Wang Zhuo, Zhu Xin-Guang, Chen Yazhu, Li Yuanyuan, Hou Jing, Li Yixue, Liu Lei
The W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, 1201 W, Gregory Dr., Urbana, Illinois 61801, USA.
BMC Genomics. 2006 Apr 30;7:100. doi: 10.1186/1471-2164-7-100.
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.
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.
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.
叶绿体起源于蓝细菌，在一次内共生事件后其基因组大幅缩减。许多祖先蓝细菌基因组的基因已通过水平基因转移转移到植物核基因组中。然而，叶绿体利用叶绿体基因组编码和核基因组编码的酶维持了一组选择性的代谢途径。作为专门进行光合作用的细胞器，叶绿体代谢网络是否具有适应更高光合作用效率的特性？我们基于从基因组数据推导的代谢图谱，比较了叶绿体与原核光合生物（主要是蓝细菌）的代谢网络特性，以识别叶绿体网络特性中与蓝细菌不同的特征，并分析这些特征可能的功能意义。
使用超图表示法分析了整个代谢网络以及由直接连接到卡尔文循环的反应组成的子网络的特性。结果表明，叶绿体和蓝细菌中的整个代谢网络都具有小世界网络特性。尽管叶绿体中的化合物和反应数量少于蓝细菌，但叶绿体的代谢网络平均路径长度更长、直径更大，且以卡尔文循环为中心，表明其整体网络结构密度较低，在叶绿体中有特定的局部高密度区域。此外，叶绿体代谢网络比蓝细菌的表现出更好的模块化组织。参与相同代谢过程的酶在叶绿体中倾向于聚集到同一个模块中。
总之，代谢网络特性的差异可能反映了内共生过程中的进化变化，这些变化导致了高等植物光合作用效率的提高。我们的发现与以下观点一致：由于即使在光合细菌中光能的吸收、转移和转换也非常高效，高等植物光合作用效率的进一步提高可能依赖于代谢网络特性的变化。
