title: Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: The W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, 1201 W, Gregory Dr., Urbana, Illinois 61801, USA. zhuowang@sjtu.edu.cn
authors.forename: Zhuo
authors.initials: Z
authors.lastname: Wang
authors.forename: Xin-Guang
authors.initials: XG
authors.lastname: Zhu
authors.forename: Yazhu
authors.initials: Y
authors.lastname: Chen
authors.forename: Yuanyuan
authors.initials: Y
authors.lastname: Li
authors.forename: Jing
authors.initials: J
authors.lastname: Hou
authors.forename: Yixue
authors.initials: Y
authors.lastname: Li
authors.forename: Lei
authors.initials: L
authors.lastname: Liu
mesh_terms: D017360:Arabidopsis / Q000378:metabolism; D005075:Biological Evolution; D002736:Chloroplasts / Q000378:metabolism*; D003198:Computer Simulation; D000458:Cyanobacteria / Q000378:metabolism*; D030541:Databases, Genetic; D004926:Escherichia coli / Q000378:metabolism; D010788:Photosynthesis / Q000502:physiology*