上海地区鸽Ⅰ型副黏病毒F基因遗传进化及生物信息学分析

doi:10.16431/j.cnki.1671-7236.2024.12.004

摘要/Abstract

摘要： 【目的】了解上海地区鸽Ⅰ型副黏病毒(PPMV-1)流行毒株F基因遗传变异情况，分析F蛋白生物信息学特征，为PPMV-1的防控提供技术支持。【方法】应用RT-PCR方法扩增分离株F基因，测序并进行遗传进化分析，并通过生物信息学在线软件对F蛋白结构功能进行预测分析。【结果】分离株F基因编码区全长为1 662 bp，编码553个氨基酸，F蛋白裂解位点序列为112R-R-Q-K-R-F117，符合强毒株序列结构特征。系统进化树分析结果显示，分离株属于新城疫病毒(NDV)Class Ⅱ群Ⅵ.2.1.1.2.2亚型，与疫苗株La Sota和Mukteswar处于不同进化分支，与国内分离株Pi/SH/CH/0617/2013和pigeon/Ningxia/2068/2016同属Ⅵ.2.1.1.2.2分支。生物信息学分析结果表明，F蛋白为亲水性蛋白，分子质量约为59.03 ku，理论等电点(PI)为7.87，半衰期为30 h，不稳定系数为35.06，脂肪系数为109.73。F蛋白主要分布在细胞质膜和内质网中，具有跨膜结构和信号肽，包含6个潜在的N-糖基化位点、13个半胱氨酸残基、103个O-糖基化位点，以及67个磷酸化位点。二级结构中α-螺旋、无规则卷曲、延伸链、β-转角分别占46.11%、31.46%、18.08%及4.34%，三级结构预测结果与二级结构相一致。B细胞抗原位点预测结果显示，F蛋白含有11个抗原表位(氨基酸数目≥7)。【结论】本研究分离获得的PPMV-1分离株属于NDV Class Ⅱ群Ⅵ.2.1.1.2.2亚型，其F蛋白具有较好的抗原表位，可作为PPMV-1疫苗研制和抗病毒治疗的靶蛋白。研究结果为有效防控PPMV-1感染提供了一定的参考依据，同时也为进一步研发新型疫苗奠定了基础。

关键词: 鸽Ⅰ型副黏病毒; F基因; 遗传进化; 生物信息学

Abstract: 【Objective】 The purpose of this study was to understand the genetic variation of F gene of Pigeon paramyxovirus type Ⅰ (PPMV-1) epidemic strain in Shanghai area,analyze the bioinformatic characteristics of F protein,and provide technical support for the prevention and control of PPMV-1.【Method】 F gene of the isolate was amplified by RT-PCR,and sequencing and genetic evolution analysis were performed.The structure and function of F protein were predicted by online bioinformatics software.【Result】 The total length of the F gene coding region of the isolate was 1 662 bp,encoding 553 amino acids,and the F protein cleavage site sequence was 112R-R-Q-K-R-F117,which was consistent with the sequence structure of the virulent strain.Phylogenetic tree analysis showed that the isolate belonged to Class Ⅱ group Ⅵ.2.1.1.2.2 subtype of Newcastle disease virus (NDV).The isolate was in a different evolutionary branch from the vaccine strains La Sota and Mukteswar,and belonged to the same branch Ⅵ.2.1.1.2.2 with the domestic isolates Pi/SH/CH/0617/2013 and pigeon/Ningxia/2068/2016.The results of bioinformatics analysis showed that F protein was a hydrophilic protein with molecular mass of 59.03 ku,theoretical isoelectric point (pI) of 7.87,half-life period of 30 h,instability coefficient of 35.06 and fat coefficient of 109.73.F protein was mainly distributed in the plasma membrane and endoplasmic reticulum of the cell,and had a transmembrane structure and signaling peptides,including 6 potential N-glycosylation sites,13 cysteine residues,103 O-glycosylation sites,and 67 phosphorylation sites.In the secondary structure,alpha helix,random coil,extended chain and beta turn account for 46.11%,31.46%,18.08% and 4.34%,respectively.The predicted result of tertiary structure was consistent with the secondary structure.B-cell antigen site prediction showed that F protein contained 11 epitopes (amino acid number ≥7).【Conclusion】 The PPMV-1 isolate belonged to NDV Class Ⅱ group Ⅵ.2.1.1.2.2 subtype of NDV，and its F protein had a good epitope,which could be used as the target protein for PPMV-1 vaccine development and antiviral therapy.The results provided a certain reference for effective prevention and control of PPMV-1 infection,and also laid a foundation for further research and development of new vaccines.

Key words: Pigeon paramyxovirus type Ⅰ; F gene; phylogenetic; bioinformatics

中图分类号:

S855.3

刘健, 周锦萍, 沈莉萍, 桂亚萍, 葛菲菲, 王晓旭, 杨显超, 刘佩红, 王建. 上海地区鸽Ⅰ型副黏病毒F基因遗传进化及生物信息学分析[J]. 中国畜牧兽医, 2024, 51(12): 5150-5161.

LIU Jian, ZHOU Jinping, SHEN Liping, GUI Yaping, GE Feifei, WANG Xiaoxu, YANG Xianchao, LIU Peihong, WANG Jian. Phylogenetic and Bioinformatics Analysis of F Gene of Pigeon Paramyxovirus Type Ⅰ from Shanghai Area[J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(12): 5150-5161.

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