Evolution of complete proteomes: guanine-cytosine pressure, phylogeny and environmental influences blend the proteomic architecture
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- 作者：Wanping Chen (11)
Yanchun Shao (10) (11)
Fusheng Chen (10) (11) (9) - 关键词：Proteome ; Evolution ; GC pressure ; Phylogeny ; Environmental influence
- 刊名：BMC Evolutionary Biology
- 出版年：2013
- 出版时间：December 2013
- 年：2013
- 卷：13
- 期：1
- 全文大小：1,346 KB
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Yanchun Shao (10) (11)
Fusheng Chen (10) (11) (9)
11. College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
10. National Key Laboratory of Agro-Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
9. Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China - ISSN：1471-2148
文摘
Background 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. Results 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. Conclusions 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.