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Hydrophobicity and aromaticity are primary factors shaping variation in amino acid usage of chicken proteome.

Rao Y, Wang Z, Chai X, Nie Q, Zhang X - PLoS ONE (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

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.

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.

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Related in: MedlinePlus

Relationship between Axis 1 and the GRAVY score of proteins, the Aromo score of proteins.a. Axis 1 is strongly correlated with the GRAVY score of proteins (r  =  0.7341, P <0.0001); b. Axis 1 is strongly correlated with the Aromo score of proteins (r  =  0.5519, P <0.0001).
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pone-0110381-g003: Relationship between Axis 1 and the GRAVY score of proteins, the Aromo score of proteins.a. Axis 1 is strongly correlated with the GRAVY score of proteins (r  =  0.7341, P <0.0001); b. Axis 1 is strongly correlated with the Aromo score of proteins (r  =  0.5519, P <0.0001).

Mentions: A correspondence analysis of the amino acid usage of this data indicated that 4 of the 19 axes account for almost 50% of the total variance (49.5%) in amino acid composition of chicken proteins. The distribution of the amino acid residues and the total genes for the first two axes is shown in figure 2. The first axis (Axis 1) accounts for 17.8% of the total variability, which is strongly correlated with the GRAVY score (general average hydropathicity) of proteins (r  =  0.7341, P <0.0001), Aromo score of proteins (r  =  0.5519, P <0.0001)(see figure 3), weakly correlated with the GCcds (r  =  0.2653, P <0.0001), GC1(r  =  −0.0739, P  =  0.0151), GC2 (r  =  0.4609, P <0.0001), GC3(r  =  0.1912, P <0.0001), and negatively correlated with the gene expression level (r  =  −0.1471, P <0.0001). As shown in figure 2a, the strong hydrophobic amino acids, Ile, Val, Phe, and Met, except for Leu, and the aromatic amino acids, Tyr, Phe, and Trp, are at the right of the plane (positive values for axis 1). The distribution of genes in figure 2b indicated that the membrane proteins were related to the distribution of axis 1, in which the majority of them show a positive value over the axis 1.


Hydrophobicity and aromaticity are primary factors shaping variation in amino acid usage of chicken proteome.

Rao Y, Wang Z, Chai X, Nie Q, Zhang X - PLoS ONE (2014)

Relationship between Axis 1 and the GRAVY score of proteins, the Aromo score of proteins.a. Axis 1 is strongly correlated with the GRAVY score of proteins (r  =  0.7341, P <0.0001); b. Axis 1 is strongly correlated with the Aromo score of proteins (r  =  0.5519, P <0.0001).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4199684&req=5

pone-0110381-g003: Relationship between Axis 1 and the GRAVY score of proteins, the Aromo score of proteins.a. Axis 1 is strongly correlated with the GRAVY score of proteins (r  =  0.7341, P <0.0001); b. Axis 1 is strongly correlated with the Aromo score of proteins (r  =  0.5519, P <0.0001).
Mentions: A correspondence analysis of the amino acid usage of this data indicated that 4 of the 19 axes account for almost 50% of the total variance (49.5%) in amino acid composition of chicken proteins. The distribution of the amino acid residues and the total genes for the first two axes is shown in figure 2. The first axis (Axis 1) accounts for 17.8% of the total variability, which is strongly correlated with the GRAVY score (general average hydropathicity) of proteins (r  =  0.7341, P <0.0001), Aromo score of proteins (r  =  0.5519, P <0.0001)(see figure 3), weakly correlated with the GCcds (r  =  0.2653, P <0.0001), GC1(r  =  −0.0739, P  =  0.0151), GC2 (r  =  0.4609, P <0.0001), GC3(r  =  0.1912, P <0.0001), and negatively correlated with the gene expression level (r  =  −0.1471, P <0.0001). As shown in figure 2a, the strong hydrophobic amino acids, Ile, Val, Phe, and Met, except for Leu, and the aromatic amino acids, Tyr, Phe, and Trp, are at the right of the plane (positive values for axis 1). The distribution of genes in figure 2b indicated that the membrane proteins were related to the distribution of axis 1, in which the majority of them show a positive value over the axis 1.

Bottom Line: 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.

View Article: PubMed Central - PubMed

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.

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.

Show MeSH
Related in: MedlinePlus