Wagner D, Przybyla D, Op den Camp R, Kim C, Landgraf F, et al. 2004. The genetic basis of singlet oxygen-induced stress responses of Arabidopsis thaliana. Science 306:1183-85
307. Walters RG, Shephard F, Rogers JJ, Rolfe SA, Horton P. 2003. Identification of mutants of Arabidopsis defective in acclimation of photosynthesis to the light environment. Plant Physiol. 131:472-81
308. Wang H, Ma L, Habashi J, Li J, Zhao H, Deng XW. 2002. Analysis of far-red light-regulated genome expression profiles of phytochrome A pathway mutants in Arabidopsis. Plant J. 32:723-33
309. Wang R, Guegler K, LaBrie ST, Crawford NM. 2000. Genomic analysis of a nutrient response in Arabidopsis reveals diverse expression patterns and novel metabolic and potential regulatory genes induced by nitrate. Plant Cell 12:1491-509
310. Weisshaar B, Armstrong GA, Block A, da Costa e Silva O, Hahlbrock K. 1991. Light-inducible and constitutively expressed DNA-binding proteins recognizing a plant promoter element with functional relevance in light responsiveness. EMBO J. 10:1777-86
311. Weisshaar B, Block A, Armstrong GA, Herrmann A, Schulze-Lefert P, Hahlbrock K. 1991. Regulatory elements required for light-mediated expression of the Petroselinum crispum chalcone synthase gene. Symp. Soc. Exp. Biol. 45:191-210
312. Whitelam GC, Johnson E, Peng J, Carol P, Anderson ML, et al. 1993. Phytochrome A null mutants of Arabidopsis display a wild-type phenotype in white light. Plant Cell 5:757-68
313. Wijnen H, Young MW. 2006. Interplay of circadian clocks and metabolic rhythms. Annu. Rev. Genet. 40:409-48
314. Wilde A, Lunser K, Ossenbuhl F, Nickelsen J, Borner T. 2001. Characterization of the cyanobacterial ycf37: mutation decreases the photosystem I content. Biochem. J. 357:211-16
315. Wilson A, Boulay C, Wilde A, Kerfeld CA, Kirilovsky D. 2007. Light-induced energy dissipation in iron-starved cyanobacteria: roles of OCP and IsiA proteins. Plant Cell 19:656-72
316. Wingler A, Lea PJ, Quick WP, Leegood RC. 2000. Photorespiration: metabolic pathways and their role in stress protection. Philos. Trans. R. Soc. London Ser. B 355:1517-29
317. Wobbe L, Schwarz C, Nickelsen J, Kruse O. 2008. Translational control of photosynthetic gene expression in phototrophic eukaryotes. Physiol. Plant
318. Wollman FA. 2001. State transitions reveal the dynamics and flexibility of the photosynthetic apparatus. EMBO J. 20:3623-30
319. Wormuth D, Heiber I, Shaikali J, Kandlbinder A, Baier M, Dietz KJ. 2007. Redox regulation and antioxidative defence in Arabidopsis leaves viewed from a systems biology perspective. J. Biotechnol. 129:229-48
320. Wraight CA, Crofts AR. 1970. Energy-dependent quenching of chlorophyll alpha fluorescence in isolated chloroplasts. Eur. J. Biochem. 17:319-27
321. Wu P, Ma L, Hou X, Wang M, Wu Y, et al. 2003. Phosphate starvation triggers distinct alterations of genome expression in Arabidopsis roots and leaves. Plant Physiol. 132:1260-71
322. Yadav V, Kundu S, Chattopadhyay D, Negi P, Wei N, et al. 2002. Light regulated modulation of Z-box containing promoters by photoreceptors and downstream regulatory components, COP1 and HY5, in Arabidopsis. Plant J. 31:741-53
323. Yamaguchi-Shinozaki K, Shinozaki K. 2006. Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annu. Rev. Plant Biol. 57:781-803
324. Yamamoto HY, Nakayama TO, Chichester CO. 1962. Studies on the light and dark interconversions of leaf xanthophylls. Arch. Biochem. Biophys. 97:168-73
325. Yang DH, Webster J, Adam Z, Lindahl M, Andersson B. 1998. Induction of acclimative proteolysis of the light-harvesting chlorophyll a/b protein of photosystem II in response to elevated light intensities. Plant Physiol. 118:827-34
326. Zelisko A, Garcia-Lorenzo M, Jackowski G, Jansson S, Funk C. 2005. AtFtsH6 is involved in the degradation of the light-harvesting complex II during high-light acclimation and senescence. Proc. Natl. Acad. Sci. USA 102:13699-704
327. Zhang C. 2007. Low-barrier hydrogen bond plays key role in active photosystem II - a new model for photosynthetic water oxidation. Biochim. Biophys. Acta 1767:493-99
328. + oxidoreductase is a subunit of the chloroplast cytochrome b6f complex. J. Biol. Chem. 276:38159-65
329. Zhang Z, Shrager J, Jain M, Chang CW, Vallon O, Grossman AR. 2004. Insights into the survival of Chlamydomonas reinhardtii during sulfur starvation based on microarray analysis of gene expression. Eukaryot Cell 3:1331-48
330. Zhou J, Wang X, Jiao Y, Qin Y, Liu X, et al. 2007. Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle. Plant Mol. Biol. 63:591-608
331. Zhu JK. 2002. Salt and drought stress signal transduction in plants. Annu. Rev. Plant Biol. 53:247-73
332. Zito F, Finazzi G, Delosme R, Nitschke W, Picot D, Wollman FA. 1999. The Qo site of cytochrome b6f complexes controls the activation of the LHCII kinase. EMBO J. 18:2961-69