Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria

Wang, Zhuo; Zhu, Xin-Guang; Chen, Yazhu; Li, Yuanyuan; Hou, Jing; Li, Yixue; Liu, Lei
January 2006
BMC Genomics;2006, Vol. 7, p100
Academic Journal
Background: Chloroplasts descended from cyanobacteria and have a drastically reduced genome following an endosymbiotic event. Many genes of the ancestral cyanobacterial genome have been transferred to the plant nuclear genome by horizontal gene transfer. However, a selective set of metabolism pathways is maintained in chloroplasts using both chloroplast genome encoded and nuclear genome encoded enzymes. As an organelle specialized for carrying out photosynthesis, does the chloroplast metabolic network have properties adapted for higher efficiency of photosynthesis? We compared metabolic network properties of chloroplasts and prokaryotic photosynthetic organisms, mostly cyanobacteria, based on metabolic maps derived from genome data to identify features of chloroplast network properties that are different from cyanobacteria and to analyze possible functional significance of those features. Results: The properties of the entire metabolic network and the sub-network that consists of reactions directly connected to the Calvin Cycle have been analyzed using hypergraph representation. Results showed that the whole metabolic networks in chloroplast and cyanobacteria both possess small-world network properties. Although the number of compounds and reactions in chloroplasts is less than that in cyanobacteria, the chloroplast's metabolic network has longer average path length, a larger diameter, and is Calvin Cycle -centered, indicating an overall less-dense network structure with specific and local high density areas in chloroplasts. Moreover, chloroplast metabolic network exhibits a better modular organization than cyanobacterial ones. Enzymes involved in the same metabolic processes tend to cluster into the same module in chloroplasts. Conclusion: In summary, the differences in metabolic network properties may reflect the evolutionary changes during endosymbiosis that led to the improvement of the photosynthesis efficiency in higher plants. Our findings are consistent with the notion that since the light energy absorption, transfer and conversion is highly efficient even in photosynthetic bacteria, the further improvements in photosynthetic efficiency in higher plants may rely on changes in metabolic network properties.


Related Articles

  • SHARP: genome-scale identification of gene–protein–reaction associations in cyanobacteria. Krishnakumar, S.; Durai, Dilip A.; Wangikar, Pramod P.; Viswanathan, Ganesh A. // Photosynthesis Research;Nov2013, Vol. 117 Issue 1-3, p181 

    Genome scale metabolic model provides an overview of an organism’s metabolic capability. These genome-specific metabolic reconstructions are based on identification of gene to protein to reaction (GPR) associations and, in turn, on homology with annotated genes from other organisms....

  • Recent advances in understanding the assembly and repair of photosystem II. Nixon, Peter J.; Michoux, Franck; Jianfeng Yu; Boehm, Marko; Komenda, Josef // Annals of Botany;Jul2010, Vol. 106 Issue 1, p1 

    Background: Photosystem II (PSII) is the light-driven water:plastoquinone oxidoreductase of oxygenic photosynthesis and is found in the thylakoid membrane of chloroplasts and cyanobacteria. Considerable attention is focused on how PSII is assembled in vivo and how it is repaired following...

  • Construction of a Genome-Scale Metabolic Model of Arthrospira platensis NIES-39 and Metabolic Design for Cyanobacterial Bioproduction. Yoshikawa, Katsunori; Aikawa, Shimpei; Kojima, Yuta; Toya, Yoshihiro; Furusawa, Chikara; Kondo, Akihiko; Shimizu, Hiroshi // PLoS ONE;12/7/2015, Vol. 10 Issue 12, p1 

    Arthrospira (Spirulina) platensis is a promising feedstock and host strain for bioproduction because of its high accumulation of glycogen and superior characteristics for industrial production. Metabolic simulation using a genome-scale metabolic model and flux balance analysis is a powerful...

  • Arabidopsis thaliana mutants lacking cpFtsY or cpSRP54 exhibit different defects in photosystem II repair. Walter, Björn; Pieta, Thomas; Schünemann, Danja // Frontiers in Plant Science;Apr2015, p1 

    Photosystem II (PS II) is a multi subunit protein complex embedded in the thylakoid membrane of cyanobacteria and chloroplasts. As the PS II reaction center protein D1 is prone to a light induced damage that inhibits PS II function especially at elevated light intensities, a highly ordered...

  • Dielectric and photoelectric properties of photosynthetic reaction centers. Chamorovsky, C.S.; Chamorovsky, S.K.; Semenov, A.Yu. // Biochemistry (00062979);Feb2005, Vol. 70 Issue 2, p257 

    A brief review of studies of dielectric and photoelectric properties of photosynthetic reaction centers of purple bacteria as well as photosystem I and photosystem II of cyanobacteria and higher plants is given. A simple kinetic model of the primary processes of electron transfer in...

  • Ocean bacteria surf the genome wave. Gunter, Chris // Nature Reviews Genetics;Oct2003, Vol. 4 Issue 10, p761 

    Discusses research being done on the genome of photosynthetic picoplanktonic marine cyanobacteria. Reference to several studies published in a 2003 issue of the "Proceedings of the National Academy of Sciences" journal; Use of genome sequencing in the experiments.

  • Complete Genome Structure of the Unicellular Cyanobacterium Synechocystis sp. PCC6803. Kaneko, Takakazu; Tabata, Satoshi // Plant & Cell Physiology;Nov1997, Vol. 38 Issue 11, p1171 

    Cyanobacteria are photoautotrophic organisms capable of oxygen-producing photosynthesis similar to that in eukaryotic algae and plants, and because of this, they have been used as model organisms for the study of the mechanism and regulation of oxygen-producing photosynthesis. To understand the...

  • Cyanobacteria: photosynthetic factories combining biodiversity, radiation resistance, and genetics to facilitate drug discovery. Cassier-Chauvat, Corinne; Dive, Vincent; Chauvat, Franck // Applied Microbiology & Biotechnology;Feb2017, Vol. 101 Issue 4, p1359 

    Cyanobacteria are ancient, abundant, and widely diverse photosynthetic prokaryotes, which are viewed as promising cell factories for the ecologically responsible production of chemicals. Natural cyanobacteria synthesize a vast array of biologically active (secondary) metabolites with great...

  • Photosynthesis genes in marine viruses yield proteins during host infection. Lindell, Debbie; Jaffe, Jacob D.; Johnson, Zackary I.; Church, George M.; Chisholm, Sallie W. // Nature;11/3/2005, Vol. 438 Issue 7064, p86 

    Cyanobacteria, and the viruses (phages) that infect them, are significant contributors to the oceanic ‘gene pool’. This pool is dynamic, and the transfer of genetic material between hosts and their phages probably influences the genetic and functional diversity of both. For example,...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics