家蚕NPV不同株系比较及宿主域差异分子机理
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摘要
杆状病毒专一寄生节肢动物,尤以昆虫纲的鳞翅目为甚。截至目前,有58种(株)杆状病毒的基因组被完全测序,它们共有31个保守基因,根据这31个基因连锁进化分析,这些杆状病毒可分为四大类,Alphabaculovirus、 Betabaculovirus、Gammabaculovirus、Deltabaculovirus。新基因组测序技术的发展带来测序的繁荣,越来越多的杆状病毒基因组被测序,也使得杆状病毒的进化发生规律越来越清晰,然而对同种杆状病毒不同株系的进化研究却鲜有报告,只有在棉铃虫杆状病毒株系有所比较研究。本论文以家蚕杆状病毒为研究对象,在全基因组水平对6个株系家蚕杆状病毒进行了比较分析,这将会填补同一宿主杆状病毒进化研究这一块的空白,也会进一步丰富对杆状病毒进化的认识。同时,我们报道了一株既可以感染Bm细胞系又可以感染High Five和Sf细胞的野生型病毒,它自野蚕中分离得到。对这株杆状病毒的研究将对杆状病毒宿主域的研究有重大意义,对杆状病毒作为杀虫剂的应用开发也有很大的借鉴意义。另外,鉴于家蚕杆状病毒对于蚕丝业的重大威胁,研究家蚕杆状病毒与家蚕的相互关系也是家蚕杆状病毒的研究热点之一。尽管之前对病毒感染之后家蚕的转录有不少研究,但还没有工作涉及转录组测序。本论文中利用RNA-Seq技术对感染杆状病毒的家蚕细胞进行了转录组测序,得到了丰富的家蚕转录信息,这将对以后继续开展家蚕与家蚕杆状病毒的互作研究提供良好的基础。本论文的主要结论如下：
1.家蚕杆状病毒不同株系的比较研究
我们在全基因组水平上比较研究了BmNPV的6个病毒株系。我们发现bro基因数目及hr区的构成是它们基因组最大差异所在。hr区中的回文序列总数影响病毒的DNA复制,但是相同hr区不同回文序列数目对其下游基因的转录似乎不影响。而对各个ORF对比发现,差异较大的是那些杆状病毒非核心基因,它们对BmNPV株系的进化影响最大。基于全基因组的进化分析表明India株与其它株亲缘关系较远,但与Cubic最近；Guangxi株与Zhejiang株相近；而Boma S1株和Cubic株尽管宿主来源不同,但是亲缘关系接近；T3株处于Boma S1株与Guangxi株(或Zhejiang株)之间。不同株系病毒不同形态的病毒粒子致病性不同。在BV毒力方面,Boma S1株和T3株稍比其它株系弱；而多角体的致死率方面,India株系最高,但Boma S1最低。然而,不同BmNPV株系的生物学差异与其分子进化的相关性比较模糊。
2.一株野蚕杆状病毒的宿主域分子决定机理研究
从野蚕分离的BomaNPV S2病毒株,它可以感染Bm细胞系,也可以感染High Five和Sf等细胞系。但病毒粒子在Bm细胞和High Five细胞中呈现的形态却有所不同。在Bm5细胞中,多角形的包含体边缘不太光滑,且包埋的ODV病毒粒子少,呈单粒包埋型(SNPV),但在High Five细胞中包含体的边缘相对光滑,但ODV病毒粒子多,却呈多粒包埋型(MNPV)。BomaNPVS2在Bm细胞中繁殖的出芽病毒量要远多于BmNPV T3株,这与核衣壳在两种病毒粒子中的平衡分配有关。基因组序列分析表明,BomaNPV S2基因组中大部分序列更类似于BmNPV基因组,但有些区段更类似于AcMNPV基因组。我们把BomaNPV S2基因组与通过BmNPV和AcMNPV共转染细胞后分离得到的一株病毒的基因组相比较后找出了一些可能与宿主域相关的序列。构建含有这些序列的重组病毒并进行转染和感染细胞实验,我们发现,这些疑似序列中gp64基因是BomaNPV S2既可以感染Bm细胞又可以感染High Five细胞的最主要原因。
3.感染家蚕杆状病毒后家蚕细胞Bm5的转录组研究
我们利用RNA-Seq技术获得BmNPV感染后家蚕细胞Bm5的转录组,这是对家蚕基因转录数据库及基因表达数据库的一个很大补充。我们发现,有90%的家蚕基因在感染病毒后得到转录,这些基因在不同染色体上的分布密度不同,对这些基因进行GO分类和KEGG分类发现,多数基因与细胞最基本的生物学功能相关。此外,只有少数的基因发生可变剪切,其中外显子跳跃(Exon skipping, ES)和内含子保留(Intron retention, IR)这两种形式可变剪切最多。值得注意的是,一些如核糖体通路等重要通路或染色体功能集、泛素系统功能集等重要功能集中有许多基因发生可变剪切。另外令人惊讶的是,同时剪切体通路也有很多基因发生可变剪切。这些结果说明了可变剪切的重要性和复杂性。
The family Baculoviridae is a highly selective virus in arthropods, especially in insects of the order Lepidoptera. Until now, genomes of58baculovimses have been sequenced, which have31common conserved genes. These baculoviruses can be classed into four genera, Alphabaculovirus, Betabaculovirus, Gammabaculovirus, Deltabaculovirus, based on linkage evolutionary analysis of31conserved genes. As development of new genome sequencing techniques are driving a boom in sequencing, more and more genomes of baculoviruses have been sequenced, and phylogenetic evolution history of baculoviruses becomes increasingly clear. However, only a few studies focus on various strains of the same species of baculovirus, except studies on Helcoverpa armigera nucleopolyhedrovirus. Taken the BmNPV as the research object, it is the first time to comparatively analyze six various strains from a host at genome level where the blank needs to be filled, and that will enrich our knowledge of evolution of the baculoviruses. Meanwhile, we firstly report a wild nucleopolyhedrovirus from Bombyx mandarina, which can successfully propagate in Bm cell lines, High Five and Sf cell lines. Study on this virus is of great important to host range researches of baculoviruses and application of baculovriuses as biocontrol pesticide. In addition, considering the great threat of BmNPV to silk industry, it is meaningful to study the interaction between BmNPV and its host. Although there were lots of researches on genes'differential transcription of silkworm infected with BmNPV, there is no reports on the whole genomic profile of gene transcription of silkworm infected with BmNPV. Using RNA-Seq technique, we report the transcriptome of Bm5cells infected with BmNPV, and obtain lots of trancription message, which will be definitely useful for studies on interaction between silkworm and BmNPV.
The main results are as following:
1. Comparatively study on various strains of BmNPV
It is the first time to comparatively analyze various strains from a host at genome level. We found differences in the number of bro gene and composition of homologous region (hr) are two main divergences within these genomes. The total number of palindromes of hrs seems to affect viral DNA replication in Bm5cells, but difference in number of palindromes in the same hr of different viruses seems to be not related to transcript level of its downstream genes. While we compared ORFs from different viruses, we noticed big differences are in the ORFs that are not core genes. This result is consistent with results from evolutionary pressure analysis of ORFs, indicating these ORFs should play important roles in evolution of BmNPV strains. Based on the cascaded DNA of134common ORFs, a phylogenetic tree of these six virus strains was constructed. India strain is closer to Cubic strain but far away from others. Guangxi strain and Zhejiang strain have a close relationship. Boma S1strain and Cubic strain are closely related, even though they are from somewhat different hosts. T3strain locates between Boma S1strain and Guangxi strain (or Zhejiang strain). Bioassays of BVs and OBs were also carried out. BVs of Boma S1strain and T3strain take longer time to kill silkworm larvae than BVs of other four viruses. OBs of India strain are significantly more competitive than OBs of other viruses, and OBs of Boma S1fall behind. There seems no obvious connection between biological characteristics and phylogenic relationship between different strains of BmNPV.
2. Study on the molecular mechanism of host range determination of a wild nucleopolyhedrovirus from B. mandarina
This virus was named "BomaNPV S2", which is isolated from B. mandarina. BomaNPV S2can successfully propagate in B. mori cell lines, Trichoplusia ni cell line (High Five) and Spodoptera frugiperda cell line (Sf9). OBs in nuclei of Bm5cells seem rough and contain less virions than that in High Five cells. Interestingly, BomaNPV S2is SNPV in Bm cells, but MNPV in High Five cells. BomaNPV S2generates much more BVs than BmNPV T3while it infects Bm5cells, indicating a complement to fewer virions in polydedra. Sequence analysis of BomaNPV S2genome has revealed that most sequences of this genome are more identical to DNAs from BmNPV (or BomaNPV S1) and some else are more identical to DNAs from AcMNPV. Compared with the genome of a hybridized virus that is isolated from cells cotransfected with BmNPV and AcMNPV, some genomic DNA regions of BomaNPV S2are thought to be associated with its host range determination. Recombinant viruses containing these sequences were constructed for analyzing their infectivity to Bm cells and High Five cells. Our result showed that gp64is the key gene for BomaNPV S2being able to infect both Bm cells and High Five cells.
3. Transcriptome of Bm5infected with BmNPV
The transcriptome of Bm5cells infected with BmNPV was obtained via RNA-Seq. This is a big addition to data library of gene transcription or gene express profile of the silkworm. We found about ninety percent of annotated genes of the silkworm was transcripted in Bm5cells infected with BmNPV. And these transcribed genes distribute different within different chromosome. Classified by GO and KEGG, most genes are related to basic biological functions. However, only a small number of genes undergo alternative splicing, of which exon skipping and intron retention are the two main kinds of alternative splicing events. Noteworthily, some pathways like Ribosome Pathway and some function Brites like Chromosome Brite and Ubiquitin Brite have lots of genes experiencing alternative splicing. Surprisingly, Spliceosome Pathway also has a number of genes undergoing alternative splicing. These results demonstrate the importance and complication of alternative splicing.
1.家蚕杆状病毒不同株系的比较研究
我们在全基因组水平上比较研究了BmNPV的6个病毒株系。我们发现bro基因数目及hr区的构成是它们基因组最大差异所在。hr区中的回文序列总数影响病毒的DNA复制,但是相同hr区不同回文序列数目对其下游基因的转录似乎不影响。而对各个ORF对比发现,差异较大的是那些杆状病毒非核心基因,它们对BmNPV株系的进化影响最大。基于全基因组的进化分析表明India株与其它株亲缘关系较远,但与Cubic最近；Guangxi株与Zhejiang株相近；而Boma S1株和Cubic株尽管宿主来源不同,但是亲缘关系接近；T3株处于Boma S1株与Guangxi株(或Zhejiang株)之间。不同株系病毒不同形态的病毒粒子致病性不同。在BV毒力方面,Boma S1株和T3株稍比其它株系弱；而多角体的致死率方面,India株系最高,但Boma S1最低。然而,不同BmNPV株系的生物学差异与其分子进化的相关性比较模糊。
2.一株野蚕杆状病毒的宿主域分子决定机理研究
从野蚕分离的BomaNPV S2病毒株,它可以感染Bm细胞系,也可以感染High Five和Sf等细胞系。但病毒粒子在Bm细胞和High Five细胞中呈现的形态却有所不同。在Bm5细胞中,多角形的包含体边缘不太光滑,且包埋的ODV病毒粒子少,呈单粒包埋型(SNPV),但在High Five细胞中包含体的边缘相对光滑,但ODV病毒粒子多,却呈多粒包埋型(MNPV)。BomaNPVS2在Bm细胞中繁殖的出芽病毒量要远多于BmNPV T3株,这与核衣壳在两种病毒粒子中的平衡分配有关。基因组序列分析表明,BomaNPV S2基因组中大部分序列更类似于BmNPV基因组,但有些区段更类似于AcMNPV基因组。我们把BomaNPV S2基因组与通过BmNPV和AcMNPV共转染细胞后分离得到的一株病毒的基因组相比较后找出了一些可能与宿主域相关的序列。构建含有这些序列的重组病毒并进行转染和感染细胞实验,我们发现,这些疑似序列中gp64基因是BomaNPV S2既可以感染Bm细胞又可以感染High Five细胞的最主要原因。
3.感染家蚕杆状病毒后家蚕细胞Bm5的转录组研究
我们利用RNA-Seq技术获得BmNPV感染后家蚕细胞Bm5的转录组,这是对家蚕基因转录数据库及基因表达数据库的一个很大补充。我们发现,有90%的家蚕基因在感染病毒后得到转录,这些基因在不同染色体上的分布密度不同,对这些基因进行GO分类和KEGG分类发现,多数基因与细胞最基本的生物学功能相关。此外,只有少数的基因发生可变剪切,其中外显子跳跃(Exon skipping, ES)和内含子保留(Intron retention, IR)这两种形式可变剪切最多。值得注意的是,一些如核糖体通路等重要通路或染色体功能集、泛素系统功能集等重要功能集中有许多基因发生可变剪切。另外令人惊讶的是,同时剪切体通路也有很多基因发生可变剪切。这些结果说明了可变剪切的重要性和复杂性。
The family Baculoviridae is a highly selective virus in arthropods, especially in insects of the order Lepidoptera. Until now, genomes of58baculovimses have been sequenced, which have31common conserved genes. These baculoviruses can be classed into four genera, Alphabaculovirus, Betabaculovirus, Gammabaculovirus, Deltabaculovirus, based on linkage evolutionary analysis of31conserved genes. As development of new genome sequencing techniques are driving a boom in sequencing, more and more genomes of baculoviruses have been sequenced, and phylogenetic evolution history of baculoviruses becomes increasingly clear. However, only a few studies focus on various strains of the same species of baculovirus, except studies on Helcoverpa armigera nucleopolyhedrovirus. Taken the BmNPV as the research object, it is the first time to comparatively analyze six various strains from a host at genome level where the blank needs to be filled, and that will enrich our knowledge of evolution of the baculoviruses. Meanwhile, we firstly report a wild nucleopolyhedrovirus from Bombyx mandarina, which can successfully propagate in Bm cell lines, High Five and Sf cell lines. Study on this virus is of great important to host range researches of baculoviruses and application of baculovriuses as biocontrol pesticide. In addition, considering the great threat of BmNPV to silk industry, it is meaningful to study the interaction between BmNPV and its host. Although there were lots of researches on genes'differential transcription of silkworm infected with BmNPV, there is no reports on the whole genomic profile of gene transcription of silkworm infected with BmNPV. Using RNA-Seq technique, we report the transcriptome of Bm5cells infected with BmNPV, and obtain lots of trancription message, which will be definitely useful for studies on interaction between silkworm and BmNPV.
The main results are as following:
1. Comparatively study on various strains of BmNPV
It is the first time to comparatively analyze various strains from a host at genome level. We found differences in the number of bro gene and composition of homologous region (hr) are two main divergences within these genomes. The total number of palindromes of hrs seems to affect viral DNA replication in Bm5cells, but difference in number of palindromes in the same hr of different viruses seems to be not related to transcript level of its downstream genes. While we compared ORFs from different viruses, we noticed big differences are in the ORFs that are not core genes. This result is consistent with results from evolutionary pressure analysis of ORFs, indicating these ORFs should play important roles in evolution of BmNPV strains. Based on the cascaded DNA of134common ORFs, a phylogenetic tree of these six virus strains was constructed. India strain is closer to Cubic strain but far away from others. Guangxi strain and Zhejiang strain have a close relationship. Boma S1strain and Cubic strain are closely related, even though they are from somewhat different hosts. T3strain locates between Boma S1strain and Guangxi strain (or Zhejiang strain). Bioassays of BVs and OBs were also carried out. BVs of Boma S1strain and T3strain take longer time to kill silkworm larvae than BVs of other four viruses. OBs of India strain are significantly more competitive than OBs of other viruses, and OBs of Boma S1fall behind. There seems no obvious connection between biological characteristics and phylogenic relationship between different strains of BmNPV.
2. Study on the molecular mechanism of host range determination of a wild nucleopolyhedrovirus from B. mandarina
This virus was named "BomaNPV S2", which is isolated from B. mandarina. BomaNPV S2can successfully propagate in B. mori cell lines, Trichoplusia ni cell line (High Five) and Spodoptera frugiperda cell line (Sf9). OBs in nuclei of Bm5cells seem rough and contain less virions than that in High Five cells. Interestingly, BomaNPV S2is SNPV in Bm cells, but MNPV in High Five cells. BomaNPV S2generates much more BVs than BmNPV T3while it infects Bm5cells, indicating a complement to fewer virions in polydedra. Sequence analysis of BomaNPV S2genome has revealed that most sequences of this genome are more identical to DNAs from BmNPV (or BomaNPV S1) and some else are more identical to DNAs from AcMNPV. Compared with the genome of a hybridized virus that is isolated from cells cotransfected with BmNPV and AcMNPV, some genomic DNA regions of BomaNPV S2are thought to be associated with its host range determination. Recombinant viruses containing these sequences were constructed for analyzing their infectivity to Bm cells and High Five cells. Our result showed that gp64is the key gene for BomaNPV S2being able to infect both Bm cells and High Five cells.
3. Transcriptome of Bm5infected with BmNPV
The transcriptome of Bm5cells infected with BmNPV was obtained via RNA-Seq. This is a big addition to data library of gene transcription or gene express profile of the silkworm. We found about ninety percent of annotated genes of the silkworm was transcripted in Bm5cells infected with BmNPV. And these transcribed genes distribute different within different chromosome. Classified by GO and KEGG, most genes are related to basic biological functions. However, only a small number of genes undergo alternative splicing, of which exon skipping and intron retention are the two main kinds of alternative splicing events. Noteworthily, some pathways like Ribosome Pathway and some function Brites like Chromosome Brite and Ubiquitin Brite have lots of genes experiencing alternative splicing. Surprisingly, Spliceosome Pathway also has a number of genes undergoing alternative splicing. These results demonstrate the importance and complication of alternative splicing.
引文
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