水稻白葉枯病抗性基因之蛋白質胺基酸組成的多變數分析

Multivariate Analysis of Amino Acid Composition in Proteins from Rice Bacterial Blight Resistance Genes

魏夢麗(Meng-Li Wei) ； 鍾依涵(Yi-Han Chung) ； 呂椿棠(Chun-Tang Lu) ； 呂秀英(Hsiu-Ying Lu)

《台灣農業研究》 57卷3期 (2008/09) Pp. 161-174

https://doi.org/10.6156/JTAR/2008.05703.02

摘要

蛋白質中的胺基酸組成隱藏甚多訊息，但其組成特性會因不同物種或物種內不同基因而異，故蛋白質的胺基酸組成分析成爲生物資訊研究的重要課題之一。胺基酸組成特性是由多個物種或基因（觀測值）與20種胺基酸之頻率（變數）所構成的資料矩陣來決定，這種多維資料形式所含之訊息，最適合利用多變數分析(multivariate analysis)之統計技術來解析。爲促進水稻白葉枯病抗病基因(Xa)蛋白質序列的結構研究，有必要針對所有已完全定序的Xa基因進行蛋白質之胺基酸組成分析。基此，本研究以NCBI公共資料庫內已知序列的Xa1、xa5、xa13、Xa13、Xa21、Xa26及Xa27等基因共17條蛋白質序列爲供試材料，綜合運用集群分析(cluster analysis)及對應分析(correspondenceanalysis)，來檢測不同Xa基因之蛋白質胺基酸組成的變異形式。結果顯示，根據胺基酸組成比例，可將Xa基因及其家族分成六群，各群基因之蛋白質序列中各有偏好的胺基酸。Xa1、Xa21、Xa26及Xa27基因之蛋白質序列中皆以白胺酸(leucine)出現頻率最高；xa13、Xa13及Xa27的丙胺酸(alanine)出現較多但絲胺酸(serine)較少；xa13及Xa13也有較多的纈胺酸(valine)；xa5出現麩胺酸(glutamic acid)和酥胺酸(threonine)的頻率遠高於其他基因；所有Xa基因皆含有高比例的疏水性胺基酸。本研究揭示出多變數分析之統計技術，可有效檢測出Xa基因間蛋白質之胺基酸組成的變異形式。

關鍵字

水稻 ； Xa基因 ； 蛋白質結構 ； 胺基酸組成及屬性 ； 集群分析 ； 對應分析

並列摘要

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.

並列關鍵字

Rice Oryza sativa L. ； Xa genes ； Protein structure ； Composition and attribution of amino acids ； Cluster analysis ； Correspondence analysis