Textbook

Introduction

Basic Energy Sciences Workshop on Solar Energy Utilization (2005). Basic Research Needs for Solar Energy Utilization. Retrieved from http://science.energy.gov/~/media/bes/pdf/reports/files/seu_rpt.pdf

Deschamps, P., Haferkamp, I., d’Hulst, C., Ekkehard Neuhaus, H., and Ball, S. G. (2008b) The relocation of starch metabolism to chloroplasts: When, why and how. Trends Plant Sci. 13: 574–582.

Deschamps, P., Moreau, H., Worden, A. Z., Dauvillee, D., and Ball, S. G. (2008a) Early gene duplication within chloroplastida and its correspondence with relocation of starch metabolism to chloroplasts. Genetics 178: 2373–2387.

Keeling, P. J. (2010) The endosymbiotic origin, diversification and fate of plastids. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 365: 729–748.

Rodríguez-Ezpeleta, N., Brinkmann, H., Burey, S. C., Roure, B., Burger, G., Löffelhardt, W., Bohnert, H. J., Philippe, H., and Lang, B. F. (2005) Monophyly of primary photosynthetic eukaryotes: Green plants, red algae, and glaucophytes. Curr. Biol. 15: 1325–1330.

Sinclair, T. R. (2009) Taking measure of biofuel limits. Am. Sci. 97: 400-407.

The Calvin–Benson Cycle

Aran, M., Ferrero, D. S., Pagano, E., and Wolosiuk, R. A. (2009) Modulation of  typical 2-Cys peroxiredoxins by covalent transformations and non-covalent interactions. FEBS J. 276: 2478–2493.

Buchanan, B. B., and Balmer, Y. (2005) Redox regulation: A broadening horizon. Annu. Rev. Plant Biol. 56: 187–220.

Buchanan, B. B., Holmgren, A., Jacquot, J. P. and Scheibe, R. (2012) Fifty years in the thioredoxin field and a bountiful harvest. Biochim. Biophys. Acta 1820: 1822–1829.

Cleland, W. W., Andrews, T. J., Gutteridge, S., Hartman, F. C., and Lorimer, G. H. (1998) Mechanism of rubisco: The carbamate as general base. Chem. Rev. 98: 549–561.

Fuchs, G. (2011) Alternative pathways of carbon dioxide fixation: Insights into the early evolution of life? Annu. Rev. Microbiol. 65: 631–658.

Heldt, H. W. (1979) Light-dependent changes of stromal H+ and Mg2+ concentrations controlling CO2 fixation. In Encyclopedia of Plant Physiology, New Series, Vol. 6, M. Gibbs and E. Latzko, eds., Springer, Berlin, pp. 202–207.

Maier, R. M., Neckermann, K., Igloi, G. L., and Koessel, H. (1995) Complete sequence of the maize chloroplast genome: Gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J. Mol. Biol. 251: 614–628.

Marri, L., Zaffagnini, M., Collin, V., Issakidis-Bourguet, E., Lemaire, S. D., Pupillo, P., Sparla, F., Miginiac-Maslow, M., and Trost, P. (2009) Prompt and easy activation by specific thioredoxins of Calvin cycle enzymes of Arabidopsis thaliana associated in the GAPDH/CP12/PRK supramolecular complex. Mol. Plant 2: 259–269.

Montrichard F., Alkhalfioui F., Yano H., Vensel W. H., Hurkman W. J., and Buchanan B. B. (2009) Thioredoxin targets in plants: The first 30 years. J. Proteomics 72: 452–474.

Mora-Garcia, S., Stolowicz, F., and Wolosiuk, R. A. (2006) Redox signal transduction in plant metabolism. Control of primary metabolism in plants. In Annual Plant Reviews, Vol. 22., W. C. Plaxton and M. T. McManus, eds., Blackwell, Oxford, UK, pp. 150–186.

Neff, M. M., Fankhauser, C., and Chory, J. (2000). Light: An indicator of time and place. Genes Dev. 14: 257–271.

Portis, A. R. (2003) Rubisco activase - Rubisco’s catalytic chaperone. Photosynth. Res. 75: 11–27.

Purton, S. (1995) The chloroplast genome of Chlamydomonas. Sci. Prog. 78: 205–216.

Wolosiuk, R. A., Ballicora, M. A., and Hagelin, K. (1993) The reductive pentose phosphate cycle for photosynthetic carbon dioxide assimilation: Enzyme modulation. FASEB J. 7: 622–637.

The C2 Oxidative Photosynthetic Carbon Cycle

Aliyev, J. A. (2012) Photosynthesis, photorespiration and productivity of wheat and soybean genotypes. Physiol. Plant. 145: 369–383.

Ashida, H., Danchin, A. and Yokota, A. (2005) Was photosynthetic RuBisCO recruited by acquisitive evolution from RuBisCO-like proteins involved in sulfur metabolism? Res. Microbiol. 156: 611–618.

Bauwe, H., Hagemann, M., Kern, R. and Timm, S. (2012) Photorespiration has a dual origin and manifold links to central metabolism. Curr. Opin. Plant Biol. 15: 269–275.

Boldt, R., Edner, C., Kolukisaoglu, U., Hagemann, M., Weckwerth, W., Wienkoop, S., Morgenthal, K., and Bauwe, H. (2005) D-Gycerate 3-kinase, the last unknown enzyme in the photorespiratory cycle in Arabidopsis, belongs to a novel kinase family. Plant Cell 17: 2413–2420.

Eisenhut, M., Ruth, W., Haimovich, M., Bauwe, H., Kaplan, A. and Hagemann, M. (2008) The photorespiratory glycolate metabolism is essential for cyanobacteria and might have been conveyed endosymbiontically to plants. Proc. Natl. Acad. Sci. USA 105: 17199–17204.

Florian, A., Araujo, W. L. and Fernie, A. R. (2013) New insights into photorespiration obtained from metabolomics. Plant Biol. 15: 656–666.

Foyer, C. H., Bloom A., Queval G., and Noctor G. (2009) Photorespiratory metabolism: Genes, mutants, energetics, and redox signaling. Annu. Rev. Plant Biol. 60: 455–484.

Foyer, C. H., Neukermans, J., Queval, G., Noctor, G. and Harbinson, J. (2012) Photosynthetic control of electron transport and the regulation of gene expression. J. Exp. Bot. 63: 1637–1661.

Hagemann, M., Fernie, A. R., Espie, G. S., Kern, R., Eisenhut, M., Reumann, S., Bauwe, H. and Weber, A. P. M. (2013) Evolution of the biochemistry of the photorespiratory C2 cycle. Plant Biol. 15: 639–647.

Kebeish, R., Niessen, M., Thiruveedhi, K., Bari, R., Hirsch, H. J., Rosenkranz, R., Stabler, N., Schonfeld, B., Kreuzaler, F., and Peterhansel, C. (2007) Chloroplastic photorespiratory bypass increases photosynthesis and biomass production in Arabidopsis thaliana. Nat. Biotechnol. 25: 593–599.

Khan, M. S. (2007) Engineering photorespiration in chloroplasts: A novel strategy for increasing biomass production. Trends Biotechnol. 25: 437–440.

Ku, S. B., and Edwards, G. E. (1978) Oxygen inhibition of photosynthesis. III. Temperature dependence of quantum yield and its relation to O2/CO2 solubility ratio. Planta 140: 1–6.

Leegood, R. C., Lea, P. J., Adcock, M. D., and Haeusler, R. D. (1995) The regulation and control of photorespiration. J. Exp. Bot. 46: 1397–1414.

Lorimer, G. H. (1983) Ribulose-1,5-bisphosphate oxygenase. Annu. Rev. Biochem. 52: 507–535.

Ogren, W. L. (1984) Photorespiration: Pathways, regulation and modification. Annu. Rev. Plant Physiol. 35: 415–422. 

Peterhansel, C., and Maurino, V. G. (2011) Photorespiration redesigned. Plant Physiol. 155: 49–55.

Peterhansel, C., Blume, C. and Offermann, S. (2013) Photorespiratory bypasses: How can they work? J. Exp. Bot. 64: 709–715.

Rachmilevitch, S., Cousins, A. B. and Bloom, A. J. (2004) Nitrate assimilation in plant shoots depends on photorespiration. Proc. Natl. Acad. Sci. USA 101: 11506–11510.

Reumann, S. and Weber, A. P. M. (2006) Plant peroxisomes respire in the light: Some gaps of the photorespiratory C2 cycle have become filled - Others remain. Biochim. Biophys. Acta 1763: 1496–1510.

Tolbert, N. E. (1981) Metabolic pathways in peroxisomes and glyoxysomes. Annu. Rev. Biochem. 50: 133–157.

Zelitch, I., Schultes, N. P., Peterson, R. B., Brown, P. and Brutnell T. P. (2009) High glycolate oxidase activity is required for survival of maize in normal air. Plant Physiol. 149: 195–204.

Inorganic Carbon–Concentrating Mechanisms

Badger, M. R., and Price, G. D. (2003) CO2 concentrating mechanisms in cyanobacteria: Molecular components, their diversity and evolution. J. Exp. Bot. 54: 609–622.

Flexas, J., Barbour, M. M., Brendel, O., Cabrera, H. M., Carriqui, M., Diaz-Espejo, A., Douthe, C., Dreyer, E., Ferrio, J. P., Gago, J., et al. (2012) Mesophyll diffusion conductance to CO2: An unappreciated central player in photosynthesis. Plant Sci. 193-194: 70–84.

Giordano, M., Beardall, J., and Raven, J. A (2005) CO2 concentrating mechanisms in algae: Mechanisms, environmental modulation, and evolution. Annu. Rev. Plant Biol. 56: 99–131.

Heckwolf, M., Pater, D., Hanson, D. T. and Kaldenhoff, R. (2011) The Arabidopsis thaliana aquaporin AtPIP1;2 is a physiologically relevant CO2 transport facilitator. Plant J. 67: 795–804.

Inorganic Carbon–Concentrating Mechanisms: The C4 Carbon Cycle

Armbrust E.V., Berges J. A., Bowler C., Green B. R., Martinez D., Putnam N. H., Zhou S., Allen, A. E., Apt, K. E., Bechner, M., et al. (2004) The genome of the diatom Thalassiosira pseudonana: Ecology, evolution, and metabolism. Science 306: 79–86.

Brautigam, A., Hoffmann-Benning, S., and Weber, A. P. M (2008) Comparative proteomics of chloroplast envelopes from C3 and C4 plants reveals specific adaptations of the plastid envelope to C4 photosynthesis and candidate proteins required for maintaining C4 metabolite fluxes. Plant Physiol. 148: 568–579. 

Brown, N. J., Newell, C. A., Stanley, S., Chen, J. E., Perrin, A. J., Kajala, K. and Hibberd, J. M. (2011). Independent and parallel recruitment of preexisting mechanisms underlying C4 photosynthesis. Science 331: 1436–1439.

Burnell, J. N., and Chastain, C. J. (2006) Cloning and expression of maize-leaf pyruvate, Pi dikinase regulatory protein gene. Biochem. Biophys. Res. Commun. 345: 675–680.

Edwards, G. E., Franceschi, V. R., and Voznesenskaya, E. V. (2004) Single-cell C4 photosynthesis versus the dual-cell (Kranz) paradigm. Annu. Rev. Plant Biol. 55: 173–196.

Fernie, A. R., Obata, T., Allen, A. E., Araujo, W. L. and Bowler, C. (2012) Leveraging metabolomics for functional investigations in sequenced marine diatoms. Trends Plant Sci. 17: 395–403.

Flügge, U. I., and Heldt, H. W. (1991) Metabolite translocators of the chloroplast envelope. Annu. Rev. Plant Physiol. Plant Mol. Biol. 42: 129–144.

Furbank, R. T. (2011) Evolution of the C4 photosynthetic mechanism: Are there really three C4 acid decarboxylation types? J. Exp. Bot. 62: 3103–3108.

Gowik, U., Bräutigam, A., Weber, K. L., Weber, A. P. M. and Westhof, P. (2011) Evolution of C4 photosynthesis in the genus Flaveria: How many and which genes does it take to make C4? Plant Cell 23: 2087–2105.

Hatch, M. D. (2002) C4 photosynthesis: Discovery and resolution. Photosynth. Res. 73: 251–256.

Hatch, M. D., and Slack, C. R. (1966) Photosynthesis by sugarcane leaves. A new carboxylation reaction and the pathway of sugar formation. Biochem. J. 101: 103–111.

Hibberd, J. M. and Covshoff, S. (2010) The regulation of gene expression required for C4 photosynthesis. Annu. Rev. Plant Biol. 61: 181–207.

Izui, K., Matsumura, H., Furumoto, T., and Kai, Y. (2004) Phosphoenolpyruvate carboxylase: A new era of structural biology. Annu. Rev. Plant Biol. 55: 69–84.

Kroth P. G., Chiovitti A., Gruber A., Martin-Jezequel V., Mock T., Parker, M. S., Stanley, M. S., Kaplan, A., Caron, L., Weber, T., et al. (2008) A model for carbohydrate metabolism in the diatom Phaeodactylum tricornutum deduced from comparative whole genome analysis. PLOS ONE 3(1): e1426.

Long, S. P. and Spence, A. K. (2013) Toward cool C4 crops. Annu. Rev. Plant Biol. 64: 701–722.

Lung, S. C., Yanagisawa, M., and Chuong, S. D. X. (2012) Isolation of dimorphic chloroplasts from the single-cell C4 species Bienertia sinuspersici. Plant Methods 8: 8–20.

Lüttge, U., and Higinbotham, N. (1979) Transport in Plants. Springer-Verlag, New York.

Maroco, J. P., Ku, M. S. B., Lea P. J., Dever, L. V., Leegood, R. C., Furbank, R. T., and Edwards, G. E. (1998) Oxygen requirement and inhibition of C4 photosynthesis: An analysis of C4 plants deficient in the C3 and C4 cycles. Plant Physiol. 116: 823–832.

Muhaidat, R., Sage, R. F., and Dengler, N. G. (2007) Diversity of Kranz anatomy and biochemistry in C4 eudicots. Amer. J. Bot. 94: 362–381.

Reinfelder, J. R., Milligan, A. J., and Morel, F. M. M. (2004) The role of the C4 pathway in carbon accumulation and fixation in a marine diatom. Plant Physiol. 135: 2106–2111.

Sage, R. F. (2002) C4 photosynthesis in terrestrial plants does not require Kranz anatomy. Trends Biochem. Sci. 7: 283–285.

Sage, R. F. and Kubien, D. S. (2003) Quo vadis C4? An ecophysiological perspective on global change and the future of C4 plants. Photosynth. Res. 77: 209–225.

Sage, R. F., Christin, P. A. and Edwards, E. J. (2011) The C4 plant lineages of planet Earth. J. Exp. Bot. 62: 3155–3169.

Weber, A. P. M., and von Caemmerer, S. (2010) Plastid transport and metabolism of C3 and C4 plants − Comparative analysis and possible biotechnological exploitation. Curr. Opin. Plant Biol. 13: 257–265.

Weber, A. P. M., Schwacke, R., and Flugge, U.-I. (2005) Solute transporters of the plastid envelope membrane. Annu. Rev. Plant Biol. 56: 133–164.

Williams, B. P., Aubry, S. and Hibberd, J. M. (2012) Molecular evolution of genes recruited into C4 photosynthesis. Trends Plant Sci. 17: 213–220.

Inorganic Carbon–Concentrating Mechanisms: Crassulacean Acid Metabolism (CAM)

Adams, P., Nelson, D. E., Yamada, S., Chmara, W., Jensen, R. G., Bohnert, H. J., and Griffiths, H. (1998) Growth and development of Mesembryanthemum crystallinum (Aizoaceae). New Phytol. 138: 171–190.

Cushman, J. C. (2001) Crassulacean acid metabolism: A plastic photosynthetic adaptation to arid environments. Plant Physiol. 127: 1439–1448.

Drincovich, M. F., Casati, P., and Andreo, C. S. (2001) NADP-malic enzyme from plants: A ubiquitous enzyme involved in different metabolic pathways. FEBS Lett. 490: 1–6.

Lawlor, D. W. (2009) Musings about the effects of environment on photosynthesis. Ann. Bot. 103: 543–549.

Lüttge, U. (2008) Clusia: Holy grail and enigma. J. Exp. Bot. 59: 1503–1514.

Mommer, L., and Visser, E. J. W. (2005) Underwater photosynthesis in flooded terrestrial plants: A matter of leaf plasticity. Ann. Bot. 96: 581–589.

Nimmo, H. G. (2003) How to tell the time: The regulation of phosphoenolpyruvate carboxylase in crassulacean acid metabolism (CAM) plants. Biochem. Soc. Trans. 31: 728–730.

Osmond, B., Neales, T. and Stange, G. (2008) Curiosity and context revisited: Crassulacean acid metabolism in the Anthropocene. J. Exp. Bot. 59: 1489–1502.

Osmond, C. B., Maxwell, K., Popp, M. and Robinson, S. (1999) On being thick: Fathoming apparently futile pathways of photosynthesis and carbohydrate metabolism in succulent CAM plants. In Carbohydrate Metabolism in Plants, J. A. Bryant, M. Burrel, and N. J. Kruger, eds., BIOS Scientific Publishers, Oxford, UK, pp. 183–200.

Accumulation and Partitioning of Photosynthates—Starch and Sucrose

Rolland, F., Baena-Gonzalez, E. and Sheen, J. (2006) Sugar sensing and signalling in plants: Conserved and novel mechanisms. Annu. Rev. Plant Biol. 57: 675–709.

Formation and Mobilization of Chloroplast Starch

Baroja-Fernandez, E., Muñoz, F. J., and Pozueta-Romero, J. (2005) Response to Neuhaus et al.: No need to shift the paradigm on the metabolic pathway to transitory starch in leaves. Trends Plant Sci. 10: 156–158.

Buléon, A., Colonna, P., Planchot, V. and Ball, S. (1998) Starch granules: Structure and biosynthesis. Int. J. Biol. Macromol. 23: 85–112.

Chia, T., Thorneycroft, D., Chapple, A., Messerli, G., Chen, J., Zeeman, S. C., Smith, S. M., and Smith, A. M. (2004) A cytosolic glucosyl-transferase is required for conversion of starch to sucrose in Arabidopsis leaves at night. Plant J. 37: 853–863.

Critchley, J. H., Zeeman, S. C., Takaha, T., Smith, A. M., and Smith, S. M. (2001) A critical role for disproportionating enzyme in starch breakdown is revealed by a knock-out mutant in Arabidopsis. Plant J. 26: 89–100.

Crumpton-Taylor, M., Grandison, S., Png, K. M. Y., Bushby, A. J. and Smith, A. M. (2012) Control of starch granule numbers in Arabidopsis chloroplasts. Plant Physiol. 158: 905–916.

Fettke, J., Chia, T., Eckermann, N., Smith, A., and Steup, M. (2006) A transglucosidase necessary for starch degradation and maltose metabolism in leaves at night acts on cytosolic heteroglycans (SHG). Plant J. 46: 668–684.

Fettke, J., Eckermann, N., Tiessen, A., Geigenberger, P., and Steup, M. (2005) Identification, subcellular localization and biochemical characterization of water-soluble heteroglycans (SHG) in leaves of Arabidopsis thaliana L.: Distinct SHG reside in the cytosol and in the apoplast. Plant J. 43: 568–586.

Graf, A. and Smith, A. M. (2011) Starch and the clock: The dark side of plant productivity. Trends Plant Sci. 16: 169–175.

Hejazi, M., Fettke, J., Haebel, S., Edner, C., Paris, O., Frohberg, C., Steup, M., and Ritte, G. (2008) Glucan, water dikinase phosphorylates crystalline maltodextrins and thereby initiates solubilisation. Plant J. 55: 323–334.

Kolbe, A., Tiessen, A., Schluepmann, H., Paul, M., Ulrich, S., and Geigenberger, P. (2005) Trehalose 6-phosphate regulates starch synthesis via post-translational redox activation of ADP-glucose pyrophosphorylase. Proc. Natl. Acad. Sci. USA 102: 11118–11123.

Kötting, O., Kossmann, J., Zeeman, S. C. and Lloyd, J. R. (2010) Regulation of starch metabolism: The age of enlightenment? Curr. Opin. Plant Biol. 13: 321–329.

Kötting, O., Pusch, K., Tiessen, A., Geigenberger, P., Steup, M., and Ritte, G. (2005) Identification of a novel enzyme required for starch metabolism in Arabidopsis leaves. The phosphoglucan, water dikinase. Plant Physiol. 137: 242–252.

Lloyd, J. R., Kossmann, J., and Ritte, G. (2005) Leaf starch degradation comes out of the shadows. Trends Plant Sci. 10: 130–137.

Mikkelsen, R., Mutenda, K. E., Mant, A., Schurmann, P., and Blennow, A. (2005) Alpha-glucan, water dikinase (GWD): A plastidic enzyme with redox-regulated and coordinated catalytic activity and binding affinity. Proc. Natl. Acad. Sci. USA 102: 1785–1790.

Neuhaus, H. E., Hausler, R. E., and Sonnewald, U. (2005) No need to shift the paradigm on the metabolic pathway to transitory starch in leaves. Trends Plant Sci. 10: 154–156.

Niittyla, T., Messerli, G., Trevisan, M., Chen, J., Smith, A. M., and Zeeman, S. C. (2004) A previously unknown maltose transporter essential for starch degradation in leaves. Science 303: 87–89.

Paul, M. J., Primavesi, L. F., Jhurreea, D., and Zhang, Y. (2008) Trehalose metabolism and signaling. Annu. Rev. Plant Biol. 59: 417–441.

Ridout, M. J., Parker, M. L., Hedley, C. L., Bogracheva, T. Y. and Morris, V. J. (2003) Atomic force microscopy of pea starch granules: Granule architecture of wild-type parent, r and rb single mutants, and the rrb double mutant. Carbohydr. Res. 338: 2135–2147.

Ritte, G., Heydenreich, M., Mahlow, S., Haebel, S., Kotting, O., and Steup, M. (2006) Phosphorylation of C6- and C3-positions of glucosyl residues in starch is catalysed by distinct dikinases. FEBS Letters 580: 4872–4876.

Smith, A. M., Zeeman, S. C., and Smith, S. M. (2005) Starch degradation. Annu. Rev. Plant Biol. 56: 73–97.

Streb, S., and Zeeman, S. C. (2012) Starch metabolism in Arabidopsis. The Arabidopsis Book 9, p. e0160. doi: 10.1199/tab.0160.

Streb, S., Egli, B., Eicke, S. and Zeeman, S. C. (2009) The debate on the pathway of starch synthesis: A closer look at low-starch mutants lacking plastidial phosphoglucomutase supports the chloroplast-localized pathway. Plant Physiol. 151: 1769–1772.

Szydlowski, N., Ragel, P., Raynaud, S., Lucas, M. M., Roldan, I., Montero, M., Muñoz, F. J., Ovecka, M., Bahaji, A., Planchot, V., et al. (2009) Starch granule initiation in Arabidopsis requires the presence of either class IV or class III starch synthases. Plant Cell 21: 2443–2457.

Veley, K. M., Marshburn, S., Clure, C. E. and Haswell, E. S. (2012) Mechanosensitive channels protect plastids from hypoosmotic stress during normal plant growth. Curr. Biol. 22: 408–413.

Yu, T. S., Kofler, H., Häusler, R. E., Hille, D., Flügge, U. I., Zeeman, S. C., Smith, A. M., Kossmann, J., Lloyd, J., Ritte, G., et al. (2001) The Arabidopsis sex1 mutant is defective in the R1 protein, a general regulator of starch degradation in plants, and not in the chloroplast hexose transporter. Plant Cell 13: 1907–1918.

Zeeman, S. C., Smith, S. M. and Smith, A. M. (2007) The diurnal metabolism of leaf starch. Biochem. J. 401: 13–28.

Sucrose Biosynthesis and Signaling

Halford, N. G. and Hey, S. J. (2009) Snf1-related protein kinases (SnRKs) act within an intricate network that links metabolic and stress signalling in plants. Biochem. J. 419: 247–259.

Huber, S. C., and Huber, J. L. (1996) Role and regulation of sucrose-phosphate synthase in higher plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 47: 431–444.

Liesche, J., Krügel, U., He, H., Chincinska, I., Hackel, A. and Kühn, C. (2011) Sucrose transporter regulation at the transcriptional, post-transcriptional and post-translational level. J. Plant Physiol. 168: 1426–1433.

Lund, J. E., Ashton, A. R., Hatch, M. D., and Heldt, H. W. (2000) Purification, molecular cloning, and sequence analysis of sucrose-6F-phosphate phosphohydrolase from plants. Proc. Natl. Acad. Sci. USA 97: 12914–12919.

Nielsen, T. H., Rung, J. H., and Villadsen, D. (2004) Fructose 2,6-bisphosphate: A traffic signal in plant metabolism. Trends Plant Sci. 9: 556–563.

Robaglia, C., Thomas, M. and Meyer, C. (2012) Sensing nutrient and energy status by SnRK1 and TOR kinases. Curr. Opin. Plant Biol. 15: 301–307.

Salerno, G. L., Echeverria, E., and Pontis, H. G. (1996) Activation of sucrose-phosphate synthase by a protein factor/sucrose-phosphate phosphatase. Cell. Mol. Biol. 42: 665–672.

Stokes, M. E., Chattopadhyay, A., Wilkins, O., Nambara, E. and Campbell, M. M. (2013) Interplay between sucrose and folate modulates auxin signaling in Arabidopsis. Plant Physiol. 162: 1552–1565.

Web Topics

Andrews, T. J. (1996) The bait in the rubisco mousetrap. Nature Struct. Biol. 3: 3–7.

Armbrust, E. V., Berges, J. A., Bowler, C., Green, B. R., Martinez, D., Putnam, N. H., Zhou, S., et al. (2004) The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science 306: 79–86.

Badger, M. R., and Price, G. D. (2003) CO2 concentrating mechanisms in cyanobacteria: Molecular components, their diversity and evolution. J. Exp. Bot. 54: 609–622.

Bassham, T. A. (1965) Photosynthesis: The path of carbon. In Plant Biochemistry, 2nd ed., J. Bonner and E. Varner, eds., Academic Press, New York, pp. 875–902.

Besse, I., and Buchanan, B. B. (1997) Thioredoxin-linked plant and animal processes: The new generation. Bot. Bull. Acad. Sinica 38: 1–11.

Bonner, W., and Bonner, J. (1948) The role of carbon dioxide in acid formation by succulent plants. Am. J. Bot. 35: 113–117.

Borland, A., Elliott, S., Patterson, S., Taybi, T., Cushman, J., Pater, B., and Barnes, J. (2006) Are the metabolic components of crassulacean acid metabolism up-regulated in response to an increase in oxidative burden? J. Exp. Bot. 57: 319–328.

Bowyer, J. R., and Leegood, R. C. (1997) Photosynthesis. In Plant Biochemistry, P. M. Dey and J. B. Harbone, eds., Academic Press, San Diego, pp. 49–110.

Buchanan, B. B. (1992) Carbon dioxide assimilation in oxygenic and anoxygenic photosynthesis. Photosynth. Res. 33: 147–162.

Buléon, A., Colonna, P., Planchot, V., and Ball, S. (1998) Starch granules: structure and biosynthesis. Int J Biol Macromol. 23: 85–112.

Carpita, N. C., Kanabus, J., and Housley, T. L. (1989) Linkage structure of fructans and fructan oligomers from Triticum aestivum and Festuca arundinacea leaves. J. Plant Physiol. 134: 162–168.

Cleland, W. W., Andrews, T. J., Gutteridge, S., Hartman, F. C., and Lorimer, G. H. (1998) Mechanism of Rubisco: The carbamate as a general base. Chem. Rev. 98: 549–561.

Crafts-Brandner, S. J., and Salvucci, M. E. (2000) Rubisco activase constrains the photosynthetic potential of leaves at high temperature. Proc. Natl. Acad. Sci. USA 97: 13430–13435.

Craig, S., and Goodchild, D. J. (1977) Leaf ultrastructure of Triodia irritans: A C4 grass possessing an unusual arrangement of photosynthetic tissues. Aust. J. Bot. 25: 277–290.

Cushman, J. C. and Bohnert, H. J. (1999) Crassulacean Acid Metabolism: Molecular Genetics. Annu. Rev. Plant Physiol. Plant Mol. Biol. 50: 305–332.

Dai, S., Schwendtmayer, C., Schürmann, P., Ramaswamy, S., and Eklund, H. (2000) Redox signaling in chloroplasts: Cleavage of disulfides by an iron-sulfur cluster. Science Jan 28, 287: 655–658.

Damager, I., Engelsen, S. B., Blennow, A., Møller, B. L., and Motawia, M. S. (2010) First principles insight into the α-glucan structures of starch: their synthesis, conformation, and hydration. Chem. Rev. 110: 2049–2080.

Dever, L. V., Bailey, K. J., Lacuesta, M., Leegood, R. C., and Lea, P. J. (1996) The isolation and characterization of mutants of the C4 plant Amaranthus edulis. In: Comptes Rendus de l'Academie des Sciences Series III. Sciences de la Vie 319: 951–959.

Drincovich, M. F., Casati, P., and Andreo, C. S. (2001) NADP-malic enzyme from plants: A ubiquitous enzyme involved in different metabolic pathways. FEBS Letters 490: 1–6.

Edwards, G. E., Franceschi, V. R., and Voznesenskaya, E. V. (2004) Single-cell C4 photosynthesis versus the dual-cell (Kranz) paradigm. Annu. Rev. Plant Biol. 55: 173–196.

Esau, B. D., Snyder, G. W., and Portis, A. R., Jr. (1996) Differential effects of N- and C-terminal deletions on the two activities of rubisco-activase. Arch. Biochem. Biophys. 326: 100–105.

Fersht, A. (1999) Structure and mechanism in protein science. A guide to enzyme catalysis and protein folding. W. H. Freeman & Co., New York, pp. 103–118.

Frederick, S. E., and Newcomb, E. H. (1969) Cytochemical localization of catalase in leaf microbodies (peroxisomes). J. Cell Biol. 43: 343–353.

Giordano, M., Beardall, J., and Raven, J. A. (2005) CO2 concentrating mechanisms in algae: Mechanisms, environmental modulation, and evolution. Annu. Rev. Plant Biol. 56: 99–131.

Goloubinoff, P., Christeller, J. T., Gatenby, A. A., and Lorimer, G. H. (1989) Reconstitution of active dimeric ribulose bisphosphate carboxylase from an unfolded state depends on two chaperonin proteins and Mg-ATP. Nature 342: 884–889

Gutierrez, M., Gracen, V. E., and Edwards, G. E. (1974) Biochemical and cytological relationships in C4 plants. Planta 119: 279–300.

Gutteridge, S. (1990) Limitations of the primary events of CO2 fixation in photosynthetic organisms: the structure and mechanism of rubisco. Biochem. Biophys. Acta 1015: 1–14.

Hanson, T. E., and Tabita, F. R. (2001) A ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO)-like protein from Chlorobium tepidum that is involved with sulfur metabolism and the response to oxidative stress. Proc. Natl. Acad. Sci. USA 98: 4397–4402.

Hartwell, J. (2005) The co-ordination of central plant metabolism by the circadian clock. Biochem. Soc. Trans. 33: 945–948.

Hatch, M. D., and Osmond, C. B. (1976) Compartmentation and transport in C4 photosynthesis. In Transport in Plants (Encyclopedia of Plant Physiology, New Series, vol. 3), C. R. Stocking and U. Heber, eds., Springer, Berlin, pp. 144–184.

Hatch, M. D., and Slack, C. R. (1966) Photosynthesis by sugarcane leaves. A new carboxylation reaction and the pathway of sugar formation. Biochem. J. 101: 103–111.

Hendry, G. (1993) Evolutionary origins and natural functions of fructans: A climatological, biogeographic and mechanistic appraisal. Phytol New. 123: 3–14.

Huber, S. C. (1986) Fructose-2,6-bisphosphate as a regulatory metabolite in plants. Annu. Rev. Plant Physiol. 37: 233–246.

Jensen, R. G. (2000) Activation of rubisco regulates photosynthesis at high temperature and CO2. Proc. Natl. Acad. Sci. USA 97: 12937–12938.

Jiao, J. A., and Chollet, R. (1991) Posttranslational regulation of phosphoenolpyruvate carboxylase in C4 and CAM plants. Plant Physiol. 95: 981–985.

Jordan, D. B., and Ogren, W. L. (1981) Species variation in the specificity of ribulose biphosphate carboxylase/oxygenase. Nature 291: 513–515.

Kallis, R. P., Ewy, R. G., and Portis, A. R., Jr. (2000) Alteration of the adenine nucleotide response and increased rubisco activation activity of Arabidopsis rubisco activase by site-directed mutagenesis. Plant Physiol. 123: 1077–1086.

Kaplan, A., Schwarz, R., Lieman-Hurwitz, J., and Reinhold, L. (1994) Physiological and molecular studies on the response of cyanobacteria to changes in the ambient inorganic carbon concentration. In The Molecular Biology of Cyanobacteria, D. Bryant, ed., Kluwer, Dordrecht, Netherlands, pp. 469–485.

Kozaki, A., and Takeba, G. (1996) Photorespiration protects C3 plants from photooxidation. Nature 384: 557–560.

Kroth, P. G., Chiovitti, A., Gruber, A., Martin-Jezequel, V., Mock, T., Parker, M. S., Stanley, M. S., Kaplan, A., Caron, L., Weber, T., Maheswari, U., Armbrust, E. V., and Bowle, C. (2008) A Model for Carbohydrate Metabolism in the Diatom Phaeodactylum tricornutum Deduced from Comparative Whole Genome Analysis. PLoS ONE 3: e1426.

Kruger, N. J., and von Schaewen, A. (2003) The oxidative pentose phosphate pathway: Structure and organisation. Curr. Opin. Plant Biol. 6: 236–246.

Ku, S. B., and Edwards, G. E. (1978) Oxygen inhibition of photosynthesis. III. Temperature dependence of quantum yield and its relation to O2 /CO2 solubility ratio. Planta 140: 1–6.

Lewis, E., and Wallace, D. Program developed for CO2 system calculations. ORNL/CDIAC-105. Carbon Dioxide Information Analysis Center, Oak Ridge National Laboratory, U.S.Departament of Energy: Oak Ridge, TN, 1998.

Lorimer, G. H. (1981) The carboxylation and oxygenation of ribulose-1,5-bisphosphate: The primary events in photosynthesis and photorespiration. Annu Rev. Plant Physiol. 32: 349–383.

Lüttge, U. (2002) CO2-concentrating: consequences in crassulacean acid metabolism. J. Exp. Bot. 53: 2131–2142.

Lüttge, U., and Higinbotham, N. (1979) Transport in Plants. Springer-Verlag, New York.

Marocco, J. P., Ku, M. S. B., Lea, P. J., Dever, L. V., Leegood, R. C., Furbank, R. T., and Edwards, G. E. (1998) Oxygen requirement and inhibition of C4 photosynthesis: An analysis of C4 plants deficient in the C3 and C4 cycles. Plant Physiol. 116: 823–832.

Maier, R. M., Neckermann, K., Igloi, G. L., and Koessel, H. (1995) Complete sequence of the maize chloroplast genome: Gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J. Mol. Biol. 251: 614–628.

Maxwell, K., Borland, A. M., Haslam, R. P., Helliker, B. R., Roberts, A., and Griffiths, H. (1999) Modulation of Rubisco Activity during the Diurnal Phases of the Crassulacean Acid Metabolism Plant Kalanchoe daigremontiana. Plant Physiol. 121: 849–856.

Morse, D., Salois, P., Markovic, P., and Hastings, J. W. (1995) A nuclear encoded form II RuBisCO in dinoflagellates. Science 268: 1622–1624.

Neuhaus, H. E., and Wagner, R. (2000) Solute pores, ion channels, and metabolite transporters in the outer and inner envelope membranes of higher plant plastids. Biochim. Biophys. Acta 1465: 307–323.

Ogawa, T., and Kaplan, A. (1987) The stoichiometry between CO2 and H+ fluxes involved in the transport of inorganic carbon in cyanobacteria. Plant Physiol. 83: 888–891.

Ott, C. M., Smith, B. D., Portis, A. R., Jr.,and Spreitzer, R. J. (2000) Activase region on chloroplast ribulose-1,5-bisphosphate carboxylase/oxygenase. J. Biol. Chem. 275: 26241–26244.

Pickersgill, R. W. (1986) An upper limit to the active site concentration of ribulose bisphosphate carboxylase in chloroplasts. Biochem. J. 236: 311.

Palmer, J. D. (1996) Rubisco surprises in dinoflagellates. Plant Cell 8: 343–345.

Pontis, H. G., and del Campillo, E. (1985) Fructans: In Biochemistry of Storage Carbohydrates in Green Plants, P. M. Dey and R. A. Dixon, eds., Academic Press, London, pp. 205–227.

Portis, A. R., Jr. (1992) Regulation of ribulose-1 5-bisphosphate carboxylase-oxygenase activity Annu. Rev. Plant Physiol. Molec. Biol. 43: 415–437.

Portis, A. R., Jr., Salvucci, M. E., and Ogren, W. L. (1986) Activation of ribulosebisphosphate carboxylase/oxygenase at physiological CO2 and ribulosebisphosphate concentrations by rubisco activase. Plant Physiol. 82: 967–971.

Raines, C. A., Harrison, E. P., Olcer, H., and Lloyd, J. C. (2000) Investigating the role of the thiol-regulated enzyme sedoheptulose-1,7-bisphosphatase in the control of photosynthesis. Physiol. Plantarum 110: 303–308.

Reinfelder, J. R., Kraepiel, A. M. L., and Morel, F. M. M. (2000) Unicellular C4 photosynthesis in a marine diatom. Nature 407: 996–999.

Reinfelder, J. R., Milligan, A. J., and Morel, F. M. M. (2004) The role of the C4 pathway in carbon accumulation and fixation in a marine diatom. Plant Physiol. 135: 2106–2111.

Reith, M. (1995) Molecular biology of rhodophyte and chromophyte plastids. Annu. Rev. Plant Physiol. Plant Mol. Biol. 46: 549–575.

Ridout, M. J., Parker, M. L., Hedley, C. L., Bogracheva, T. Y., and Morris, V. J. (2003) Atomic force microscopy of pea starch granules: granule architecture of wild-type parent, r and rb single mutants, and the rrb double mutant. Carbohyd Res. 338: 2135–2147.

Ritsema, T., and Smeekens, S. (2003) Fructans: Beneficial for plants and humans. Curr. Opin. Plant Biol. 6: 223–230.

Sage, R. F. (2002) C4 photosynthesis in terrestrial plants does not require Kranz anatomy. Trends Biochem. Sci. 7: 283–285.

Salvucci, M. E., and Ogren, W. L. (1996) The mechanism of Rubisco activase: Insights from studies of the properties and structure of the enzyme. Photosynth. Res. 47: 1–11.

Salvucci, M. E., Werneke, J. M., Ogren, W. L., and Portis, A. R., Jr. (1987) Purification and species distribution of rubisco activase. Plant Physiol. 84: 930–936.

Scheibe, R. (1990) Light/dark modulation: Regulation of chloroplast metabolism in a new light. Bot. Acta 103: 327–334.

Schürmann, P., and Jacquot, J.-P (2000) Plant thioredoxin systems revisited. Ann. Rev. Plant Physiol. Plant Mol. Biol. 51: 1040–2519.

Shtilerman, M., Lorimer, G. H., and Englander, S. W. (1999) Chaperonin function: Folding by forced unfolding. Science 284: 822–825.

Tang, H., Mitsunaga, T., and Kawamura, Y. (2006) Molecular arrangement in blocklets and starch granule architecture. Carbohyd Polym. 63: 555–560.

Taylor, T. C., and Andersson, I. (1996) Structural transitions during activation and ligand binding in hexadecameric Rubisco inferred from the crystal structure of the activated unliganded spinach enzyme. Nature Struct. Biol. 3: 95–101.

Van den Ende, W., De Coninck, B., and Van Laere, A. (2004) Plant fructan exohydrolases: A role in signaling and defense? T. Plant Sci. 9: 523–528.

Vernon, D. M., Ostrem, J. A., and Bohnert, H. J. (1993) Stress perception and response in a facultative halophyte: The regulation of salinity-induced genes in Mesembryanthemum crystallinum. Plant Cell Environ. 16: 437–444.

Weber, A. P. M. (2004) Solute transporters as connecting elements between cytosol and plastid stroma. Curr. Op. Plant Biol. 7: 247–253.

Weber, A. P. M., Schwacke, R., and Flugge, U. I. (2005) Solute transporters of the plastid envelope membrane. Annu. Rev. Plant Biol. 56: 133–164.

Weston, R. E. (2000) Climate changes and its effects on coral reefs. J. Chem. Ed. 77: 1574–1577.

Whitney, S. M., Shaw, D. C., and Yellowlees, F. (1995) Evidence that some dinoflagellates contain a ribulose-1,5-bisphosphate carboxylase/oxygenase related to that of the α-proteobacteria. Proc. R. Soc. Lond. B 259: 271–275.

Wolosiuk, R. A., Ballicora, M. A., and Hagelin, K. (1993) The reductive pentose phosphate cycle for photosynthetic carbon dioxide assimilation: Enzyme modulation. FASEB J. 7: 622–637.

Xiang, Y., Zhang, J., and Weeks, D. P. (2001) The Cia5 gene controls formation of the carbon concentrating mechanism in Chlamydomonas reinhardtii. Proc. Natl. Acad. Sci. USA 98: 5341–5346.

Zhang, N., and Portis, A. R. (1999) Mechanism of light regulation of Rubisco: A specific role for the larger Rubisco activase isoform involving reductive activation by thioredoxin-f. Proc. Natl. Acad. Sci. USA. 96: 9438–9443.