標題: Evolution of Domain Architectures and Catalytic Functions of Enzymes in Metabolic Systems
作者: Suen, Summit
Lu, Henry Horng-Shing
Yeang, Chen-Hsiang
統計學研究所
Institute of Statistics
關鍵字: protein domain architecture;metabolic reaction;parsimony;max-product;protein duplication
公開日期: 2012
摘要: Domain architectures and catalytic functions of enzymes constitute the centerpieces of a metabolic network. These types of information are formulated as a two-layered network consisting of domains, proteins, and reactions-a domain-protein-reaction (DPR) network. We propose an algorithm to reconstruct the evolutionary history of DPR networks across multiple species and categorize the mechanisms of metabolic systems evolution in terms of network changes. The reconstructed history reveals distinct patterns of evolutionary mechanisms between prokaryotic and eukaryotic networks. Although the evolutionary mechanisms in early ancestors of prokaryotes and eukaryotes are quite similar, more novel and duplicated domain compositions with identical catalytic functions arise along the eukaryotic lineage. In contrast, prokaryotic enzymes become more versatile by catalyzing multiple reactions with similar chemical operations. Moreover, different metabolic pathways are enriched with distinct network evolution mechanisms. For instance, although the pathways of steroid biosynthesis, protein kinases, and glycosaminoglycan biosynthesis all constitute prominent features of animal-specific physiology, their evolution of domain architectures and catalytic functions follows distinct patterns. Steroid biosynthesis is enriched with reaction creations but retains a relatively conserved repertoire of domain compositions and proteins. Protein kinases retain conserved reactions but possess many novel domains and proteins. In contrast, glycosaminoglycan biosynthesis has high rates of reaction/protein creations and domain recruitments. Finally, we elicit and validate two general principles underlying the evolution of DPR networks: 1) duplicated enzyme proteins possess similar catalytic functions and 2) the majority of novel domains arise to catalyze novel reactions. These results shed new lights on the evolution of metabolic systems.
URI: http://hdl.handle.net/11536/20938
http://dx.doi.org/10.1093/gbe/evs072
ISSN: 1759-6653
DOI: 10.1093/gbe/evs072
期刊: GENOME BIOLOGY AND EVOLUTION
Volume: 4
Issue: 9
起始頁: 976
結束頁: 993
顯示於類別:期刊論文


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  1. 000313212900008.pdf