水稻抗白葉枯病基因之密碼子使用偏性

Synonymous Condon Usage Bias in Rice Genes with Resistance to Bacterial Blight (Xanthomonas oryza)

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》 58卷3期 (2009/09) Pp. 155-168

https://doi.org/10.6156/JTAR/2009.05803.01

摘要

密碼子使用偏性分析對水稻白葉枯病抗病基因(Xa)之抗性分子機制之瞭解相當重要，因此本研究自NCBI (National Center for Biotechnology Information)公共資料庫下載已完全定序的Xa基因 （Xa1，xa5，xa13，Xa13，Xa21，Xa26及Xa27）及其家族之17個編碼區序列(coding domain sequence, CDS)進行密碼子使用偏性分析。首先進行各Xa基因之同義密碼子相對使用度(relative synonymous codon usage, RSCU)的集群分析和對應分析，可將Xa基因之CDS明顯區分成4群。進而再分別計算各群基因之同義密碼子相對使用頻率(relative frequency of synonymous codon, RFSC)以篩選出高頻密碼子，結果發現蛋白質序列具有多白胺酸重複(leucine-rich repeat, LRR)區域結構且CDS長度大於1000 bp的Xa1、Xa21及Xa26，其大多數胺基酸並無密碼子使用偏好性，僅少數胺基酸偏好以A或U結尾的同義密碼子；而不具LRR區域蛋白質結構且CDS 長度較短的xa5、xa13、Xa13及Xa27，則幾乎所有胺基酸都偏好以C或G結尾的同義密碼子。Xa1、Xa21、Xa26及Xa27的表現蛋白質皆含豐富之白胺酸(leucine, Leu)，但Xa1、Xa21及Xa26的Leu並無偏好任何密碼子，亦即其表現蛋白質的Leu可選擇任意同義密碼子轉譯，而Xa27的Leu則高度偏好使用CUC。由此顯見，同樣對白葉枯病菌產生抗性的不同Xa基因間，呈現出密碼子使用偏性的多樣性。

關鍵字

Xa基因 ； 同義密碼子相對使用度 ； 同義密碼子相對使用頻率 ； 集群分析 ； 對應分析

並列摘要

Analysis of codon usage is important in understanding the molecular mechanism of rice genes with resistance to bacterial blight caused by Xanthomonas oryzae pv. oryzae. A total of 17 coding domain sequences (CDSs) of the completely sequenced genes, i.e., Xa1, xa5, xa13, Xa13, Xa21, Xa26, and Xa27 were obtained through the access from public database of NCBI (National Center for Biotechnology Information) and they were used to analyze the condon usage bias. The use of correspondence analysis and cluster analysis of relative synonymous codon usage (RSCU) clearly separated the CDSs of Xa genes into four distinct groups. The relative frequency of synonymous codon (RFSC) was further used to indentify the high-frequency codons for each gene group. The results showed that Xa1, Xa21, and Xa26 with leucine-rich repeat (LRR) domain protein structure and CDS length more than 1000 bp were found no codon usages in most amino acids, and preferred A- or U-ending codons in a few amino acids; whereas xa5, xa13, Xa13, and Xa27 with non-LRR domain protein structure and shorter CDSs preferred C- or G-ending codons in almost all amino acids. The protein sequences of Xa1, Xa21, Xa26, and Xa27 has been known to have abundant leucine (Leu). The Xa1, Xa21, and Xa26 showed no significant codon bias in their Leu, that is they could choose any synonymous codon for Leu when translating to protein; whereas, Xa27 exhibited CUC as the most preferred codon in Leu. It indicated that codon usage bias varied among rice genes with resistance to bacterial blight.

並列關鍵字

Xa genes ； Relative synonymous codon usage ； Relative frequency of synonymous codon ； Cluster analysis ； Correspondence analysis