淋巴囊肿病毒中国分离株（LCDV-cn）系统关系分析与功能基因研究
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摘要
淋巴囊肿病毒(Lymphocystis disease virus, LCDV),属于虹彩病毒科(Iridoviridae),淋巴囊肿病毒属(Lymphocystivirus),其分布遍及全球;能引起9个目34科计140种以上淡、海水鱼的淋巴囊肿病,在淡、海水鱼组织细胞中可以增殖并引起宿主细胞病变,在病鱼体表等处形成囊肿物。该病毒病在发病的养殖场的感染率可达90%以上,病鱼不仅外形丑陋,且会发生死亡,严重影响了商品价值和市场销售。
1962年,Walker首次在鲽形目鱼类中发现淋巴囊肿病的病原,并命名为淋巴囊肿病毒(LCDV);1997年Tidona等测得了LCDV-1的全基因组序列,报告LCDV-1基因组长102653 bp、编码195个ORF。在中国,1997年底首次在威海地区呈亚急性暴发;1998年,孙修勤等从患病养殖牙鲆体内首次分离出淋巴囊肿病毒、称之为淋巴囊肿病毒中国分离株LCDV-cn,并开始对淋巴囊肿病毒进行了系统的研究。2000年,徐洪涛等获得了LCDV-cn mcp基因的部分序列,认为LCDV-cn的mcp基因序列与LCDV-1的mcp基因序列的同源性为78%。2004年,张奇亚等LCDV-C的全基因组序列,认为基因组长186250 bp、编码240个ORF。
本文以LCDV-cn核衣壳蛋白基因(mcp)为分子标记,通过PCR扩增和克隆测序获得了长度为1356 bp的、含178个信息位点的mcp基因序列;用最大简约法、最大似然法、邻接法和Bayesian法构建了分子系统树并进行了置信度检验,从DNA水平上分析了LCDV-cn与淋巴囊肿病毒韩国鲈鱼分离株(LCDV- sb)、淋巴囊肿病毒日本牙鲆分离株(LCDV-jf)、淋巴囊肿病毒欧洲分离株(LCDV-1)、淋巴囊肿病毒日本岩鱼分离株(LCDV-rf)及淋巴囊肿病毒中国军曹鱼分离株(LCDV-rc)的系统关系。结果表明,LCDV-cn的mcp基因序列与LCDV-C的mcp基因序列是一致的,构建的淋巴囊肿病毒ML、NJ、MP和Bayesian系统树的拓扑结构也一致,LCDV-rc与LCDV-sb聚为一支;LCDV-cn与LCDV-jf聚为一支;LCDV-1独为一支;LCDV-rf也独为一支。在对35种虹彩病毒的系统关系分析中,LCDV-cn与其他淋巴囊肿病毒分离株聚为一大支,说明LCDV-cn与淋巴囊肿病毒的关系近于其他虹彩病毒。遗传距离和系统关系分析认为,LCDV-1属于基因型Ⅰ型,LCDV-cn和LCDV-jf属于基因型Ⅱ型,LCDV-rf属于基因型Ⅲ型,LCDV-rc和LCDV-sb属于基因型Ⅳ型。
本研究经PCR扩增、克隆和测序,证明了获得的11个LCDV-cn的基因DNA序列与已登陆的LCDV-C相应序列一致。据此,本研究以LCDV-C基因组序列为参考序列进行分析,结果表明,LCDV-cn基因组中有119个ORF与其它虹彩病毒无同源区域、是LCDV特有的;而LCDV-cn还有52个自身特有的、含有功能结构或重复序列的ORF,该52个ORF与其他淋巴囊肿病毒和LCDV无同源区域。
锌指蛋白在基因的表达调控、细胞分化、胚胎发育及疾病的发生等生命过程中发挥重要作用。本文通过PCR法从LCDV-cn基因组DNA中获得了锌指蛋白基因序列,将DNA序列装入pET24a(+)表达载体,在E.coli中进行蛋白表达并获得成功。生物信息学软件分析表明:lcn61编码的锌指蛋白含有4个C2H2型锌指结构域,lcn140编码的锌指蛋白含有4个C3H1型锌指结构域和4个简单重复序列。LCDV-cn锌指蛋白的研究将有助于进一步了解LCDV的发生与发展,为阐明病毒致病的分子机理提供科学依据。
迄今,病毒DNA疫苗在抗病毒性疾病上取得了很大成功,但在抑制病毒编码功能蛋白时却可能影响宿主细胞内的功能蛋白。RNAi是一种新型基因沉默方法,已成功应用于多种生物体和组织细胞的基因功能研究。有文献报道,RNAi也存在于海洋生物中、并在海洋生物功能基因等研究中得到应用。本文根据LCDV-cn和LCDV的特有基因序列设计siRNA,将siRNA注射入牙鲆体内,首次研究了RNAi对LCDV-cn基因表达的影响,结果发现,注射mcp-siRNA1和mcp-siRNA3后,LCDV-cn的mcp基因表达量有所减少,说明LCDV的mcp基因在RNAi技术处理后有所抑制。
Lymphocystis disease virus, which is iridoviridae lymphocystivirus and spreads all over on the world, can lead to lymphocystis disease in more than 100 different seawater and freshwater fish species. The infection ratio is about 70% after exposure. Lymphocystis disease virus can lead to pathological changes in cells of the seawater and freshwater fish and cyst on surface of fish. Such change will eventually result in a much lower market value and related loss in aquaculture. The infection will also lead to fish death.
Since 1962, when Walker isolated lymphocystis disease virus firstly, a prodigious progress have been achieved in LCDV study. The shape, the configuration, chemical component and characteristics of LCDV have been studied. The study of many years indicated that there was prodigious difference in different isolated LCDV. in 1997, Tidona obtained the genome sequences of LCDV-1 and revealed that the genome had 102653 bp which coding 195 open reading frames(ORF). In China, lymphocystis disease badly broke out in Weihai for the first time. lymphocystis disease virus China(LCDV-cn) was isolated from paralichthys olivaceus by Prof. Sun Xiuqin in 1998. LCDV-cn was then studied systemically and the part sequence of mcp gene was revealed in 2000. The homologous relationship of mcp gene in LCDV-1 compared with that of in LCDV-cn was 78%. Zhang qiya acquired the genome sequences of LCDV-C in 2004. Whereas, the genome of LCDV-C has 186250 bp and 240 ORF.
In order to reveal phylogenetic station of LCDV-cn, phylogenetic relationships of LCDV-rc ,LCDV-cn, LCDV-jf, LCDV-sb, LCDV-rf, LCDV-1 and other iridovirus were analysed on the molecular level. Taking mcp gene as the molecular marker, partial nucleotide sequences(1356 bp) containing 178 infromative sites of mcp gene were acquired by PCR and cloning sequencing. Phylogenetic trees were reconstructed using maximum parsimony, maximum likelihood, neighbor joining and bayesian methods based on mcp gene sequences. Supporting values were also calculated. The results indicates that the mcp gene of LCDV-cn was same as the mcp gene of LCDV-C. One cluster belongs to genotypeⅣcontains LCDV-rc isolated from China cobio and LCDV-sb isolated from Korea weever. Another cluster belongs to genotypeⅡcontains LCDV-cn isolated from China flounder and LCDV-jf isolated from Japan flounder. The third cluster belong to genotypeⅢcontains LCDV-rf isolated from Japan rockfish. LCDV-1 is the last cluster and belong to genotypeⅠ.
By PCR, cloning and sequencing, sequences of eleven genes had been acquired and identified as same genes of LCDV-C. So, the genome of LCDV-C as the central reference sequence was been analysed. The result is that there are 119 ORF without homological sequences in iridovirus; there are 52 ORF without homological sequences in LCDV.
Zinc-finger proteins play various roles in a lot of organisms, i.e. adjusting the cellular differentiation, the embryogenesis. Further more, zinc-finger proteins are related to diseases. Two ORF (lcn61 and lcn140) of lymphocystis disease virus China (LCDV-cn) are predicted to encode putative zinc finger proteins. They were amplified and inserted into pET24a(+) vector, then expressed in E. coli BL21 (DE3). His-tag fusion proteins with the high yield were obtained. It was found that fusion proteins existed mainly as inclusion body in E. coli. Analysis of LCN61 and LCN140 protein by bioinformatic software indicated that LCN61 was C2H2 type zinc-finger protein containing four C2H2 zinc-finger motifs and LCN140 is C3H1 type zinc-finger protein containing four C3H1 zinc-finger motifs. The expression of lcn61 and lcn140 genes and analysis of LCN61 and LCN140 protein set a satisfactory foundation for their functional researches.
Viral bacterins have gained distinct achievements, but there are some problems in the scopes: the inhibition of viral proteins may affect the function of proteins in the host; the antigenic excursion induced by the gene mutation can make viral bacterins study frustrate continuously. RNA interference(RNAi) is a phenomenon of specific silencing of genes in diverse organisms including Drodophia, Caenorhabditis elegans, epiphyte, mammalian and etc. RNAi also exists in aquicolous organisms. RNAi is an effective method to study the gene function of aquicolous organisms as was validated zebra fish, ascidian and so on. Controlling viral infection in aquiculture is a technological challenge worldwide, and RNAi could be a way of viral infection of cultured animals. siRNAs were designed based on LCDV-cn own genes and LCDV own genes. siRNAs were injected into China flounder in order to study the effect of LCDV-cn copy and infection. The results indicated that the expression quantity of mcp gene in LCDV-cn was reduced in three days after infection of mcp-siRNA1 and mcp-siRNA3. This show that RNAi can restrain the copy of LCDV-cn.
1962年,Walker首次在鲽形目鱼类中发现淋巴囊肿病的病原,并命名为淋巴囊肿病毒(LCDV);1997年Tidona等测得了LCDV-1的全基因组序列,报告LCDV-1基因组长102653 bp、编码195个ORF。在中国,1997年底首次在威海地区呈亚急性暴发;1998年,孙修勤等从患病养殖牙鲆体内首次分离出淋巴囊肿病毒、称之为淋巴囊肿病毒中国分离株LCDV-cn,并开始对淋巴囊肿病毒进行了系统的研究。2000年,徐洪涛等获得了LCDV-cn mcp基因的部分序列,认为LCDV-cn的mcp基因序列与LCDV-1的mcp基因序列的同源性为78%。2004年,张奇亚等LCDV-C的全基因组序列,认为基因组长186250 bp、编码240个ORF。
本文以LCDV-cn核衣壳蛋白基因(mcp)为分子标记,通过PCR扩增和克隆测序获得了长度为1356 bp的、含178个信息位点的mcp基因序列;用最大简约法、最大似然法、邻接法和Bayesian法构建了分子系统树并进行了置信度检验,从DNA水平上分析了LCDV-cn与淋巴囊肿病毒韩国鲈鱼分离株(LCDV- sb)、淋巴囊肿病毒日本牙鲆分离株(LCDV-jf)、淋巴囊肿病毒欧洲分离株(LCDV-1)、淋巴囊肿病毒日本岩鱼分离株(LCDV-rf)及淋巴囊肿病毒中国军曹鱼分离株(LCDV-rc)的系统关系。结果表明,LCDV-cn的mcp基因序列与LCDV-C的mcp基因序列是一致的,构建的淋巴囊肿病毒ML、NJ、MP和Bayesian系统树的拓扑结构也一致,LCDV-rc与LCDV-sb聚为一支;LCDV-cn与LCDV-jf聚为一支;LCDV-1独为一支;LCDV-rf也独为一支。在对35种虹彩病毒的系统关系分析中,LCDV-cn与其他淋巴囊肿病毒分离株聚为一大支,说明LCDV-cn与淋巴囊肿病毒的关系近于其他虹彩病毒。遗传距离和系统关系分析认为,LCDV-1属于基因型Ⅰ型,LCDV-cn和LCDV-jf属于基因型Ⅱ型,LCDV-rf属于基因型Ⅲ型,LCDV-rc和LCDV-sb属于基因型Ⅳ型。
本研究经PCR扩增、克隆和测序,证明了获得的11个LCDV-cn的基因DNA序列与已登陆的LCDV-C相应序列一致。据此,本研究以LCDV-C基因组序列为参考序列进行分析,结果表明,LCDV-cn基因组中有119个ORF与其它虹彩病毒无同源区域、是LCDV特有的;而LCDV-cn还有52个自身特有的、含有功能结构或重复序列的ORF,该52个ORF与其他淋巴囊肿病毒和LCDV无同源区域。
锌指蛋白在基因的表达调控、细胞分化、胚胎发育及疾病的发生等生命过程中发挥重要作用。本文通过PCR法从LCDV-cn基因组DNA中获得了锌指蛋白基因序列,将DNA序列装入pET24a(+)表达载体,在E.coli中进行蛋白表达并获得成功。生物信息学软件分析表明:lcn61编码的锌指蛋白含有4个C2H2型锌指结构域,lcn140编码的锌指蛋白含有4个C3H1型锌指结构域和4个简单重复序列。LCDV-cn锌指蛋白的研究将有助于进一步了解LCDV的发生与发展,为阐明病毒致病的分子机理提供科学依据。
迄今,病毒DNA疫苗在抗病毒性疾病上取得了很大成功,但在抑制病毒编码功能蛋白时却可能影响宿主细胞内的功能蛋白。RNAi是一种新型基因沉默方法,已成功应用于多种生物体和组织细胞的基因功能研究。有文献报道,RNAi也存在于海洋生物中、并在海洋生物功能基因等研究中得到应用。本文根据LCDV-cn和LCDV的特有基因序列设计siRNA,将siRNA注射入牙鲆体内,首次研究了RNAi对LCDV-cn基因表达的影响,结果发现,注射mcp-siRNA1和mcp-siRNA3后,LCDV-cn的mcp基因表达量有所减少,说明LCDV的mcp基因在RNAi技术处理后有所抑制。
Lymphocystis disease virus, which is iridoviridae lymphocystivirus and spreads all over on the world, can lead to lymphocystis disease in more than 100 different seawater and freshwater fish species. The infection ratio is about 70% after exposure. Lymphocystis disease virus can lead to pathological changes in cells of the seawater and freshwater fish and cyst on surface of fish. Such change will eventually result in a much lower market value and related loss in aquaculture. The infection will also lead to fish death.
Since 1962, when Walker isolated lymphocystis disease virus firstly, a prodigious progress have been achieved in LCDV study. The shape, the configuration, chemical component and characteristics of LCDV have been studied. The study of many years indicated that there was prodigious difference in different isolated LCDV. in 1997, Tidona obtained the genome sequences of LCDV-1 and revealed that the genome had 102653 bp which coding 195 open reading frames(ORF). In China, lymphocystis disease badly broke out in Weihai for the first time. lymphocystis disease virus China(LCDV-cn) was isolated from paralichthys olivaceus by Prof. Sun Xiuqin in 1998. LCDV-cn was then studied systemically and the part sequence of mcp gene was revealed in 2000. The homologous relationship of mcp gene in LCDV-1 compared with that of in LCDV-cn was 78%. Zhang qiya acquired the genome sequences of LCDV-C in 2004. Whereas, the genome of LCDV-C has 186250 bp and 240 ORF.
In order to reveal phylogenetic station of LCDV-cn, phylogenetic relationships of LCDV-rc ,LCDV-cn, LCDV-jf, LCDV-sb, LCDV-rf, LCDV-1 and other iridovirus were analysed on the molecular level. Taking mcp gene as the molecular marker, partial nucleotide sequences(1356 bp) containing 178 infromative sites of mcp gene were acquired by PCR and cloning sequencing. Phylogenetic trees were reconstructed using maximum parsimony, maximum likelihood, neighbor joining and bayesian methods based on mcp gene sequences. Supporting values were also calculated. The results indicates that the mcp gene of LCDV-cn was same as the mcp gene of LCDV-C. One cluster belongs to genotypeⅣcontains LCDV-rc isolated from China cobio and LCDV-sb isolated from Korea weever. Another cluster belongs to genotypeⅡcontains LCDV-cn isolated from China flounder and LCDV-jf isolated from Japan flounder. The third cluster belong to genotypeⅢcontains LCDV-rf isolated from Japan rockfish. LCDV-1 is the last cluster and belong to genotypeⅠ.
By PCR, cloning and sequencing, sequences of eleven genes had been acquired and identified as same genes of LCDV-C. So, the genome of LCDV-C as the central reference sequence was been analysed. The result is that there are 119 ORF without homological sequences in iridovirus; there are 52 ORF without homological sequences in LCDV.
Zinc-finger proteins play various roles in a lot of organisms, i.e. adjusting the cellular differentiation, the embryogenesis. Further more, zinc-finger proteins are related to diseases. Two ORF (lcn61 and lcn140) of lymphocystis disease virus China (LCDV-cn) are predicted to encode putative zinc finger proteins. They were amplified and inserted into pET24a(+) vector, then expressed in E. coli BL21 (DE3). His-tag fusion proteins with the high yield were obtained. It was found that fusion proteins existed mainly as inclusion body in E. coli. Analysis of LCN61 and LCN140 protein by bioinformatic software indicated that LCN61 was C2H2 type zinc-finger protein containing four C2H2 zinc-finger motifs and LCN140 is C3H1 type zinc-finger protein containing four C3H1 zinc-finger motifs. The expression of lcn61 and lcn140 genes and analysis of LCN61 and LCN140 protein set a satisfactory foundation for their functional researches.
Viral bacterins have gained distinct achievements, but there are some problems in the scopes: the inhibition of viral proteins may affect the function of proteins in the host; the antigenic excursion induced by the gene mutation can make viral bacterins study frustrate continuously. RNA interference(RNAi) is a phenomenon of specific silencing of genes in diverse organisms including Drodophia, Caenorhabditis elegans, epiphyte, mammalian and etc. RNAi also exists in aquicolous organisms. RNAi is an effective method to study the gene function of aquicolous organisms as was validated zebra fish, ascidian and so on. Controlling viral infection in aquiculture is a technological challenge worldwide, and RNAi could be a way of viral infection of cultured animals. siRNAs were designed based on LCDV-cn own genes and LCDV own genes. siRNAs were injected into China flounder in order to study the effect of LCDV-cn copy and infection. The results indicated that the expression quantity of mcp gene in LCDV-cn was reduced in three days after infection of mcp-siRNA1 and mcp-siRNA3. This show that RNAi can restrain the copy of LCDV-cn.
引文
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