Journal of Taiwan Agricultural Research

Author:Meng-Li Wei, Yi-Han Chung, Chun-Tang Lu, and Hsiu-Ying Lu*

Abstract:

    Much information is stored in amino acid composition of proteins, while amino acid compositional features vary among species and among genes within species; thus, the analysis of amino acid composition of proteins becomes one of the important topics in bioinformatics research.  The total amino acid usage is determined by obtaining a data matrix of multiple species or genes (observations) and 20 amino acid frequencies (variables).  The multivariate analysis is well suited for exploring this multidimensional information.  To accelerate the analysis of protein structure in rice bacterial blight resistance gene (Xa), it is essential to examine the amino acid composition of all completely sequenced Xa genes.  Thus, using a total of 17 protein sequences of rice bacterial blight resistance genes, i.e., Xa1, xa5, xa13, Xa13, Xa21, Xa26, and Xa27 collected from NCBI, as test data, the pattern of variation of amino acid composition in Xa genes was detected by the complementary use of correspondence analysis and cluster analysis.  The results showed that Xa genes were divided into six groups according to their percentage compositions of amino acids.  The Xa1, Xa21, Xa26, and Xa27 genes were found to have leucine mostly.  The xa13, Xa13, and Xa27genes had fewer serine but more alanine and glycine.  The xa13 and Xa13 genes also contained much valine.  The xa5 gene had much glutamic acid and threonine compared to other Xa genes.  All of Xa genes had high-frequency hydrophobic amino acid in proteins.  This research showed that multivariate statistical technique is useful for detecting the variation pattern of amino acid composition of proteins among Xa genes.

Key words:Rice (Oryza sativa L.), Xa genes, Protein structure, Composition and attribution of amino acids, Cluster analysis, Correspondence analysis

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