E-photosynthesis: A comprehensive modeling approach to understand chlorophyll fluorescence transients and other complex dynamic features of photosynthesis in fluctuating light

Photosynthesis Research

Volumn 93, Issue 1-3, 2007, Pages 223-234

  Nedbal, Ladislav ^a,b   Červený, Jan ^a,b,c   Rascher, Uwe ^d   Schmidt, Henning ^e  

^a INSTITUTE OF LANDSCAPE ECOLOGY   (Czech Republic)

^b UNIVERSITY OF SOUTH BOHEMIA   (Czech Republic)

^c CZECH TECHNICAL UNIVERSITY IN PRAGUE   (Czech Republic)

^d FORSCHUNGSZENTRUM JÜLICH   (Germany)

^e FRAUNHOFER CHALMERS CENTRE   (Sweden)

Author keywords

Chlorophyll fluorescence emission; Forced oscillations; Model reduction; Non linearity; Photosystem II; System biology; System decomposition

Indexed keywords

CHLOROPHYLL;

BIOLOGICAL MODEL; FLUORESCENCE; LIGHT; METABOLISM; PHOTOSYNTHESIS; RADIATION EXPOSURE; REVIEW; SYSTEMS BIOLOGY;

CHLOROPHYLL; FLUORESCENCE; LIGHT; MODELS, BIOLOGICAL; PHOTOSYNTHESIS; SYSTEMS BIOLOGY;

EID: 34548192057     PISSN: 01668595     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11120-007-9178-9     Document Type: Review

References (71)

1. Beck F, Blasius B, Lüttge U et al (2001) Stochastic noise interferes coherently with a model biological clock and produces specific dynamic behaviour. Proc Roy Soc Lond Ser B Biol Sci 268:1307-1313
2. Bernhardt K, Trissl HW (1999) Theories for kinetics and yields of fluorescence and photochemistry: how, if at all, can different models of antenna organization be distinguished experimentally? Biochim Biophys Acta Bioenergetics 1409:125-142
3. Black CC, Osmond CB (2003) Crassulacean acid metabolism photosynthesis: 'working the night shift'. Photosynth Res 76:329-341
4. Blasius B, Beck F, Lüttge U (1998) Oscillatory model of crassulacean acid metabolism: structural analysis and stability boundaries with a discrete hysteresis switch. Plant Cell Environ 21:775-784
5. Blasius B, Neff R, Beck F et al (1999) Oscillatory model of crassulacean acid metabolism with a dynamic hysteresis switch. Proc Roy Soc Lond Ser B Biol Sci 266:93-101
6. Blankenship RE (2002) Molecular mechanisms of photosynthesis. Blackwell Publishing, Oxford, UK
7. Bohn A, Geist A, Rascher U et al (2001) Responses to different external light rhythms by the circadian rhythm of crassulacean acid metabolism in Kalanchoë daigremontiana. Plant Cell Environ 24:811-820
8. Bohn A, Rascher U, Hütt MT et al (2002) Responses of a plant circadian rhythm to thermoperiodic perturbations with asymmetric temporal patterns and the rate of temperature change. Biol Rhythm Res 33:151-170
9. Csete ME, Doyle JC (2002) Reverse engineering of biological complexity. Science 295:1664-1669
10. Danø S, Madsen M, Schmidt H et al (2006) Reduction of a biochemical model with preservation of its basic dynamic properties. FEBS J 273:4862-4877
11. Dau H (1994) Molecular mechanism and quantitative models of variable photosystem II fluorescence. Photochem Photobiol 60:1-23
12. Duysens LNM, Sweers HE (1963) Mechanism of the two photochemical reactions in algae as studied by means of fluorescence. In: Japanese Society of Plant Physiologists (eds) Studies on microalgae and photosynthetic bacteria. University of Tokyo Press, Tokyo, Japan, pp 353-372
13. Farquhar GD, von Caemmerer S, Berry JA (2001) Models of photosynthesis. Plant Physiol 125:42-45
14. Fietz S, Nicklisch A (2002) Acclimation of the diatom Stephanodiscus neoastraea and the cyanobacterium Planktothrix agardhii to simulated natural light fluctuations. Photosynth Res 72:95-106
15. Genty B, Briantais JM, Baker NR (1989) The relationship between the quantum yield of photosynthetic electron-transport and quenching of chlorophyll fluorescence. Biochem Biophys Acta 990:87-92
16. Golbeck JH (ed) (2006) Photosystem I. The light-driven plastocyanin: ferredoxin oxidoreductase. Advances in photosynthesis and respiration, vol 24. Springer, Dordrecht, The Netherlands
17. Govindjee (1990) Photosystem II heterogeneity: electron acceptor side. Photosynth Res 25:151-160
18. Govindjee (1995) Sixty-three years since Kautsky: chlorophyll a fluorescence. Aust J Plant Physiol 22:131-160
19. Grams TEE, Borland AM, Roberts A et al (1997) On the mechanism of reinitiation of endogenous Crassulacean acid metabolism rhythm by temperature changes. Plant Physiol 113:1309-1317
20. Hindmarsh AC, Brown PN, Grant KE et al (2005) SUNDIALS: Suite of nonlinear and differential/algebraic equation solvers. Acm Transact Math Software 31:363-396
21. Holzwarth AR, Müller MG, Niklas J et al (2006) Ultrafast transient absorption studies on Photosystem I reaction centers from Chlamydomonas reinhardtii. 2: mutations near the P700 reaction center chlorophylls provide new insight into the nature of the primary electron donor. Biophys J 90:552-565
22. Holzwarth AR, Müller MG, Reus M et al (2006) Kinetics and mechanism of electron transfer in intact photosystem II and in the isolated reaction center: Pheophytin is the primary electron acceptor. Proc Natl Acad Sci USA 103:6895-6900
23. Hucka M, Finney A, Sauro HM et al (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19:524-531
24. Hütt MT, Lüttge U (2002) Nonlinear dynamics as a tool for modelling in plant physiology. Plant Biol 4:281-297
25. Joliot A, Joliot P (1964) Etudes cinétique de la réaction photochimique libérant l'oxygéne au cours de la photosynthése. CR Acad Sci Paris 258D:4622-4625
26. Kautsky H, Hirsch A (1931) Neue Versuche zur Kohlensä ureassimilation. Naturwiss 19:964
27. Kitano H (2001) Foundations of systems biology. MIT Press, Cambridge
28. Kitano H (2002) Systems biology: a brief overview. Science 295:1662-1664
29. Korn RW (2005) The emergence principle in biological hierarchies. Biol Philos 20:137-151
30. Kulheim C, Agren J, Jansson S (2002) Rapid regulation of light harvesting and plant fitness in the field. Science 297:91-93
31. Lavergne J, Trissl H (1995) Theory of fluorescence induction in Photosystem II: Derivation of analytical expressions in a model including exciton-radical-pair equilibrium and restricted energy transfer between photosynthetic units. Biophys J 68:2474-2492
32. Lavergne J, Briantais J-M (1996) Photosystem II heterogeneity. In: Ort DR, Yocum CF (eds) Oxygenic photosynthesis: the light reactions. advances in photosynthesis, vol 4. Kluwer, Dordrecht, The Netherlands, pp 265-287
33. Lazár D (1999) Chlorophyll a fluorescence induction. Biochim Biophys Acta 1412:1-28
34. Lazár D (2006) The polyphasic chlorophyll a fluorescence rise measured under high intensity of exciting light. Funct Plant Biol 33:9-30
35. Liebermeister W, Baur U, Klipp E (2005) Biochemical network models simplified by balanced truncation. FEBS J 272:4034-4043
36. Ljung L (1981) Reglerteori, Moderna analys-och syntesmetoder. Studentlitteratur, Lund
37. 2 exchange in CAM plants without a concomitant rhythm of malate levels. Z Pflanzenphysiol 90:69-77
38. Lüttge U, Beck F (1992) Endogenous rhythms and chaos in crassulacean acid metabolism. Planta 188:28-38
39. Lüttge U, Grams TEE, Hechler B et al (1996) Frequency resonances of the circadian rhythm of CAM under external temperature rhythms of varied period lengths in continuous light. Bot Acta 109:422-426
40. Maertens J, Donckels BMR, Lequeux G et al (2005) Metabolic model reduction by metabolite pooling on the basis of dynamic phase planes and metabolite correlation analysis. Conference on modeling and simulation in biology. Linköping, Sweden, pp 147-151
41. Minorsky PV (2003) Achieving the in silico plant. Systems biology and the future of plant biological research. Plant Physiol 132:404-409
42. Müller MG, Niklas J, Lubitz W et al (2003) Ultrafast transient absorption studies on Photosystem I reaction centers from Chlamydomonas reinhardtii. 1. A new interpretation of the energy trapping and early electron transfer steps in Photosystem I. Biophys J 85:3899-3922
43. Nedbal L, Březina V, Adamec F et al (2003) Negative feedback regulation is responsible for the non-linear modulation of photosynthetic activity in plants dynamic light and cyanobacteria exposed to a environment. Biochim Biophys Acta 1607:5-17
44. Nedbal L, Březina V, Červený J et al (2005) Photosynthesis in dynamic light: systems biology of unconventional chlorophyll fluorescence transients in Synechocystis sp PCC 6803. Photosynth Res 84:99-106
45. Neubauer C, Schreiber U (1987) The polyphasic rise of chlorophyll fluorescence upon onset of strong continuous illumination: I. Saturation characteristics and partial control by the Photosystem II acceptor side. Z Naturforsch 42C:1246-1254
46. Novoderezhkin VI, Andrizhiyevskaya EG, Dekker JP, van Grondelle R (2005) Pathways and timescales of primary charge separation in the photosystem II reaction center as revealed by a simultaneous fit of time-resolved fluorescence and transient absorption. Biophys J 89:1464-1481
47. Okino MS, Mavrovouniotis ML (1998) Simplification of mathematical models of chemical reaction systems. Chem Rev 98:391-408
48. Papageorgiou GC, Govindjee (Eds) (2004) Chlorophyll a fluorescence: a signature of photosynthesis. Advances in photosynthesis and respiration, vol. 19, Springer, Dordrecht, The Netherlands
49. Poolman MG, Fell DA, Thomas S (2000) Modelling photosynthesis and its control. J Exp Bot 51:319-328
50. Poolman MG, Assmus HE, Fell DA (2004) Applications of metabolic modelling to plant metabolism. J Exp Bot 55:1177-1186
51. Popper KR (1990) The logic of scientific discovery. Unwin Hyman, London
52. Prigogine I (1969) Structure, dissipation and life. Theoretical physics and biology. North-Holland Publ. Company, Amsterdam
53. Prokhorenko VI, Holzwarth AR (2000) Primary processes and structure of the photosystem II reaction center: a photon echo study. J Phys Chem B 104:11563-11578
54. Quackenbush J (2006) Standardizing the standards. Mol Syst Biol 2:3-5
55. 2 exchange in the CAM plant Kalanchoë daigremontiana can be shifted by slow temperature changes. Planta 207:76-82
56. Rascher U, Hütt MT, Siebke K et al (2001) Spatiotemporal variation of metabolism in a plant circadian rhythm: the biological clock as an assembly of coupled individual oscillators. Proc Natl Acad Sci USA 98:11801-11805
57. Rascher U, Lüttge U (2002) High-resolution chlorophyll fluorescence imaging serves as a non-invasive indicator to monitor the spatio-temporal variations of metabolism during the day-night cycle and during the endogenous rhythm in continuous light in the CAM plant Kalanchoë daigremontiana. Plant Biol 4:671-681
58. Rascher U, Nedbal L (2006) Dynamics of plant photosynthesis under fluctuating natural conditions. Curr Opin Plant Biol 9:671-678
59. Rugh WJ (1996) Linear system theory, 2nd edn. Prentice-Hall
60. Sabbah S, Shashar N (2006) Underwater light polarization and radiance fluctuations induced by surface waves. Appl Opt 45:4726-4739
61. Schmidt H, Jacobsen EW (2004) Linear systems approach to analysis of complex dynamic behaviours in biochemical networks. Syst Biol 1:149-158
62. Schreiber U (2004) Pulse-amplitude-modulation (PAM) fluorometry and saturation pulse method: an overview. In: Papageorgiou GC, Govindjee (eds) Chlorophyll a fluorescence: a signature of photosynthesis. Advances in photosynthesis and respiration, vol 19, Springer, Dordrecht, pp 279-319
63. Schreiber U, Schliwa U, Bilger W (1986) Continuous recording of photochemical and nonphotochemical chlorophyll fluorescence quenching with a new type of modulation fluorometer. Photosynth Res 10:51-62
64. Schrödinger E (1945) What is life? The physical aspect of the living cell. Macmillan, New York
65. Sims DA, Pearcy RW (1993) Sunfleck frequency and duration affects growth-rate of the understorey plant, Alocasia-Macrorrhiza. Funct Ecol 7:683-689
66. Strasser R, Srivastava A, Govindjee (1995) Polyphasic chlorophyll a fluorescence transient in plants and cyanobacteria. Photochem Photobiol 61:32-42
67. van Grondelle R, Novoderezhkin VI (2006) Energy transfer in photosynthesis: experimental insights and quantitative models. Phys Chem Chem Phys 8:793-807
68. Warren DM, Wilkins MB (1961) An endogenous rhythm in the rate of dark-fixation of carbon dioxide in leaves of Bryophyllum Fedtschenkoi. Nature 191:686-688
69. Wiener N (1948) Cybernetics, or control and communication in the animal and the machine. Wiley, New York
70. Wydrzynski TJ, Satoh K (eds) (2005) Photosystem II the light-driven water: plastoquinone oxidoreductase. Advances in photosynthesis and respiration, vol. 22. Springer, Dordrecht, The Netherlands
71. Zimmermann P, Schildknecht B, Craigon D et al (2006) MIAME/Plant-adding value to plant microarrray experiments. Plant Meth 2:1, doi:10.1186/1746-4811-2- 1