Abstract
In the present study, we carried out an examination of the amino acid usage in the zebra finch (Taeniopygia guttata) proteome. We found that tRNA abundance, base composition, hydrophobicity and aromaticity, protein second structure, cysteine residue (Cys) content and protein molecular weight had significant impact on the amino acid usage of the zebra finch. The above factors explained the total variability of 22.85%, 25.37%, 10.91%, 5.06%, 4.21%, and 3.14%, respectively. Altogether, approximately 70% of the total variability in zebra finch could be explained by such factors. Comparison of the amino acid usage between zebra finch, chicken (Gallus gallus) and human (Homo sapiens) suggested that the average frequency of various amino acid usage is generally consistent among them. Correspondence analysis indicated that base composition was the primary factor affecting the amino acid usage in zebra finch. This trend was different from chicken, but similar to human. Other factors affecting the amino acid usage in zebra finch, such as isochore structure, protein second structure, Cys frequency and protein molecular weight also showed the similar trends with human. We do not know whether the similar amino acid usage trend between human and zebra finch is related to the distinctive neural and behavioral traits, but it is worth studying in depth.
Highlights
Amino acids are utilized with different frequencies in various proteins and organisms
We carried out a genome scale analysis of the amino acid usage in the zebra finch (Taeniopygia guttata)
The effects of tRNA abundance, base composition, hydrophobicity and aromaticity, protein second structure, cysteine residue (Cys) frequency and protein molecular weight on amino acid usage were investigated in detail
Summary
Amino acids are utilized with different frequencies in various proteins and organisms Such biases in amino acid usage have been demonstrated extensively in prokaryote and eukaryote genomes, and likely reflect a balance or near balance between the action of mutation, selection, and genetic drift [1,2,3]. Base composition in a number of species has been shown to correlate with the amino acid content of proteins. This trend has been attributed to the neutral processes or mutation[1, 4,5,6,7,8,9,10,11].
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