Though with constraints imposed by endosymbiosis,preferential attachment is still a plausible mechanism responsible for the evolution of the chloroplast metabolic network |
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Authors: | Z. WANG X.‐G. ZHU X. CHANG Y. Z. CHEN Y. X. LI L. LIU |
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Affiliation: | 1. College of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China;2. Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China;3. Department of Plant Biology, University of Illinois at Urbana‐Champaign, Urbana, IL, USA;4. Plant Systems Biology Group, Partner Institute of Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China;5. Shanghai Center for Bioinformation Technology, Shanghai, China |
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Abstract: | Chloroplasts evolved as a result of endosymbiosis, during which sophisticated mechanisms evolved to translocate nucleus‐encoded plastid‐targeted enzymes into the chloroplast to form the chloroplast metabolic network. Given the constraints and complexity of endosymbiosis, will preferential attachment still be a plausible mechanism for chloroplast metabolic network evolution? We answer this question by analysing the metabolic network properties of the chloroplast and a cyanobacterium, Synechococcus sp. WH8102 (syw). First, we found that enzymes related to more ancient pathways are more connected, and synthetases have the highest connectivity. Most of the enzymes shared by the two densest cores between the chloroplast and syw are synthetases. Second, the highly conserved functional modules mainly consist of highly connected enzymes. Finally, isozymes and enzymes from endosymbiotic gene transfer (EGT) were distributed mainly in conserved modules and showed higher connectivity than nonisozymes or non‐EGT enzymes. These results suggest that even with severe evolutionary constraints imposed by endosymbiosis, preferential attachment is still a plausible mechanism responsible for the evolution of the chloroplast metabolic network. However, the current analysis may not completely differentiate whether the chloroplast network properties reflect the evolution of the chloroplast network through preferential attachment or has been inherited from its cyanobacterial ancestor. To fully differentiate these two possibilities, further analyses of the metabolic network structure properties of organisms at various intermediate evolutionary stages between cyanobacteria and the chloroplast are needed. |
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Keywords: | chloroplast endosymbiotic gene transfer evolution metabolic network photosynthesis preferential attachment |
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