title: Hydrophobicity and aromaticity are primary factors shaping variation in amino acid usage of chicken proteome.
abstract: Amino acids are utilized with different frequencies both among species and among genes within the same genome. Up to date, no study on the amino acid usage pattern of chicken has been performed. In the present study, we carried out a systematic examination of the amino acid usage in the chicken proteome. Our data indicated that the relative amino acid usage is positively correlated with the tRNA gene copy number. GC contents, including GC1, GC2, GC3, GC content of CDS and GC content of the introns, were correlated with the most of the amino acid usage, especially for GC rich and GC poor amino acids, however, multiple linear regression analyses indicated that only approximately 10-40% variation of amino acid usage can be explained by GC content for GC rich and GC poor amino acids. For other intermediate GC content amino acids, only approximately 10% variation can be explained. Correspondence analyses demonstrated that the main factors responsible for the variation of amino acid usage in chicken are hydrophobicity, aromaticity and genomic GC content. Gene expression level also influenced the amino acid usage significantly. We argued that the amino acid usage of chicken proteome likely reflects a balance or near balance between the action of selection, mutation, and genetic drift.
authors.affiliation: Department of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, China; Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China.
authors.forename: Yousheng
authors.initials: Y
authors.lastname: Rao
authors.affiliation: Department of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, China.
authors.forename: Zhangfeng
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Department of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, China.
authors.forename: Xuewen
authors.initials: X
authors.lastname: Chai
authors.affiliation: Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China.
authors.forename: Qinghua
authors.initials: Q
authors.lastname: Nie
authors.affiliation: Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China.
authors.forename: Xiquan
authors.initials: X
authors.lastname: Zhang
mesh_terms: D000596:Amino Acids / Q000235:genetics / Q000378:metabolism*; D000818:Animals; D001482:Base Composition / Q000235:genetics; D002645:Chickens / Q000235:genetics*; D003062:Codon / Q000235:genetics; D018628:Gene Dosage / Q000235:genetics*; D057927:Hydrophobic and Hydrophilic Interactions; D009154:Mutation; D020543:Proteome / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics* / Q000378:metabolism
chemical_list: D000596:Amino Acids; D003062:Codon; D020543:Proteome; D012343:RNA, Transfer