马铃薯Y病毒pipo基因的分子变异及结构特征分析
收稿日期: 2013-04-15
修回日期: 2013-07-08
网络出版日期: 2013-09-25
基金资助
国家现代农业马铃薯产业技术体系(编号：CARS-10), 福建省自然科学基金项目(编号：2013J01088), 福建省教育厅科技项目(编号：JA12119)和福建出入境检验检疫局科技项目(编号：FK2011-07)资助
Sequence variation and protein structure of pipo gene in Potato virus Y
Received date: 2013-04-15
Revised date: 2013-07-08
Online published: 2013-09-25
为揭示马铃薯Y病毒(Potato virus Y, PVY) pipo基因的分子变异和结构特征, 文章根据文献报道的马铃薯Y病毒属(Potyvirus) pipo 基因保守区序列设计一对简并引物, 从感染PVY的马铃薯病叶中克隆获得pipo基因的cDNA全长序列, 分析其核苷酸序列和氨基酸序列的特征, 并基于氨基酸序列使用贝叶斯法重建了Potyvirus的系统发育树。结果显示：20个PVY分离物成功扩增出预期大小(约235 bp)的特异性片段, 其核苷酸序列与已报道的其它PVY 株系的pipo基因核苷酸序列一致性均在92%以上; 5′端均含有典型的G1-2A6-7 基序(motif), 无碱基插入/缺失, 所有的核苷酸变异都是碱基置换, 共发现13个多态性位点, 其中4个简约信息位点, 9个单一变异位点, 表明该基因高度保守, 但不同分离物也存在一定的分子变异; PIPO蛋白理论等电点11.26~11.62, 无信号肽和跨膜区, 是可溶的亲水性蛋白; 整个蛋白含有3个保守区, 其中位于10~59aa的基序最为保守。该蛋白主要定位于线粒体中, 可能是线粒体导肽。系统发育分析结果显示, 源于PVY不同株系优先相聚成簇, 而向日葵褪绿斑驳病毒(Sunflower chlorotic mottle virus, SuCMoV)与辣椒重花叶病毒(Pepper severe mosaic virus, PepSMV)的亲缘关系较PVY相比更近, 与前人的结果相一致, 表明PIPO蛋白可以作为研究Potyvirus系统发育关系的新的分子标记。
高芳銮 沈建国 史凤阳 常飞 谢联辉 詹家绥 . 马铃薯Y病毒pipo基因的分子变异及结构特征分析[J]. 遗传, 2013 , 35(9) : 1125 -1134 . DOI: 10.3724/SP.J.1005.2013.01125
The objectives of this study were to understand the sequence variation and the putative protein structure of pipo gene in the Potato virus Y (PVY) collected from Solanum tuberosum. The pipo gene in PVY was cloned using a pair of degenerate primers designed from its conserved region and its sequences were used to re-construct phylogenetic tree in Potyvirus genera by a Bayesian inference method. An expected fragment of 235 bp was amplified in all 20 samples by RT-PCR and the pipo genes in the 20 samples assayed shared more than 92% nucleotide sequence similarity with the published sequences of PVY strains. Among the 20 pipo gene sequences, 13 polymorphic sites were detected, including 4 parsimony informative sites and 9 singleton variable sites. These results indicate that PVY pipo gene is highly conserved but some sequence variations exist. Further analyses suggest that the pipo gene encodes a hydrophilic protein without signal peptide and transmembrane region. The protein has theoretical isoelectric points (pI) ranging from 11.26 to 11.62 and contains three highly conserved regions, especially between aa 10 and 59. The protein is likely located in the mitochondria and has α-helix secondary structure. Bayesian inference of phylogenetic trees reveals that PVY isolates are clustered in the same branch with high posterior probability, while Sunflower chlorotic mottle virus (SoCMoV) and Pepper severe mosaic virus (PepSMV) are closely related, consisting with the classification of Potyvirus genera using other approaches. Our analyses suggest that the pipo gene can be a new marker for phylogenetic analysis of the genera. The results reported in this paper provide useful insights in the genetic variation and the evolution of PVY and can stimulate further research on structure and function of the PIPO protein.
Key words： evolution of virus; Potato virus Y; pipo gene
[1] 祝雯, 詹家绥. 植物病原物的群体遗传学. 遗传, 2012, 34(2): 157–166.<\P>
[2] King AM, Lefkowitz E, Adams MJ, Carstens EB. Virus taxonomy: Ninth report of the international committee on taxonomy of viruses. Amsterdam: Elsevier Academic Press, 2011.<\P>
[3] Gibbs A, Ohshima K. Potyviruses and the digital revolution. Annu Rev Phytopathol, 2010, 48(1): 205–223.<\P>
[4] Chung BY, Miller WA, Atkins JF, Firth AE. An overlapping essential gene in the Potyviridae. Proc Natl Acad Sci USA, 2008, 105(15): 5897–5902.<\P>
[5] Wen RH, Hajimorad MR. Mutational analysis of the putative pipo of soybean mosaic virus suggests disruption of PIPO protein impedes movement. Virology, 2010, 400(1): 1–7.<\P>
[6] Wei TY, Zhang CW, Hong J, Xiong RY, Kasschau KD, Zhou XP, Carrington JC, Wang AM. Formation of complexes at plasmodesmata for Potyvirus intercellular movement is mediated by the viral protein P3N-PIPO. PLoS Pathog, 2010, 6(6): e1000962.<\P>
[7] Cuevas JM, Delaunay A, Visser JC, Bellstedt DU, Jacquot E, Elena SF. Phylogeography and molecular evolution of Potato virus Y. PLoS ONE, 2012, 7(5): e37853.<\P>
[8] Ohshima K, Sako K, Hiraishi C, Nakagawa A, Matsuo K, Ogawa T, Shikata E, Sako N. Potato tuber necrotic ringspot disease occurring in Japan: its association with Potato virus Y necrotic strain. Plant Dis, 2000, 84(10): 1109–1115.<\P>
[9] 孙琦, 张春庆. PVYN与PVYO病毒RT-PCR快速检测体系研究. 中国农业科学, 2005, 38(1): 213–216.<\P>
[10] Ogawa T, Tomitaka Y, Nakagawa A, Ohshima K. Genetic structure of a population of Potato virus Y inducing potato tuber necrotic ringspot disease in Japan; comparison with North American and European populations. Virus Res, 2008, 131(2): 199–212.<\P>
[11] 陈士华, 刘晓磊, 张晓婷, 吴兴泉. 河南PVY高致病性株系的发现及其分子特征研究. 河南农业大学学报, 2010, 44(4): 443–447.<\P>
[12] 陈士华, 刘晓磊, 张晓婷, 吴兴泉. 中国部分马铃薯产区马铃薯Y病毒 (PVY) 的株系分化与鉴定. 河南农业大学学报, 2011, 45(5): 548–551.<\P>
[13] Hu XX, Nie XZ, He CZ, Xiong XY. Differential pathogenicity of two different recombinant PVYNTN isolates in Physalis floridana is likely determined by the coat protein gene. Virol J, 2011, 8(1): 207.<\P>
[14] Ogawa T, Nakagawa A, Hataya T, Ohshima K. The genetic structure of populations of Potato virus Y in Japan; based on the analysis of 20 full genomic sequences. J Phytopathol, 2012, 160(11-12): 661–673.<\P>
[15] 高芳銮, 沈建国, 史凤阳, 方治国, 谢联辉, 詹家绥. 中国马铃薯Y病毒的检测鉴定及CP基因的分子变异. 中国农业科学, 2013, 46(15): 3125–3133.<\P>
[16] Librado P, Rozas J. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 2009, 25(11): 1451–1452.<\P>
[17] Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol Biol Evol, 2013, 30(4): 772–780.<\P>
[18] Abascal F, Zardoya R, Posada D. ProtTest: selection of best-fit models of protein evolution. Bioinformatics, 2005, 21(9): 2104–2105.<\P>
[19] Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hohna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol, 2012, 61(3): 539–542.<\P>
[20] Martincorena I, Seshasayee AS, Luscombe NM. Evidence of non-random mutation rates suggests an evolutionary risk management strategy. Nature, 2012, 485(7396): 95–98.<\P>
[21] 吴祖建, 高芳銮, 沈建国. 生物信息学分析实践. 北京: 科学出版社, 2010: 107–110.<\P>
[22] Guruprasad K, Reddy BV, Pandit MW. Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Eng, 1990, 4(2): 155–161.<\P>
[23] Bejerman N, Giolitti F, de Breuil S, Lenardon S.
/
| 〈 |
|
〉 |
www.chinagene.cn
备案号：京ICP备09063187号-4
总访问:,今日访问:,当前在线:
