Advertisement

Natural Computing

, 8:847 | Cite as

A photosynthetic process modelled by a metabolic P system

  • Vincenzo Manca
  • Roberto Pagliarini
  • Simone Zorzan
Article

Abstract

Photosynthesis is the process used by plants, algae and some bacteria to obtain biochemical energy from sunlight. It is the most important process allowing life on earth. In this work, by applying the Log Gain theory of Metabolic P Systems, we define a mathematical model of an important photosynthetic phenomenon, called Non Photochemical Quenching (shortly NPQ), that determines the plant accommodation to the environmental light. Starting from experimental data of this phenomenon, we are able to deduce a Metabolic P system which provides, in a specific simplified case, the regulation mechanism underling the NPQ process. The dynamics of our model, generated by suitable computational tools, reproduce, with a very good approximation, the observed behaviour of the natural system.

Keywords

P systems Metabolic P systems Discrete dynamical systems Biomolecular dynamics Photosynthesis Non photochemical quenching process 

Notes

Acknowledgments

The authors are grateful to Prof. Bassi’s group of Biotechnological Department, at University of Verona, for laboratory analysis and Dr. Petronia Carillo, Department of Life Sciences, Second University of Naples, for CO2 uptake measurements.

References

  1. Ahn TK, Avenson TJ, Ballottari M, Cheng YC, Niyogi KK, Bassi R, Fleming GR (2008) Architecture of a charge-transfer state regulating light harvesting in a plant antenna protein. Science 320(5877):794–797Google Scholar
  2. Alder NN, Theg SM (2003) Energetics of protein transport across biological membranes: a study of the thylakoid \(\Updelta\) pH-dependent/cptat pathway. Cell 112:231–242CrossRefGoogle Scholar
  3. Allen JF (1995) Thylakoid protein phosphorylation, state 1-state 2 transitions, and photosystem stoichiometry adjustment: redox control at multiple levels of gene expression. Physiol Plant 93:196–205CrossRefGoogle Scholar
  4. Benson A, Calvin M (1950) Carbon dioxide fixation by green plants. Annu Rev Plant Physiol Plant Mol Biol 1:25–42Google Scholar
  5. Bianco L, Fontana F, Franco G, Manca V (2006a) P systems for biological dynamics. In: Ciobanu G, Păun G, Pérez-Jiménez MJ (eds) Applications of membrane computing. Springer, Berlin, pp 81–126Google Scholar
  6. Bianco L, Fontana G, Manca V (2006) P systems with reaction maps. International Journal of Foundations of Computer Science 17(1):27–48zbMATHCrossRefMathSciNetGoogle Scholar
  7. Calzone L, Fages F, Soliman S (2006) BIOCHAM: an environment for modelling biological systems and formalizing experimental knowledge. Bioinformatics Application Note 22(14):1805–1807Google Scholar
  8. Castellini A, Manca V (2008) MetaPlab: a computational framework for metabolic P systems. In: Pre-Proceeding of the Ninth Workshop on membrane computing, July 28–31, 2008, Heriot-Watt University, EdinburghGoogle Scholar
  9. Castellini A, Franco G, Manca V (2008) Toward a representation of hybrid functional Petri nets by MP systems. In: Suzuki Y et al (eds) IWNC 2007. Springer, Berlin, pp 28–37Google Scholar
  10. Ciobanu G, Păun G, Pérez-Jiménez MJ (eds) (2006) Applications of membrane computing. Springer, BerlinGoogle Scholar
  11. Evron Y, McCarty RE (2000) Simultaneous measurement of deltapH and electron transport in chloroplast thylakoids by 9-aminoacridine fluorescence. Plant Physiol 124:407–414CrossRefGoogle Scholar
  12. Fontana F, Manca V (2007) Discrete solution to differential equations by metabolic P systems. Theor Comput Sci 372:165–182zbMATHCrossRefMathSciNetGoogle Scholar
  13. Fontana F, Bianco L, Manca V (2005) P systems and the modeling of biochemical oscillations. In: Freud R, Păun G, Rozenberg G, Salomaa A (eds) Membrane computing, WMC 2005, LNCS 3850. Springer, Berlin, pp. 199–208Google Scholar
  14. Fork DC, Herbert SK (1993) Electron transport and photophosphorylation by photosystem I in vivo in plants and cyanobacteria. Photosynth Res 36:149–168CrossRefGoogle Scholar
  15. Gilmore AM, Mohanty N, Yamamoto HY (1994) Epoxidation of zeaxanthin and antheraxanthin reverses non-photochemical quenching of photosystem II chlorophyll a fluorescence in the presence of trans-thylakoid \(\Updelta\) pH. FEBS Lett 350:271–274CrossRefGoogle Scholar
  16. Gisselsson A, Szilagyi A, Akerlund H (2004) Role of histidines in the binding of violaxanthin de-epoxidase to the thylakoid membrane as studied by site-directed mutagenesis. Physiol Plant 122:337–343CrossRefGoogle Scholar
  17. Holt NE, Zigmantas D, Valkunas L, Li X-P, Niyogi KK, Fleming GR (2005) Carotenoid cation formation and the regulation of photosynthetic light harvesting. Science 307:433–436CrossRefGoogle Scholar
  18. Holzwarth AR (1989) Applications of ultrafast laser spectroscopy for the study of biological systems. Q Rev Biophys 22:239–295CrossRefGoogle Scholar
  19. Kanazawa A, Kramer DM (2002) In vivo modulation of nonphotochemical exciton quenching (NPQ) by regulation of the chloroplast ATP synthase. PNAS 99(20):12789–12794CrossRefGoogle Scholar
  20. Kurka P (2003) Topological and symbolic dynamics. Société Mathématique de France, ParisGoogle Scholar
  21. Manca V (2006) Topics and problems in metabolic P systems. In: Păun G, Pérez-Jiménez MJ (eds) Membrane computing (BWMC4). Fenix Editora, Sevilla, SpainGoogle Scholar
  22. Manca V (2007a) Metabolic P systems for biochemical dynamics. Prog Nat Sci 17(4):384–391zbMATHCrossRefMathSciNetGoogle Scholar
  23. Manca V (2007b) MP systems approaches to biochemical dynamics: biological rhythms and oscillation. In: Hoogeboom HJ, Păun G, Rozenberg G, Salomaa A (eds) Membrane computing, WMC 2006. LNCS 4361, Springer, Berlin, p 8699Google Scholar
  24. Manca V (2008a) Log-gain principles for metabolic P systems. In: G. Rozenberg’s Festschrift. Springer (to appear)Google Scholar
  25. Manca V (2008b) The Metabolic algorithm: principles and applications. Theor Comput Sci 404:142–157zbMATHCrossRefMathSciNetGoogle Scholar
  26. Manca V (2008c) Discrete simulation of biochemical dynamics. In: Garzon MH, Yan H (eds) DNA 13. LNCS 4848, Springer, Berlin, pp 231–235Google Scholar
  27. Manca V, Bianco L (2008) Biological networks in metabolic P systems. BioSystems 91(3):489–498CrossRefGoogle Scholar
  28. Manca V, Bianco L, Fontana F (2005a) Evolutions and oscillations of P systems: applications to biological phenomena. In: Mauri G, Pérez-Jiménez MJ, Păun G, Rozenberg G, Salomaa A (eds) Membrane computing, WMC 2004. LNCS 3365, Springer, Berlin, pp 63–84Google Scholar
  29. Manca V, Franco G, Scollo (2005) State transition dynamics: basic concepts and molecular computing perspectives. In: Gheorghe M (ed) Molecular computational models: unconventional approachers Chapter 2. Idea Group Inc, UK, pp 32–55Google Scholar
  30. Müller P, Li XP, Niyogi KK (2001) Non-photochemical quenching. A response to excess light energy. Plant Physiol 125(4):1558–1566CrossRefGoogle Scholar
  31. Nelson N, Ben-Shem A (2006) The complex architecture of oxygenic photosynthesis. Nat Rev Mol Cell Biol (5):971–982CrossRefGoogle Scholar
  32. Nelson N, Yocum C (2006) Structure and Function of Photosystems I and II. Annu Rev Plant Biol (35):521–565CrossRefGoogle Scholar
  33. Obtulowicz A (2003) Probabilistic P systems. In: Păun G, Rozenberg G, Salomaa A (eds) Membrane computing. LNCS 2597. Springer, Berlin, pp 377–387Google Scholar
  34. Păun G (2000) Computing with membranes. J Comput Syst Sci 61(1):108–143zbMATHCrossRefGoogle Scholar
  35. Păun G (2002) Membrane computing. Springer, BerlinGoogle Scholar
  36. Pescini D, Besozzi D, Mauri G, Zandron C (2006) Dynamical probabilistic P systems. Int J Found Comput Sci 17(1):183–204zbMATHCrossRefMathSciNetGoogle Scholar
  37. Siefermann D, Yamamoto HY (1975) NADPH and oxygen-dependent epoxidation of zeaxanthin in isolated chloroplasts. Biochem Biophys Res Commun 62:456–461CrossRefGoogle Scholar
  38. Trubitsin BV, Tikhonov AN (2003) Determination of a transmembrane pH difference in chloroplasts with a spin label tempamine. J Magn Reson 163:257–269CrossRefGoogle Scholar
  39. Voit EO (2000) Computational analysis of biochemical systems. Cambridge University Press, CambridgeGoogle Scholar
  40. von Bertalanffy L (1967) General systems theory: foundations, developments, applications. George Braziller Inc., New York, NYGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Vincenzo Manca
    • 1
  • Roberto Pagliarini
    • 1
  • Simone Zorzan
    • 2
  1. 1.Computer Science DepartmentThe University of VeronaVeronaItaly
  2. 2.Biotechnological DepartmentThe University of VeronaVeronaItaly

Personalised recommendations