山羊氨基酸代谢网络的重构与关键代谢基因的解析

Reconstruction of Amino Acid Metabolic Network and Investigation of Essential Metabolic Genes in Goats

氨基酸是参与生物体生命活动的基本物质之一,其代谢对山羊的诸多经济性状(如羊肉品质、山羊绒)有重要影响。随着生物信息学的快速发展,系统生物学方法被广泛用来研究生物体内代谢机制。为了阐明山羊体内氨基酸的代谢机制,本文通过构建代谢网络解析山羊氨基酸代谢机制,并通过网络分析发现关键代谢基因。研究首先使用山羊氨基酸代谢基因重新构建山羊氨基酸代谢网络,其次采用Cytoscape软件对该网络进行可视化,并利用R语言中的igraph程序包对氨基酸代谢网络的聚类系数、接近中心度、网络直径及密度等网络参数进行计算和分析。结果发现,山羊氨基酸代谢网络直径为13,密度为0.03,说明该代谢网络的拓扑结构表现出直径较大、密度较小、整个氨基酸代谢网络较复杂等特征。在该代谢网络中,发现10个相互没有联系的子网络模块,根据子网络的基因个数由多到少及其各自的主要功能将它们分别定义为谷胱甘肽转移酶模块、甲基转移酶模块、硒复合代谢模块、赖氨酸降解模块等。山羊氨基酸代谢网络的结构特点与氨基酸的生理功能是相辅相成的,这是山羊长期进化适应环境的结果。此外,本文从网络拓扑结构的角度确定13个对维持整个山羊氨基酸代谢网络具有重要意义的关键代谢基因,例如ABAT,AGXT2,ALDH3B1等。上述结果发现的代谢网络模块及关键代谢基因有助于从遗传层面进一步完善山羊氨基酸代谢的分子机制,可以为全面深入解析山羊与氨基酸代谢相关的经济性状的形成机制奠定了基础,同时也可以为改良相关的重要经济性状、品种培育提供了新的理论参考。

Amino acids are the most basic substances related to biological activities,and their metabolism has an important impact on the economic traits of goats(such as mutton quality and cashmere).With the rapid development of bioinformatics,system biology has been widely applied to investigate metabolic mechanism.In order to clarify the metabolic mechanism of amino acids in goats,this paper analyzes the metabolic network of amino acids in goats by constructing metabolic network,and identifies the key metabolic genes by network analysis.The metabolic network was visualized with Cytoscape.The network parameters(e.g.,clustering coefficient,proximity centrality,network diameter and density)were calculated and analyzed with the igraph package in R language.The results suggested that the network diameter and the density were 13 and 0.03 respectively,indicating that the whole amino acid metabolic network was complex.10 subnetwork modules were discovered and were independent from each other.According to gene number in the subnetwork and their biological functions,subnetwork modules were defined as glutathione transferase module,methyltransferase module,selenium complex metabolism module and lysine degradation module.These characteristics of amino acid metabolism network were in accordance to the physiological functions of amino acids and could be the result of long-term evolution and adaptation of goat environment.In addition,13 essential metabolic genes were identified,which played key roles in maintaining network topology of this metabolic network.For example,ABAT,AGXT2,ALDH3B1 were such essential metabolic genes.In summary,this study provides a comprehensive insight to molecular mechanism of amino acid metabolism in goat,which can lay a foundation for a comprehensive and in-depth understanding of formation mechanism of economic traits related to amino acid metabolism in goats,as well as new theoretical reference for improving important economic traits related to amino acids in goats.