南方水稻黑条矮缩病毒S9片段基因编码产物的生物信息学分析

doi:10.11924/j.issn.1000-6850.2012-1089

中国农学通报 ›› 2013, Vol. 29 ›› Issue (6): 12-19.doi: 10.11924/j.issn.1000-6850.2012-1089

所属专题：生物技术；水稻

南方水稻黑条矮缩病毒S9片段基因编码产物的生物信息学分析

胡秀弟朱静吴文斗任国敏李凡

收稿日期:2012-03-26 修回日期:2012-04-19 出版日期:2013-02-25 发布日期:2013-02-25
基金资助:
云南省中青年学术和技术带头人后备人才培养项目 “云南主要水稻病毒的分子变异及致病性分化” (2006PY01-37)。

Bioinformatic Analysis for the Functions of S9 Encoded Proteins of Southern Rice Black Streaked Dwarf Virus

Received:2012-03-26 Revised:2012-04-19 Online:2013-02-25 Published:2013-02-25

摘要/Abstract

摘要： 预测南方水稻黑条矮缩病毒(SRBSDV) S9片段编码蛋白的功能，为进一步深入分析相关基因编码产物的功能提供理论依据。应用RT-PCR克隆了SRBSDV云南芒市分离物(SRBSDV-YNMShi)的S9片段，测定其全序列，并对S9及其编码蛋白进行生物信息学分析。结果表明，S9片段全长1900 nt，编码P9-1和P9-2 2个蛋白。S9核苷酸序列与广东、海南、湖北分离物的同源性分别为99.5%、99.1%和98.7%。系统进化分析再次印证了SRBSDV是斐济病毒属的成员，SRBSDV-YNMShi与广东、越南分离物聚成一枝，与海南分离物有一定的进化分离趋势。P9-1为一个不稳定疏水蛋白，亚细胞定位于细胞核内，无规则卷曲是该蛋白质的主要结构元件，与其亲缘关系最近的水稻黑条矮缩病毒(RBSDV)有着类似结构。P9-2是有2个跨膜结构域的亲水性稳定蛋白，亚细胞定位于质膜，α-螺旋是其主要结构元件，有1个保守的G蛋白偶联受体。P9-1可能为SRBSDV复制的关键因子，P9-2可能为膜蛋白，具有转运的功能。

关键词: 抗药性, 抗药性

Abstract: Bioinformatic analysis was carried out to predict the functions of S9 segment encoded proteins of Southern rice black streaked dwarf virus (SRBSDV) to provide the scientific basis for further biological function analysis of the encoded proteins of SRBSDV. The S9 segment of SRBSDV Manshi isolate (SRBSDV-YNMShi), which was collected in Manshi, Dehong Prefecture of Yunnan, was amplified by RT-PCR with specific primers. The amplicon was then cloned and sequenced, and the nucleotide sequence of S9 and the amino acid sequences of the encoded proteins were analyzed by bioinformatics. The results showed that, S9 segment of SRBSDV-YNMShi comprises of 1900 nt, and encoded two proteins of P9-1 and P9-2. The nucleotide sequence of S9 segment of SRBSDV-YNMShi shared 99.5%, 99.1%, 98.7% identity with those of Guangdong (GD), Hainan (HN) and Hubei (HB) SRBSDV isolates. Phylogenetic analysis results reconfirmed that SRBSDV was a member of genus Fijivirus, and the isolate of YNMShi could be grouped into the clade of isolates GD and Vietnam other than isolate HN. Bioinformatic analysis results indicated that P9-1 was an unstable hydrophobic protein, and subcellular localized in the nucleus. Random coil was the main structural element of P9-1. Comparison of the amino acid sequences showed that SRBSDV had high homology and similar structure with Rice black streaked dwarf virus (RBSDV) and Maize rough dwarf virus (MRCV). P9-2 was a stabilized hydrophilic protein with two transmembrane domains, and subcellular localized on the plasma membrane.ɑ-helix was the main structural element of P9-2, and a conserved G protein-coupled receptor was detected in the P9-2. P9-1 might be one of the key factors for viral replication, and P2-1 might be a membrane protein with the function of transportation.

胡秀弟朱静吴文斗任国敏李凡. 南方水稻黑条矮缩病毒S9片段基因编码产物的生物信息学分析[J]. 中国农学通报, 2013, 29(6): 12-19.

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南方水稻黑条矮缩病毒S9片段基因编码产物的生物信息学分析

Bioinformatic Analysis for the Functions of S9 Encoded Proteins of Southern Rice Black Streaked Dwarf Virus

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