真核生物非逆转录病毒内生化与进化基因组学研究
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摘要
病毒是地球上目前所知的最古老、数量最多、适应性最强的生物实体(biological entities),代表着巨大、多样的新基因源,病毒进化因而很可能也影响到宿主的进化。研究病毒进化不仅可以了解病毒的多样性,预测和解释新病毒病的出现,而且可以深入认识病毒-宿主间的互作关系,揭示病毒-宿主之间遗传信息的交流。病毒基因组比较是研究病毒互作与进化的重要方式,但是常常会受到数据的限制,比如可用的病毒基因组数据量偏少,或着样本不具代表性。更重要的是,病毒没有化石,病毒进化研究只能局限在现存病毒上。由于逆转录病毒(retroviruses)能够发生基因组整合,在数百万年的进化历程中它们偶尔会内生化(endogenization)到宿主基因组中形成内源逆转录病毒(endogenous retroviruses)。这些内源病毒序列实际上代表着古老病毒基因组的“分子化石”,保留了古代病毒与宿主互作的重要信息,因此对研究病毒-宿主长期的互作与进化历史极为宝贵。此前一直认为非逆转录病毒通常并不能够发生基因组整合,形成“病毒化石”的例子就更加罕见。
本研究一方面立足于所在实验室长期研究的核盘菌(Sclerotinia sclerotiorum)——一种重要植物病原真菌,从中分子克隆和测序分析未知真菌病毒的全基因组序列；另一方面立足于不断增长的生物信息学数据库,运用生物信息学方法和技术,从公共的EST数据库中电子克隆(cloning in silico)未知病毒的基因组序列,更重要的是,从真核生物基因组数据库中挖掘(data mining)作为“病毒化石”的内源非逆转录病毒序列。最后利用这些新得到的病毒基因组序列结合已有的相关病毒的数据,在比较基因组学的框架内,以系统发育分析病毒基因和基因组序列为主要研究方式,全面了解病毒的多样性、宿主范围的广泛性和非逆转录病毒内生化现象,探讨病毒内生化机制、病毒起源进化以及病毒-宿主在基因组水平上的互作关系,揭示病毒在真核生物进化中的重要作用。本研究所取得的主要研究结果如下：
1.从核盘菌弱致病力菌株Ep-1PN中克隆到一种新RNA病毒,命名为核盘菌RNA病毒L (SsRV-L)。SsRV-L基因组全长6043 bp(不包括3’-末端的polyA尾),仅具单个开放阅读框(ORF),编码蛋白具有甲基转移酶、RNA解旋酶和依赖RNA的RNA聚合酶(RdRp)保守结构域。序列比较表明该蛋白与隶属ss(+)RNA病毒“类甲病毒”超组的人类戊型肝炎病毒(HEV)的复制酶具有显著相似性,这是首次在真菌中报道与人类病毒具有显著亲缘关系的ss(+)RNA病毒。系统发育分析表明SsRV-L可归于“类甲病毒”超组内的“类风疹病毒”世系,与植物长线形病毒(closteroviruses)、烟草花叶病毒(tobamoviruses)、甜菜坏死黄脉病毒(benyviruses)、昆虫四病毒(tetraviruses),以及脊椎动物戊型肝炎病毒(hepeviruses)和风疹病毒(rubiviruses)都具有较近的亲缘关系。并且这些病毒的系统进化关系与宿主的分化相一致,表明其祖先可能起源于宿主植物、真菌和动物分化之前,随后在长期的进化历程中与宿主保持协同进化,该发现对理解众多的RNA病毒进化世系的起源进化以及新病毒的出现具有深远影响。另外,实验证明了SsRV-L能够在宿主核盘菌细胞内独立复制,对宿主生长速度和致病力可造成轻微的影响,进一步明确了引起Ep-1PN菌株弱致病力的原因,对研究病毒介导的植物病原真菌弱毒特性的分子机理具有重要意义。
2从核盘菌强致病力菌株Sunf-M中克隆到一种新单分体(monopartite) dsRNA病毒,命名为核盘菌dsRNA真菌病毒L (SsMV-L)。SsMV-L基因组全长9124 bp,无polyA尾,具两个长ORF (ORF1和ORF2),5’-非翻译区相对较长(1088 bp)而3’-非翻译区相对较短(54 bp)。ORF1推定编码1304个氨基酸的蛋白,该蛋白具有磷酸庚糖异构酶(Sugar ISomerase)保守结构域的部分序列,但功能未知；ORF2推定编码1337个氨基酸的蛋白,该蛋白具有RNA病毒典型的RdRp保守结构域,推测为病毒的复制酶。对SsMV-L及其相关的dsRNA病毒类群进行了全面的系统发育分析和基因组结构比较,研究结果表明SsMV-L代表一类新单分体dsRNA病毒世系,而单分体dsRNA病毒实际上具有多样化的病毒世系,当前的病毒分类系统已不能满足需要,可考虑成立新的病毒科或在已有单分病毒科(Totiviridae)内增加新属以容纳这些不同的病毒进化世系。系统发育分析还表明基因组为4节段的产黄青霉病毒(chrysoviruses)可能由单分体dsRNA病毒进化而来。令人惊奇的是,SsRV-L复制酶RdRp结构域的下游还具有植物呼肠孤病毒属(Phytoreovirus)成员所特有的S7核心蛋白结构域的同源序列,通过PSI-BLAST分析,发现该结构域广泛存在于多种RNA病毒类群中,包括产黄青霉病毒、内源RNA病毒(endornaviruses)以及一些未归类的单分体dsRNA病毒。结构域排列比较和系统发育分析表明S7结构域序列可能起源于植物呼肠孤病毒属病毒,并且在不同种类的dsRNA病毒间发生过多次水平基因转移事件。该发现首次证明遗传关系非常疏远的dsRNA病毒类群间也能够发生基因水平转移事件,揭示了dsRNA病毒宏观进化(macroevolution)的分子机制。
3.从核盘菌Sunf-M菌株中克隆到一种新双分体(bipartite) dsRNA病毒,命名为核盘菌双分病毒S(SsPV-S)。SsPV-S基因组包含大小相似的两个片段：S-1和S-2,长度分别为1856和1783 bp(不包括正链3’-末端的polyA尾),各含一个ORF,分别编码病毒的RdRp和衣壳蛋白(CP)。对SsPV-S及目前已报道的双分病毒(partitiviruses)进行全面的系统发育分析,结果表明这些病毒主要形成4个单系类群。同一单系类群中可包括侵染真菌的双分病毒(Partitivirus)和侵染植物的双分病毒(Alphacryptovirus),表明双分病毒可能在植物和真菌间发生过水平转移,同时也说明当前双分病毒科(Partitiviridae)的分类并不能反映病毒真实的进化关系。值得说明的是,SsPV-S的CP蛋白与拟南芥生长素-亮氨酸抗性蛋白2(ILR2)具有最高的氨基酸相似性,而与其它双分病毒的CP蛋白相似性都较低,表明病毒与拟南芥基因组之间可能发生过水平基因转移事件。
4.通过电子克隆技术从NCBI EST数据库中克隆到120多条类似单分病毒、双分病毒、产黄青霉病毒和内源RNA病毒的新RNA病毒基因组序列,其中类似双分病毒的新病毒序列达到106条,几乎使已知双分病毒的种类翻了一倍。这些序列不仅代表先前未报道的病毒,而且很多来自新的宿主甚至新的宿主类群。例如许多类似单分病毒和内源RNA病毒的序列来自动物,而目前这类病毒并未发现侵染动物。更重要的是,通过对这些新得到的病毒序列以及已报道的相关病毒序列进行全面的系统发育分析,揭示了这些病毒与宿主的互作与进化关系,即这些病毒的祖先可能起源于真核宿主超群(supergroup)分化之前,在漫长的进化历史中与宿主协同进化并伴随频率的宿主转移事件。该研究证明电子克隆方法具有发现新病毒的巨大潜力,通过该方法的运用极大地增强了我们对dsRNA病毒多样性、宿主范围广泛性以及病毒-宿主互作与进化的认识。
5.通过对dsRNA病毒和真核生物基因组进行系统地数据比较,鉴定真核基因组中内源dsRNA病毒序列,研究结果表明单分病毒和双分病毒都存在广泛的内生化现象。总共从来自植物、节肢动物、真菌、线虫、腹足动物和原生动物等类群的20多种真核生物的核基因组中鉴定出22个类似双分病毒和34个类似单分病毒RdRp或CP基因的序列。通过PCR扩增、测序以及计算分析证明这些序列是真正存在于真核生物基因组中的内源病毒序列。序列比较和系统发育分析进一步证明这些序列来自单分病毒和双分病毒的内生化。鉴于许多内源病毒序列来自目前还未报道被单分病毒和双分病毒侵染的真核类群,本研究延伸了这些病毒的宿主范围。另外,通过分析内源病毒基因的保守性和表达情况,证明一些内源病毒基因,例如拟南芥和白菜(Brassica rapa)基因组中的双分病毒CP类似基因和果蝇(Drosophila grimshawi)基因组中的双分病毒RdRp类似基因不仅存在序列保守性而且能够表达,尤其是拟南芥中的CP类似基因(ILR2)已被证明具有调节植物激素吲哚乙酸生物合成的功能。本研究提供翔实的证据证明dsRNA病毒的遗传材料可以水平转移到多样的真核生物基因组中,并可能产生有重要功能的新基因,表明RNA病毒在真核生物进化中扮演了重要角色。
6.通过对线性ssDNA病毒和真核生物基因组进行系统地数据比较,鉴定真核基因组中内源线性ssDNA病毒的序列,研究结果表明细小病毒(parvoviruses)和浓核病毒(densoviruses)都存在广泛的内生化现象。总共从来自哺乳动物、鸟类、鱼类和背囊动物等类群的37种真核生物核基因组中鉴定出62个细小病毒非结构蛋白(NS)类似序列和77个CP类似序列：从来自甲壳纲、蛛形纲和昆虫纲动物以及扁形虫等类群的9种真核生物核基因组中鉴定出92个浓核病毒NS类似序列和44个CP类似序列。通过PCR扩增、测序以及计算分析证明这些序列是真正存在于真核生物基因组中的内源病毒序列。值得说明的是鱼类、背囊动物和扁形虫当前并未发现被细小病毒侵染,但其基因组中存在内源病毒序列清楚的表明它们被或曾经被相关病毒侵染。序列比较和系统发育分析证明许多内源病毒序列非常古老,至少在动物基因组中存在了数百万年。特别是在人类和其它哺乳动物的基因组中鉴定出一个类似细小病毒CP基因的直系同源(orthologous)序列,表明细小病毒与哺乳动物宿主共存至少有9,800万年的历史,此类病毒的进化时间超出前人想象,同时,这也是迄今发现的最古老的“病毒化石”。另外,通过表达分析证明部分内源细小病毒基因在真核生物基因组中可以表达,表明细小病毒可能作为宿主未曾预料的遗传革新源(source of genetic innovation)。总之,内源细小病毒和浓核病毒的发现提供了表征病毒入侵的“化石记录”,从而有助于揭示其与宿主的进化历史,增强了我们对病毒一宿主互作的认识。
7.通过对环形ssDNA病毒和真核生物基因组进行系统地数据比较,鉴定真核基因组中类似环形ssDNA病毒的序列,研究结果表明类似双生病毒(geminiviruses)、矮缩病毒(nanoviruses)和圆环病毒(circoviruses)的内源序列广泛存在于真核生物核基因组中。总共从来自真菌、植物和原生动物等类群的12种真核生物核基因组中鉴定出31个双生病毒复制相关蛋白(Rep)类似序列和1个CP类似序列；从来自绿藻类、硅藻类、脊椎动物和无脊椎动物等类群的23种真核生物核基因组中鉴定出271个圆环病毒和矮缩病毒Rep类似序列和2个CP类似序列。通过PCR扩增、测序以及计算分析证明这些序列是真正存在于真核生物基因组中的内源病毒序列。通过将这些内源病毒序列与已知的环状ssDNA病毒以及真核或原核滚环复制质粒进行序列比较和系统发育分析,不仅揭示了环状ssDNA病毒的多样性和宿主范围的广泛性,而且重构了这些病毒与宿主长期的进化历史,并对双生病毒、矮缩病毒和圆环病毒的起源和进化产生了新的认识。另外,本研究不仅通过表达分析证明了部分内源病毒基因在真核生物基因组中可以表达,预示可能执行生物学功能,而且在内生真菌和半索类海生动物基因组中鉴定出类似双生病毒和类似细小病毒的两种新转座子,证明了ssDNA病毒对真核宿主的进化起到了重要作用。
Viruses are the most ancient, numerous and adaptable biological entities we now know. They represent a vast and diverse source of novel genes and thereby their evolution can also affect host evolution. The study of virus evolution provides an integrating framework for not only understanding the diversity of viruses and providing explanations for the emergence of new viral disease, but also advancing our knowledge of host-virus interactions and revealing the exchange of genetic information between viruses and hosts. The large-scale comparison of viral genome sequences may provides a valuable way to study their evolution and interactions. However, this way is often limited by data, such as the available viral sample sizes are often both small and biased. Moreover, since viruses lack the geological fossil record, the study of virus evolution is confined to the present. Retroviruses normally integrate into the genome of the host cell as an obligate step in their replication strategy, and occasionally these viruses may integrate into the germline genome of their host, and become inherited endogenous retroviruses over millions of years. The endogenous retroviral sequences effectively represent the 'molecular fossils' of ancient viral genomes, preserving information about ancient virus and host interactions, and hence constitute an invaluable resource for reconstructing the long-term history of virus and host evolution. For non-retroviral viruses, which do not normally integrate their genomes into host DNA, the formation of 'viral fossils' should be far less likely.
On the one hand, base our study on the Sclerotinia sclerotiorum, a long-term studied plant pathogens fungus in our lab, from which we performed molecular cloning and sequencing of the complete genome sequences of novel mycoviruses. On the other hand, base on the increasing availability of bioinformatics database, we used bioinformatics methods and technologies to discover genomic sequences of new viruses from EST database by cloning in silico, and more importantly, to identify the non-retroviral endogenous virus sequences, the 'molecular fossils' of ancient viral genomes, from the eukaryotic genomic databases by data mining. Finally, we used the new viral genome sequences combining with the related known viral sequences in the database and sited squarely within the framework of comparative genomics, with the phylogenetic analysis of viral gene and genome sequences as the main analytical tool to reveal novel virus diversity, the widespread endogenization and host range of non-retroviral viruses, the contribution of virus to eukaryotic host evolution, and discuss the origin and evolution of relevant viruses, the potential integration mechanism of non-retroviral viruses, and the interaction and evolution of virus-host in the genome level. The main results of this study are listed as following,
1. We cloned and sequenced a novel RNA virus, named Sclerotinia sclerotiorum RNA virus L (SsRV-L), from a debilitated strain Ep-1PN of S. sclerotiorum. The complete genomic sequence of the SsRV-L is 6,043 nucleotides in length, excluding the poly (A) tail. Sequence analysis revealed the presence of a single open reading frame (ORF) that encodes a protein containing conserved methyltransferase, helicase, and RNA dependent RNA polymerase domains, which has significant sequence similarity to the replicase of Hepatitis E virus, a virus infecting humans belonging to "alphavirus-like" supergroup of positive-strand RNA viruses. As far as we know, this is the first report of a positive-strand RNA mycovirus that is related to a human virus. Genome comparison and phylogenetic analysis of SsRV-L with representative members of "alphavirus-like" supergroup showed that it clustered with the rubi-like viruses and that it is related to the plant clostero-, beny-and tobamoviruses, to the insect tetraviruses, and to the vertebrate hepeviruses and rubiviruses. Moreover, the viral phylogeny is consistent with the host phylogeny, suggesting that the progenitor of these viruses was originated anciently possibly prior to the separation of host fungi, plants, and animals and subsequently co-evolved with their hosts over long evolutionary history. This finding has potentially far-reaching implications for the understanding the origin and evolution of the large evolutionary lineage of RNA viruses as well as the emergence of new viruses. In addition, we presented convincing evidence that SsRV-L could replicate independently with only a slight impact on growth and virulence of its host. These results represent a significant contribution to future studies on the basis of virus-mediated hypovirulence for this plant pathogenic fungus.
2. We cloned and sequenced a novel monopartite dsRNA virus, named S. sclerotiorum dsRNA mycovirus L (SsMV-L), from a virulence strain Sunf-M of S. sclerotiorum. The complete genomic sequence of the SsMV-L is 9,124 nucleotides in length and no poly (A) tail. Sequence analysis revealed the presence of two large ORFs (ORF1 and ORF2) and the 5'-untranslated region (UTR) and 3'-UTR were 1088 and 54 bp in length, respectively. ORF1 of SsMV-L was predicted to encode a 1,034-aa protein containing partial sequence of conserved Sugar ISomerase domain but its function is unknown. ORF2 was predicted to encode a 1,337-aa protein containing conserved RdRp domain characteristic of RNA viruses, suggesting that it is function as viral replicase. Genome comparison and phylogenetic analysis of SsMV-L with related dsRNA viruses revealed that SsMV-L represents a species of a new taxon of monopartite dsRNA viruses and the current taxonomy of monopartite dsRNA virus cannot meet the needs. Hence, it should be considered to establish new virus families or new genera within the existent family Totiviridae to accommodate the different viral evolutionary lineages. In addition, the phylogeny also suggests that the ancestor of chrysoviruses whose genome encompasses four segments is likely to be originated from monopartite dsRNA viruses. Intriguingly, a 'phytoreo S7 domain' was found downstream from the RdRp domain in the putative replicase of SsMV-L. This domain consists of P7 proteins of phytoreoviruses known to be viral core proteins with nucleic acid binding activities. PSI-BLAST searches showed that the S7 domain has also been found in various RNA viruses, including chrysoviruses, endornaviruses as well as some unclassified monopartite dsRNA viruses. Domain organization and phylogenetic analysis suggested that the S7 domain sequences were most likely to be derived from those of ancestral phytoreoviruses and then be occurred multiple horizontal gene transfers (HGTs) among diverse RNA viruses. This finding provides convincing evidence that the recombination events have occurred between the virus families with very distant genetic relationships from different host taxa and reveals the macroevolutionary mechanism of dsRNA viruses.
3. We cloned and sequenced a novel bipartite dsRNA virus, named S. sclerotiorum partitivirus S (SsPV-S), from the strain Sunf-M. The genome of SsPV-S encompasses two segments:S-1 and S-2 and each contain one ORF. S-1 is 1,856 bp in length and encodes an RdRp; S-2 is 1,783 bp in length and encodes a coat protein (CP). Comprehensive phylogenetic analysis of SsPV-S with all known partitiviruses led to the identification of four major clades. One clade can consist of a mixture of plant partitiviruses (genus Alphacryptovirus) and fungal partitiviruses (genus Partitivirus), suggesting that horizontal transfer of members of the family Partitiviridae between fungi and plants were most likely to occur. Meanwhile, it suggests that current classification of partitivirus does not reflect the true evolutionary relationships of viruses, and therefore the taxonomy of the family Partitiviridae will probably need to be reconsidered. Intriguingly, SsPV-S CP has the highest aa sequence similarity to IAA-leucine-resistant protein 2 (ILR2) of Arabidopsis, its similarity to CPs of other partitiviruses is considerably lower. This raises the interesting possibility that HGT may have occurred between partitiviruses and genome of an Arabidopsis ancestor.
4. We identified large numbers of novel viral sequences similar to partiti-, toti-, chryso-or endornaviruses from NCBI EST database by cloning in silico. Among these, the number of partitivirus-like sequences is 106, almost doubled the known partitiviral species. The viral sequences obtained from this study not only represented previously unknown viruses, many but also were from the new host even new host taxa. For example, many partiti- or endornavirus-like sequences were from animals, while these viruses presently have not been reported to infect animals. More importantly, Comprehensive phylogenetic analysis of these new viral sequences with related known dsRNA viruses revealed the long-term history of virus-host evolution and interaction, namely, the progenitors of these viruses were originated anciently possibly prior to the separation of host supergroups and subsequently likely to co-evolve with their hosts over long evolutionary timescales concomitant of frequent viral host changes. This study demonstrates the potential of virus cloning in silico for discovering novel viruses directly from database, which can greatly increase our knowledge of viral diversity, host ranges as well as the interaction and evolution of virus-host.
5. We constructed a systematic search for sequences related to known dsRNA viruses in the publicly available eukaryotic genome databases. The results show that the RdRp and CP genes of partitiviruses and totiviruses have been widely endogenized into a broad range of eukaryotic genomes. Altogether,22 partitivirus and 34 totivirus RdRp or CP-like sequences were identified from the nuclear genomes of more than 20 eukaryotic organisms, including plants, arthropods, fungi, nematodes, and protozoa. PCR amplification, sequencing and comparative analysis supports the conclusion that these viral homologs are real and occur in eukaryotic genomes. Sequence comparison and phylogenetic analysis further demonstrated that these endogenous viral sequences were derived from endogenization of partitiviruses and totiviruses. Given that many of endogenous viral sequences were found in eukaryotic species which previously is not known to be infected by partitiviruses or totiviruses, our findings extends the host range of these viruses. Though analysis of conservation and expression of endogenous viral genes, we found that some of these, such as the partitiviral CP-like genes in Arabidopsis and Chinese cabbage (Brassica rapa), and the partitiviral RdRp-like gene in fruit fly (Drosophila grimshawi), were not only conserved but also expressed. Particularly, the ILR2 gene, a homolog of partitivirus CP, has been demonstrated to function in regulating the synthesis of the auxin indole-3-acetic acid (IAA). Hence, our findings imply that horizontal transfer of double-stranded RNA viral genes is widespread among eukaryotes and may give rise to functionally important new genes, thus entailing that RNA viruses may play significant roles in the evolution of eukaryotes.
6. We performed extensive sequence similarity searches for sequences related to known linear ssDNA viruses in the publicly available eukaryotic genome databases. The results show that parvoviruses and densoviruses have been widely endogenized into a broad range of eukaryotic genomes. Altogether,62 nonstructural protein (NS)-like and 77 CP-like sequences of parvoviruses were identified from the nuclear genomes of 37 eukaryotic organisms, including mammals, fish, birds and tunicates; 92 NS-like and 44 CP-like sequences of densoviruses were identified from the nuclear genomes of 9 eukaryotic organisms, including crustaceans, arachnids, insects and flatworms. PCR amplification, sequencing and comparative analysis supports the conclusion that these viral homologs are real and occur in eukaryotic genomes. It is worth to note that some animal lineages (such as fishes, tunicates and flatworms) are not known to be infected by parvoviruses. Many endogenous parvoviral sequences were found in their genomes, however, clearly suggesting that these species can also be infected by parvoviruses, at least past. Sequence comparison and phylogenetic analysis suggested that many of endogenous viral sequences were ancient and occurred at least millions years. Especially, the identification of orthologous endogenous parvoviral CP-like sequences in the genomes of humans and other mammals suggests that parvoviruses have coexisted with mammals at least 98 million years, which implies that these viruses are much older than previously thought. As far as we know, this is the oldest'viral fossil'known. In addition, we also reveal that some of the endogenous viral genes were expressed, suggesting that parvoviruses might act as an unforeseen source of genetic innovation in their hosts. In summary, our discovery provides fossil records of past viral invasions, thereby helps to shed light on the evolutionary history of viruses and hosts, and advance our knowledge of host-virus interactions.
7. We performed comprehensive sequence similarity searches for sequences related to known circular ssDNA viruses in the publicly available eukaryotic genome databases. The results show that sequences related geminiviruses, nanoviruses and circoviruses have been widely occurred in a broad range of eukaryotic genomes. Altogether,31 replication initiation protein (Rep)-like and 1 CP-like sequences of geminiviruses were identified from the nuclear genomes of 12 eukaryotic organisms, including plants, fungi, and protozoans; 271 Rep-like and 2 CP-like sequences of nanoviruses and circoviruses were identified from the nuclear genomes of 23 eukaryotic organisms, including green algae, diatoms, invertebrates and vertebrates. PCR amplification, sequencing and comparative analysis supports the conclusion that these viral homologs are real and occur in eukaryotic genomes. Though comprehensive sequence comparison and phylogenetic analysis of endogenous circular ssDNA virus-like sequences with related known viruses and eukaryotic or bacterial rolling-circle replicating (RCR) plasmids, our studies not only revealed the diversity of circular ssDNA viruses and their widespread host range, but also reconstructed the long-term history of virus and host evolution and advanced our understanding of the evolution of geminiviruses, nanoviruses and circoviruses. Furthermore, we also demonstrated that some of the endogenous viral genes were conserved and expressed, suggesting that these genes are also functional in the host genomes. We also identified a geminivirus-like and parvovirus-like transposable element in genomes of fungi and lower animals, respectively, and thereby provide direct evidence that eukaryotic transposons could derive from relevant viruses. It revealed that capture and functional assimilation of exogenous viral genes may represent an important force in eukaryotic evolution.
本研究一方面立足于所在实验室长期研究的核盘菌(Sclerotinia sclerotiorum)——一种重要植物病原真菌,从中分子克隆和测序分析未知真菌病毒的全基因组序列；另一方面立足于不断增长的生物信息学数据库,运用生物信息学方法和技术,从公共的EST数据库中电子克隆(cloning in silico)未知病毒的基因组序列,更重要的是,从真核生物基因组数据库中挖掘(data mining)作为“病毒化石”的内源非逆转录病毒序列。最后利用这些新得到的病毒基因组序列结合已有的相关病毒的数据,在比较基因组学的框架内,以系统发育分析病毒基因和基因组序列为主要研究方式,全面了解病毒的多样性、宿主范围的广泛性和非逆转录病毒内生化现象,探讨病毒内生化机制、病毒起源进化以及病毒-宿主在基因组水平上的互作关系,揭示病毒在真核生物进化中的重要作用。本研究所取得的主要研究结果如下：
1.从核盘菌弱致病力菌株Ep-1PN中克隆到一种新RNA病毒,命名为核盘菌RNA病毒L (SsRV-L)。SsRV-L基因组全长6043 bp(不包括3’-末端的polyA尾),仅具单个开放阅读框(ORF),编码蛋白具有甲基转移酶、RNA解旋酶和依赖RNA的RNA聚合酶(RdRp)保守结构域。序列比较表明该蛋白与隶属ss(+)RNA病毒“类甲病毒”超组的人类戊型肝炎病毒(HEV)的复制酶具有显著相似性,这是首次在真菌中报道与人类病毒具有显著亲缘关系的ss(+)RNA病毒。系统发育分析表明SsRV-L可归于“类甲病毒”超组内的“类风疹病毒”世系,与植物长线形病毒(closteroviruses)、烟草花叶病毒(tobamoviruses)、甜菜坏死黄脉病毒(benyviruses)、昆虫四病毒(tetraviruses),以及脊椎动物戊型肝炎病毒(hepeviruses)和风疹病毒(rubiviruses)都具有较近的亲缘关系。并且这些病毒的系统进化关系与宿主的分化相一致,表明其祖先可能起源于宿主植物、真菌和动物分化之前,随后在长期的进化历程中与宿主保持协同进化,该发现对理解众多的RNA病毒进化世系的起源进化以及新病毒的出现具有深远影响。另外,实验证明了SsRV-L能够在宿主核盘菌细胞内独立复制,对宿主生长速度和致病力可造成轻微的影响,进一步明确了引起Ep-1PN菌株弱致病力的原因,对研究病毒介导的植物病原真菌弱毒特性的分子机理具有重要意义。
2从核盘菌强致病力菌株Sunf-M中克隆到一种新单分体(monopartite) dsRNA病毒,命名为核盘菌dsRNA真菌病毒L (SsMV-L)。SsMV-L基因组全长9124 bp,无polyA尾,具两个长ORF (ORF1和ORF2),5’-非翻译区相对较长(1088 bp)而3’-非翻译区相对较短(54 bp)。ORF1推定编码1304个氨基酸的蛋白,该蛋白具有磷酸庚糖异构酶(Sugar ISomerase)保守结构域的部分序列,但功能未知；ORF2推定编码1337个氨基酸的蛋白,该蛋白具有RNA病毒典型的RdRp保守结构域,推测为病毒的复制酶。对SsMV-L及其相关的dsRNA病毒类群进行了全面的系统发育分析和基因组结构比较,研究结果表明SsMV-L代表一类新单分体dsRNA病毒世系,而单分体dsRNA病毒实际上具有多样化的病毒世系,当前的病毒分类系统已不能满足需要,可考虑成立新的病毒科或在已有单分病毒科(Totiviridae)内增加新属以容纳这些不同的病毒进化世系。系统发育分析还表明基因组为4节段的产黄青霉病毒(chrysoviruses)可能由单分体dsRNA病毒进化而来。令人惊奇的是,SsRV-L复制酶RdRp结构域的下游还具有植物呼肠孤病毒属(Phytoreovirus)成员所特有的S7核心蛋白结构域的同源序列,通过PSI-BLAST分析,发现该结构域广泛存在于多种RNA病毒类群中,包括产黄青霉病毒、内源RNA病毒(endornaviruses)以及一些未归类的单分体dsRNA病毒。结构域排列比较和系统发育分析表明S7结构域序列可能起源于植物呼肠孤病毒属病毒,并且在不同种类的dsRNA病毒间发生过多次水平基因转移事件。该发现首次证明遗传关系非常疏远的dsRNA病毒类群间也能够发生基因水平转移事件,揭示了dsRNA病毒宏观进化(macroevolution)的分子机制。
3.从核盘菌Sunf-M菌株中克隆到一种新双分体(bipartite) dsRNA病毒,命名为核盘菌双分病毒S(SsPV-S)。SsPV-S基因组包含大小相似的两个片段：S-1和S-2,长度分别为1856和1783 bp(不包括正链3’-末端的polyA尾),各含一个ORF,分别编码病毒的RdRp和衣壳蛋白(CP)。对SsPV-S及目前已报道的双分病毒(partitiviruses)进行全面的系统发育分析,结果表明这些病毒主要形成4个单系类群。同一单系类群中可包括侵染真菌的双分病毒(Partitivirus)和侵染植物的双分病毒(Alphacryptovirus),表明双分病毒可能在植物和真菌间发生过水平转移,同时也说明当前双分病毒科(Partitiviridae)的分类并不能反映病毒真实的进化关系。值得说明的是,SsPV-S的CP蛋白与拟南芥生长素-亮氨酸抗性蛋白2(ILR2)具有最高的氨基酸相似性,而与其它双分病毒的CP蛋白相似性都较低,表明病毒与拟南芥基因组之间可能发生过水平基因转移事件。
4.通过电子克隆技术从NCBI EST数据库中克隆到120多条类似单分病毒、双分病毒、产黄青霉病毒和内源RNA病毒的新RNA病毒基因组序列,其中类似双分病毒的新病毒序列达到106条,几乎使已知双分病毒的种类翻了一倍。这些序列不仅代表先前未报道的病毒,而且很多来自新的宿主甚至新的宿主类群。例如许多类似单分病毒和内源RNA病毒的序列来自动物,而目前这类病毒并未发现侵染动物。更重要的是,通过对这些新得到的病毒序列以及已报道的相关病毒序列进行全面的系统发育分析,揭示了这些病毒与宿主的互作与进化关系,即这些病毒的祖先可能起源于真核宿主超群(supergroup)分化之前,在漫长的进化历史中与宿主协同进化并伴随频率的宿主转移事件。该研究证明电子克隆方法具有发现新病毒的巨大潜力,通过该方法的运用极大地增强了我们对dsRNA病毒多样性、宿主范围广泛性以及病毒-宿主互作与进化的认识。
5.通过对dsRNA病毒和真核生物基因组进行系统地数据比较,鉴定真核基因组中内源dsRNA病毒序列,研究结果表明单分病毒和双分病毒都存在广泛的内生化现象。总共从来自植物、节肢动物、真菌、线虫、腹足动物和原生动物等类群的20多种真核生物的核基因组中鉴定出22个类似双分病毒和34个类似单分病毒RdRp或CP基因的序列。通过PCR扩增、测序以及计算分析证明这些序列是真正存在于真核生物基因组中的内源病毒序列。序列比较和系统发育分析进一步证明这些序列来自单分病毒和双分病毒的内生化。鉴于许多内源病毒序列来自目前还未报道被单分病毒和双分病毒侵染的真核类群,本研究延伸了这些病毒的宿主范围。另外,通过分析内源病毒基因的保守性和表达情况,证明一些内源病毒基因,例如拟南芥和白菜(Brassica rapa)基因组中的双分病毒CP类似基因和果蝇(Drosophila grimshawi)基因组中的双分病毒RdRp类似基因不仅存在序列保守性而且能够表达,尤其是拟南芥中的CP类似基因(ILR2)已被证明具有调节植物激素吲哚乙酸生物合成的功能。本研究提供翔实的证据证明dsRNA病毒的遗传材料可以水平转移到多样的真核生物基因组中,并可能产生有重要功能的新基因,表明RNA病毒在真核生物进化中扮演了重要角色。
6.通过对线性ssDNA病毒和真核生物基因组进行系统地数据比较,鉴定真核基因组中内源线性ssDNA病毒的序列,研究结果表明细小病毒(parvoviruses)和浓核病毒(densoviruses)都存在广泛的内生化现象。总共从来自哺乳动物、鸟类、鱼类和背囊动物等类群的37种真核生物核基因组中鉴定出62个细小病毒非结构蛋白(NS)类似序列和77个CP类似序列：从来自甲壳纲、蛛形纲和昆虫纲动物以及扁形虫等类群的9种真核生物核基因组中鉴定出92个浓核病毒NS类似序列和44个CP类似序列。通过PCR扩增、测序以及计算分析证明这些序列是真正存在于真核生物基因组中的内源病毒序列。值得说明的是鱼类、背囊动物和扁形虫当前并未发现被细小病毒侵染,但其基因组中存在内源病毒序列清楚的表明它们被或曾经被相关病毒侵染。序列比较和系统发育分析证明许多内源病毒序列非常古老,至少在动物基因组中存在了数百万年。特别是在人类和其它哺乳动物的基因组中鉴定出一个类似细小病毒CP基因的直系同源(orthologous)序列,表明细小病毒与哺乳动物宿主共存至少有9,800万年的历史,此类病毒的进化时间超出前人想象,同时,这也是迄今发现的最古老的“病毒化石”。另外,通过表达分析证明部分内源细小病毒基因在真核生物基因组中可以表达,表明细小病毒可能作为宿主未曾预料的遗传革新源(source of genetic innovation)。总之,内源细小病毒和浓核病毒的发现提供了表征病毒入侵的“化石记录”,从而有助于揭示其与宿主的进化历史,增强了我们对病毒一宿主互作的认识。
7.通过对环形ssDNA病毒和真核生物基因组进行系统地数据比较,鉴定真核基因组中类似环形ssDNA病毒的序列,研究结果表明类似双生病毒(geminiviruses)、矮缩病毒(nanoviruses)和圆环病毒(circoviruses)的内源序列广泛存在于真核生物核基因组中。总共从来自真菌、植物和原生动物等类群的12种真核生物核基因组中鉴定出31个双生病毒复制相关蛋白(Rep)类似序列和1个CP类似序列；从来自绿藻类、硅藻类、脊椎动物和无脊椎动物等类群的23种真核生物核基因组中鉴定出271个圆环病毒和矮缩病毒Rep类似序列和2个CP类似序列。通过PCR扩增、测序以及计算分析证明这些序列是真正存在于真核生物基因组中的内源病毒序列。通过将这些内源病毒序列与已知的环状ssDNA病毒以及真核或原核滚环复制质粒进行序列比较和系统发育分析,不仅揭示了环状ssDNA病毒的多样性和宿主范围的广泛性,而且重构了这些病毒与宿主长期的进化历史,并对双生病毒、矮缩病毒和圆环病毒的起源和进化产生了新的认识。另外,本研究不仅通过表达分析证明了部分内源病毒基因在真核生物基因组中可以表达,预示可能执行生物学功能,而且在内生真菌和半索类海生动物基因组中鉴定出类似双生病毒和类似细小病毒的两种新转座子,证明了ssDNA病毒对真核宿主的进化起到了重要作用。
Viruses are the most ancient, numerous and adaptable biological entities we now know. They represent a vast and diverse source of novel genes and thereby their evolution can also affect host evolution. The study of virus evolution provides an integrating framework for not only understanding the diversity of viruses and providing explanations for the emergence of new viral disease, but also advancing our knowledge of host-virus interactions and revealing the exchange of genetic information between viruses and hosts. The large-scale comparison of viral genome sequences may provides a valuable way to study their evolution and interactions. However, this way is often limited by data, such as the available viral sample sizes are often both small and biased. Moreover, since viruses lack the geological fossil record, the study of virus evolution is confined to the present. Retroviruses normally integrate into the genome of the host cell as an obligate step in their replication strategy, and occasionally these viruses may integrate into the germline genome of their host, and become inherited endogenous retroviruses over millions of years. The endogenous retroviral sequences effectively represent the 'molecular fossils' of ancient viral genomes, preserving information about ancient virus and host interactions, and hence constitute an invaluable resource for reconstructing the long-term history of virus and host evolution. For non-retroviral viruses, which do not normally integrate their genomes into host DNA, the formation of 'viral fossils' should be far less likely.
On the one hand, base our study on the Sclerotinia sclerotiorum, a long-term studied plant pathogens fungus in our lab, from which we performed molecular cloning and sequencing of the complete genome sequences of novel mycoviruses. On the other hand, base on the increasing availability of bioinformatics database, we used bioinformatics methods and technologies to discover genomic sequences of new viruses from EST database by cloning in silico, and more importantly, to identify the non-retroviral endogenous virus sequences, the 'molecular fossils' of ancient viral genomes, from the eukaryotic genomic databases by data mining. Finally, we used the new viral genome sequences combining with the related known viral sequences in the database and sited squarely within the framework of comparative genomics, with the phylogenetic analysis of viral gene and genome sequences as the main analytical tool to reveal novel virus diversity, the widespread endogenization and host range of non-retroviral viruses, the contribution of virus to eukaryotic host evolution, and discuss the origin and evolution of relevant viruses, the potential integration mechanism of non-retroviral viruses, and the interaction and evolution of virus-host in the genome level. The main results of this study are listed as following,
1. We cloned and sequenced a novel RNA virus, named Sclerotinia sclerotiorum RNA virus L (SsRV-L), from a debilitated strain Ep-1PN of S. sclerotiorum. The complete genomic sequence of the SsRV-L is 6,043 nucleotides in length, excluding the poly (A) tail. Sequence analysis revealed the presence of a single open reading frame (ORF) that encodes a protein containing conserved methyltransferase, helicase, and RNA dependent RNA polymerase domains, which has significant sequence similarity to the replicase of Hepatitis E virus, a virus infecting humans belonging to "alphavirus-like" supergroup of positive-strand RNA viruses. As far as we know, this is the first report of a positive-strand RNA mycovirus that is related to a human virus. Genome comparison and phylogenetic analysis of SsRV-L with representative members of "alphavirus-like" supergroup showed that it clustered with the rubi-like viruses and that it is related to the plant clostero-, beny-and tobamoviruses, to the insect tetraviruses, and to the vertebrate hepeviruses and rubiviruses. Moreover, the viral phylogeny is consistent with the host phylogeny, suggesting that the progenitor of these viruses was originated anciently possibly prior to the separation of host fungi, plants, and animals and subsequently co-evolved with their hosts over long evolutionary history. This finding has potentially far-reaching implications for the understanding the origin and evolution of the large evolutionary lineage of RNA viruses as well as the emergence of new viruses. In addition, we presented convincing evidence that SsRV-L could replicate independently with only a slight impact on growth and virulence of its host. These results represent a significant contribution to future studies on the basis of virus-mediated hypovirulence for this plant pathogenic fungus.
2. We cloned and sequenced a novel monopartite dsRNA virus, named S. sclerotiorum dsRNA mycovirus L (SsMV-L), from a virulence strain Sunf-M of S. sclerotiorum. The complete genomic sequence of the SsMV-L is 9,124 nucleotides in length and no poly (A) tail. Sequence analysis revealed the presence of two large ORFs (ORF1 and ORF2) and the 5'-untranslated region (UTR) and 3'-UTR were 1088 and 54 bp in length, respectively. ORF1 of SsMV-L was predicted to encode a 1,034-aa protein containing partial sequence of conserved Sugar ISomerase domain but its function is unknown. ORF2 was predicted to encode a 1,337-aa protein containing conserved RdRp domain characteristic of RNA viruses, suggesting that it is function as viral replicase. Genome comparison and phylogenetic analysis of SsMV-L with related dsRNA viruses revealed that SsMV-L represents a species of a new taxon of monopartite dsRNA viruses and the current taxonomy of monopartite dsRNA virus cannot meet the needs. Hence, it should be considered to establish new virus families or new genera within the existent family Totiviridae to accommodate the different viral evolutionary lineages. In addition, the phylogeny also suggests that the ancestor of chrysoviruses whose genome encompasses four segments is likely to be originated from monopartite dsRNA viruses. Intriguingly, a 'phytoreo S7 domain' was found downstream from the RdRp domain in the putative replicase of SsMV-L. This domain consists of P7 proteins of phytoreoviruses known to be viral core proteins with nucleic acid binding activities. PSI-BLAST searches showed that the S7 domain has also been found in various RNA viruses, including chrysoviruses, endornaviruses as well as some unclassified monopartite dsRNA viruses. Domain organization and phylogenetic analysis suggested that the S7 domain sequences were most likely to be derived from those of ancestral phytoreoviruses and then be occurred multiple horizontal gene transfers (HGTs) among diverse RNA viruses. This finding provides convincing evidence that the recombination events have occurred between the virus families with very distant genetic relationships from different host taxa and reveals the macroevolutionary mechanism of dsRNA viruses.
3. We cloned and sequenced a novel bipartite dsRNA virus, named S. sclerotiorum partitivirus S (SsPV-S), from the strain Sunf-M. The genome of SsPV-S encompasses two segments:S-1 and S-2 and each contain one ORF. S-1 is 1,856 bp in length and encodes an RdRp; S-2 is 1,783 bp in length and encodes a coat protein (CP). Comprehensive phylogenetic analysis of SsPV-S with all known partitiviruses led to the identification of four major clades. One clade can consist of a mixture of plant partitiviruses (genus Alphacryptovirus) and fungal partitiviruses (genus Partitivirus), suggesting that horizontal transfer of members of the family Partitiviridae between fungi and plants were most likely to occur. Meanwhile, it suggests that current classification of partitivirus does not reflect the true evolutionary relationships of viruses, and therefore the taxonomy of the family Partitiviridae will probably need to be reconsidered. Intriguingly, SsPV-S CP has the highest aa sequence similarity to IAA-leucine-resistant protein 2 (ILR2) of Arabidopsis, its similarity to CPs of other partitiviruses is considerably lower. This raises the interesting possibility that HGT may have occurred between partitiviruses and genome of an Arabidopsis ancestor.
4. We identified large numbers of novel viral sequences similar to partiti-, toti-, chryso-or endornaviruses from NCBI EST database by cloning in silico. Among these, the number of partitivirus-like sequences is 106, almost doubled the known partitiviral species. The viral sequences obtained from this study not only represented previously unknown viruses, many but also were from the new host even new host taxa. For example, many partiti- or endornavirus-like sequences were from animals, while these viruses presently have not been reported to infect animals. More importantly, Comprehensive phylogenetic analysis of these new viral sequences with related known dsRNA viruses revealed the long-term history of virus-host evolution and interaction, namely, the progenitors of these viruses were originated anciently possibly prior to the separation of host supergroups and subsequently likely to co-evolve with their hosts over long evolutionary timescales concomitant of frequent viral host changes. This study demonstrates the potential of virus cloning in silico for discovering novel viruses directly from database, which can greatly increase our knowledge of viral diversity, host ranges as well as the interaction and evolution of virus-host.
5. We constructed a systematic search for sequences related to known dsRNA viruses in the publicly available eukaryotic genome databases. The results show that the RdRp and CP genes of partitiviruses and totiviruses have been widely endogenized into a broad range of eukaryotic genomes. Altogether,22 partitivirus and 34 totivirus RdRp or CP-like sequences were identified from the nuclear genomes of more than 20 eukaryotic organisms, including plants, arthropods, fungi, nematodes, and protozoa. PCR amplification, sequencing and comparative analysis supports the conclusion that these viral homologs are real and occur in eukaryotic genomes. Sequence comparison and phylogenetic analysis further demonstrated that these endogenous viral sequences were derived from endogenization of partitiviruses and totiviruses. Given that many of endogenous viral sequences were found in eukaryotic species which previously is not known to be infected by partitiviruses or totiviruses, our findings extends the host range of these viruses. Though analysis of conservation and expression of endogenous viral genes, we found that some of these, such as the partitiviral CP-like genes in Arabidopsis and Chinese cabbage (Brassica rapa), and the partitiviral RdRp-like gene in fruit fly (Drosophila grimshawi), were not only conserved but also expressed. Particularly, the ILR2 gene, a homolog of partitivirus CP, has been demonstrated to function in regulating the synthesis of the auxin indole-3-acetic acid (IAA). Hence, our findings imply that horizontal transfer of double-stranded RNA viral genes is widespread among eukaryotes and may give rise to functionally important new genes, thus entailing that RNA viruses may play significant roles in the evolution of eukaryotes.
6. We performed extensive sequence similarity searches for sequences related to known linear ssDNA viruses in the publicly available eukaryotic genome databases. The results show that parvoviruses and densoviruses have been widely endogenized into a broad range of eukaryotic genomes. Altogether,62 nonstructural protein (NS)-like and 77 CP-like sequences of parvoviruses were identified from the nuclear genomes of 37 eukaryotic organisms, including mammals, fish, birds and tunicates; 92 NS-like and 44 CP-like sequences of densoviruses were identified from the nuclear genomes of 9 eukaryotic organisms, including crustaceans, arachnids, insects and flatworms. PCR amplification, sequencing and comparative analysis supports the conclusion that these viral homologs are real and occur in eukaryotic genomes. It is worth to note that some animal lineages (such as fishes, tunicates and flatworms) are not known to be infected by parvoviruses. Many endogenous parvoviral sequences were found in their genomes, however, clearly suggesting that these species can also be infected by parvoviruses, at least past. Sequence comparison and phylogenetic analysis suggested that many of endogenous viral sequences were ancient and occurred at least millions years. Especially, the identification of orthologous endogenous parvoviral CP-like sequences in the genomes of humans and other mammals suggests that parvoviruses have coexisted with mammals at least 98 million years, which implies that these viruses are much older than previously thought. As far as we know, this is the oldest'viral fossil'known. In addition, we also reveal that some of the endogenous viral genes were expressed, suggesting that parvoviruses might act as an unforeseen source of genetic innovation in their hosts. In summary, our discovery provides fossil records of past viral invasions, thereby helps to shed light on the evolutionary history of viruses and hosts, and advance our knowledge of host-virus interactions.
7. We performed comprehensive sequence similarity searches for sequences related to known circular ssDNA viruses in the publicly available eukaryotic genome databases. The results show that sequences related geminiviruses, nanoviruses and circoviruses have been widely occurred in a broad range of eukaryotic genomes. Altogether,31 replication initiation protein (Rep)-like and 1 CP-like sequences of geminiviruses were identified from the nuclear genomes of 12 eukaryotic organisms, including plants, fungi, and protozoans; 271 Rep-like and 2 CP-like sequences of nanoviruses and circoviruses were identified from the nuclear genomes of 23 eukaryotic organisms, including green algae, diatoms, invertebrates and vertebrates. PCR amplification, sequencing and comparative analysis supports the conclusion that these viral homologs are real and occur in eukaryotic genomes. Though comprehensive sequence comparison and phylogenetic analysis of endogenous circular ssDNA virus-like sequences with related known viruses and eukaryotic or bacterial rolling-circle replicating (RCR) plasmids, our studies not only revealed the diversity of circular ssDNA viruses and their widespread host range, but also reconstructed the long-term history of virus and host evolution and advanced our understanding of the evolution of geminiviruses, nanoviruses and circoviruses. Furthermore, we also demonstrated that some of the endogenous viral genes were conserved and expressed, suggesting that these genes are also functional in the host genomes. We also identified a geminivirus-like and parvovirus-like transposable element in genomes of fungi and lower animals, respectively, and thereby provide direct evidence that eukaryotic transposons could derive from relevant viruses. It revealed that capture and functional assimilation of exogenous viral genes may represent an important force in eukaryotic evolution.
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