Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria.
Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria.
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通过对叶绿体和光合细菌之间代谢网络的比较分析来探索光合作用的演变。
DOI：
10.1186/1471-2164-7-100
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发表时间：
2006-04-30
期刊：
影响因子：
4.4
通讯作者：
Liu, Lei
中科院分区：
文献类型：
--
作者：
Wang, Zhuo;Zhu, Xin-Guang;Chen, Yazhu;Li, Yuanyuan;Hou, Jing;Li, Yixue;Liu, Lei
叶绿体起源于蓝藻，并在内共生事件后急剧减少基因组。祖先蓝藻基因组的许多基因已经通过水平基因转移转移到植物核基因组。然而，叶绿体中有一组选择性的代谢途径是通过叶绿体基因组编码酶和核基因组编码酶来维持的。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？基于基因组数据的代谢图谱，我们比较了叶绿体和原核光合生物（主要是蓝藻）的代谢网络特性，找出了与蓝藻不同的叶绿体网络特性特征，并分析了这些特征可能的功能意义。用超图表示分析了整个代谢网络和直接与卡尔文循环相连的反应组成的子网络的性质。结果表明，叶绿体和蓝藻的整个代谢网络都具有小世界网络特性。虽然叶绿体中化合物和反应的数量比蓝藻少，但叶绿体代谢网络的平均路径长度更长，直径更大，并且以卡尔文循环为中心，表明叶绿体中具有特定和局部高密度区域的整体不那么密集的网络结构。此外，叶绿体代谢网络表现出比蓝藻更好的模块化组织。在叶绿体中，参与相同代谢过程的酶往往聚集在同一个模块中。综上所述，代谢网络特性的差异可能反映了高等植物内共生过程中的进化变化，从而导致光合效率的提高。由于光能的吸收、转移和转化在光合细菌中也是非常高效的，因此高等植物光合效率的进一步提高可能依赖于代谢网络特性的变化。
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.