Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China.
BMC Evol Biol. 2013 Oct 3;13:219. doi: 10.1186/1471-2148-13-219.
Guanine-cytosine (GC) composition is an important feature of genomes. Likewise, amino acid composition is a distinct, but less valued, feature of proteomes. A major concern is that it is not clear what valuable information can be acquired from amino acid composition data. To address this concern, in-depth analyses of the amino acid composition of the complete proteomes from 63 archaea, 270 bacteria, and 128 eukaryotes were performed.
Principal component analysis of the amino acid matrices showed that the main contributors to proteomic architecture were genomic GC variation, phylogeny, and environmental influences. GC pressure drove positive selection on Ala, Arg, Gly, Pro, Trp, and Val, and adverse selection on Asn, Lys, Ile, Phe, and Tyr. The physico-chemical framework of the complete proteomes withstood GC pressure by frequency complementation of GC-dependent amino acid pairs with similar physico-chemical properties. Gln, His, Ser, and Val were responsible for phylogeny and their constituted components could differentiate archaea, bacteria, and eukaryotes. Environmental niche was also a significant factor in determining proteomic architecture, especially for archaea for which the main amino acids were Cys, Leu, and Thr. In archaea, hyperthermophiles, acidophiles, mesophiles, psychrophiles, and halophiles gathered successively along the environment-based principal component. Concordance between proteomic architecture and the genetic code was also related closely to genomic GC content, phylogeny, and lifestyles.
Large-scale analyses of the complete proteomes of a wide range of organisms suggested that amino acid composition retained the trace of GC variation, phylogeny, and environmental influences during evolution. The findings from this study will help in the development of a global understanding of proteome evolution, and even biological evolution.
鸟嘌呤-胞嘧啶（GC）组成是基因组的一个重要特征。同样，氨基酸组成是蛋白质组的一个独特但价值较低的特征。人们主要关心的是，从氨基酸组成数据中可以获得哪些有价值的信息还不清楚。为了解决这个问题，对来自 63 种古菌、270 种细菌和 128 种真核生物的完整蛋白质组的氨基酸组成进行了深入分析。
对氨基酸矩阵的主成分分析表明，蛋白质组结构的主要贡献者是基因组 GC 变化、系统发育和环境影响。GC 压力导致 Ala、Arg、Gly、Pro、Trp 和 Val 发生正选择，Asn、Lys、Ile、Phe 和 Tyr 发生负选择。完整蛋白质组的物理化学框架通过具有相似物理化学性质的 GC 依赖氨基酸对的频率互补来抵抗 GC 压力。Gln、His、Ser 和 Val 负责系统发育，它们的组成成分可以区分古菌、细菌和真核生物。环境生态位也是决定蛋白质组结构的一个重要因素，特别是对于古菌，其主要氨基酸是 Cys、Leu 和 Thr。在古菌中，高温菌、嗜酸菌、中温菌、嗜冷菌和嗜盐菌依次沿着基于环境的主成分聚集。蛋白质组结构与遗传密码之间的一致性也与基因组 GC 含量、系统发育和生活方式密切相关。
对广泛的生物体完整蛋白质组的大规模分析表明，氨基酸组成在进化过程中保留了 GC 变化、系统发育和环境影响的痕迹。本研究的结果将有助于全面了解蛋白质组进化，甚至是生物进化。
