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. 2018 Dec 5;13(12):e0204796.
doi: 10.1371/journal.pone.0204796. eCollection 2018.

Base composition is the primary factor responsible for the variation of amino acid usage in zebra finch (Taeniopygia guttata)

Yousheng Rao  1   2 , Zhangfeng Wang  1   2 , Wen Luo  2 , Wentao Sheng  1   2 , Rendian Zhang  1   2 , Xuewen Chai  1   2
Affiliations

Base composition is the primary factor responsible for the variation of amino acid usage in zebra finch (Taeniopygia guttata)

Yousheng Rao et al. PLoS One. .

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.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Relationship between the relative amino acid usage and the isoaccepting tRNA gene copy number.
The tRNA gene copy numbers for each codon in the Taeniopygia guttata genome was taken from http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/eukaryota/Tgutt2/ (August 2, 2017). The isoaccepting tRNA gene number was summed for each amino acid. The relative amino acid usage (RAAU) for each amino acid was calculated by CodonW 1.4.2. The average RAAU values of amino acid was correlated with the isoaccepting tRNA gene copy numbers significantly (r = 0.478, p = 0.038).
Fig 2
Fig 2. Distribution of the amino acids and genes on the first two axes of the correspondence analysis.
a. Representation of the first two axes of the correspondence analysis performed on the amino acid frequency of Taeniopygia guttata protein. b. Representation of the first two axes of the correspondence analysis performed on the amino acid frequencies of 8109 Taeniopygia guttata genes. Membrane proteins are indicated by red dots. The total number of membrane proteins was 298. The percentage of membrane proteins with the positive value account for 72%.
Fig 3
Fig 3. Relationship between GC content and axis 1,axis 2.
a. Axis 1 positively correlated with GCcds significantly. b. Axis 1 strongly correlated with GC2 positively. c. Axis 1 weakly correlated with GC3 positively. d. Axis 2 negatively correlated with GCcds significantly. e. Axis 2 negatively correlated with GC1 significantly. f. Axis 2 negatively correlated with GC2 significantly.
Fig 4
Fig 4. Relationship between axis 2 and the GRAVY score of proteins, the Aromo score of proteins.
a. Axis 2 strongly correlated with the GRAVY score of proteins. b. Axis 2 strongly correlated with the Aromo score of proteins.
Fig 5
Fig 5. Comparison of the average frequency of various amino acids usage among zebra finch (Taeniopygia guttata), chicken (Gallus gallus) and human (Homo sapiens).
See this image and copyright information in PMC

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