Sputnik噬病毒体的生物学特性、行为及效应CSCD

噬病毒体是一种能感染其他病毒,通过损害宿主病毒来完成自我复制的病毒。目前发现的几种噬病毒体的宿主病毒都是巨病毒目病毒。噬病毒体能对宿主病毒产生负面影响,使得宿主病毒里异常颗粒增多,并损害宿主病毒的感染和裂解能力。Sputnik是第一种被发现的噬病毒体,本文对Sputnik噬病毒体的生物学性状、生物学行为和调控作用进行简单的介绍。     

Sputnik噬病毒体的生物学特性、行为及效应

噬病毒体是一种能感染其他病毒,通过损害宿主病毒来完成自我复制的病毒。目前发现的几种噬病毒体的宿主病毒都是巨病毒目病毒。噬病毒体能对宿主病毒产生负面影响,使得宿主病毒里异常颗粒增多,并损害宿主病毒的感染和裂解能力。Sputnik是第一种被发现的噬病毒体,本文对Sputnik噬病毒体的生物学性状、生物学行为和调控作用进行简单的介绍。     

噬病毒体启动子模体的初步预测分析

噬病毒体作为遗传信息的承载者和传播者,在生态系统中有着举足轻重的作用。为了探索噬病毒体以及噬病毒体与其宿主巨病毒间的调控模式和进化关系,本文基于MEME启动子预测分析工具,对噬病毒体ORF上游部分序列(包括起始密码子ATG)中的启动子模体进行了预测分析。依据预测得到的启动子模体E值和在基因组上的位置、数量和长度等信息,共得到17个潜在的启动子模体。sputnik的模体2和zamilon的模体2都存在一个富含AT的区域,广泛分布在基因组上,可能调控大部分ORF的表达;mavirus启动子模体中存在TCTA盒子,而ALM启动子模体中存在ATCT盒子,这两个模体可能为后期启动子模体;OLV的模体2、YSLV1和2的模体3、YSLV3的模体1以及YSLV4的模体1和2都存在富含AT的区域,广泛存在各基因组上,为各噬病毒体的潜在启动子模体。该结果为进一步研究噬病毒体ORF的表达时序及其与宿主巨病毒之间的协同调控表达奠定了一定的理论基础。     

自噬与微生物感染

自噬作为一种维持胞内代谢稳态的机制,与机体微生物感染有着紧密的关系。一方面,自噬能够协助宿主清除病原体;而另一方面也有细菌通过进化,利用自噬体为其增殖提供必要条件,甚至在其中潜伏增殖。同时,病原体也可诱导过度自噬,促进细胞死亡。总之,自噬与微生物感染的关系,可能远比我们知道的复杂。本篇综述即是从自噬分子机制出发,寻找多种病原体与宿主细胞自噬之间的最新进展,深入探讨了自噬之于微生物感染的作用和意义。     

感染丝状蓝藻的噬藻体的裂解周期和释放量的测定

近年来,随着浮游病毒的认识的深入,人们认识到浮游病毒对水体中初级生产力的影响是巨大的[1],其主要证据就是发现噬藻体在海洋蓝藻的种群控制上发挥着重要作用[2]. 噬藻体的释放量和裂解周期是衡量噬藻体感染力的重要指标,很多重要的生态指标如病毒在生态系统中对宿主的致死率、病毒种群得以维持的阈浓度等都需要使用病毒的释放量和裂解周期来加以推算[3,4], 因此准确地测定这两个基本参数是十分重要的.在自然界,很多丝状蓝藻,如颤藻、鱼腥藻、螺旋藻、席藻等是能够形成水华的,其中有些还具有产毒的功能[5].丝状蓝藻的形态特征有别于单细胞蓝藻, 在被噬藻体感染时,丝状蓝藻的感染周期和光合生理也与单细胞蓝藻有较大的差异[6],因此研究裂解丝状蓝藻的噬藻体的方法可能不同于感染单细胞的噬藻体.本次试验以一种感染丝状宿主的噬藻体为材料,探讨了确定其裂解周期和释放量的研究方法.     

自噬对胞内感染病原菌的清除及促进增殖作用

自噬作为一种新的程序性细胞死亡,其在病原体感染中的地位日益受到广泛关注。自噬在病原体感染中具有"双刃剑"样作用,一方面,机体可利用自噬清除感染入侵的病原体;另一方面,自噬可被某些病原体利用、修饰或干扰,以促进自身在宿主细胞内的存活与增殖。本文拟就近年来自噬与人类疾病关系密切的胞内病原菌感染中的作用及地位进行综述,同时结合本室研究进行一定深入探讨,为探索通过调控及合理利用自噬途径预防和控制感染性疾病的发生发展提供理论依据。     

巨大病毒的发现及研究进展

人们发现第一个病毒以来,病毒学科取得了迅猛的发展,人们对病毒大小的认知也已经基本成型。21世纪初,科学家发现了拟菌病毒,开启了巨大病毒的大门,此后人们又陆续发现了多种巨大病毒。这些病毒体积较大,基因复杂,已经超出了以往以大小区分病毒的标准,其体积和基因组大小甚至与很多原核和真核生物相当。此外,科学家们还发现了数种能够感染巨大病毒和其他核质大DNA病毒(nucleocytoplasmic large DNA virus,NCLDV)的病毒,将其命名为噬病毒体。这一系列新发现极大地触动了人们对病毒认识的知识体系,并导致了关于病毒起源与进化问题的讨论,这在病毒学史上具有重大的意义。     

细胞自噬在冠状病毒感染中的作用

细胞自噬是一种保守的广泛存在于真核细胞内的溶酶体依赖性分解代谢途径,其通过形成双层膜结构的自噬体降解蛋白质和细胞器,参与物质循环和稳态维持。同时,自噬也能作为机体免疫防御的一部分发挥抗病毒的作用,或是被病毒利用以促进其自身增殖。冠状病毒是一种有囊膜的单股正链RNA病毒,能够诱导双层膜囊泡形成转录复合物,进一步指导病毒基因组的合成。研究表明多个冠状病毒成员能够诱导自噬发生,自噬参与了病毒增殖的多个环节。本文拟对细胞自噬的概况及作用、自噬在病毒感染特别是冠状病毒感染中的作用进行综述,以期为揭示冠状病毒的致病机理提供参考,并为开发冠状病毒的治疗方案提供新思路。     

噬藻体感染相关基因的研究进展

噬藻体是感染蓝细菌(蓝藻)的病毒,能调控蓝细菌种群的丰度和多样性,在许多水生生态系统的食物网动态变化和生物地球化学循环中起关键作用。噬藻体与宿主细胞发生各种相互作用,包括吸附、入侵和复制,参与感染过程,从而完成噬藻体的生命周期。本文在综述噬藻体生命周期与基因组结构相互关联的基础上,重点介绍噬藻体与宿主蓝细菌相互作用的蛋白,如噬藻体吸附蛋白、内肽酶、穿孔素、DNA聚合酶、藻胆体降解蛋白A(NblA)、毒力因子、抗CRISPR蛋白(Acr)和小分子热休克蛋白等,分析它们的分子特性,阐述它们在噬藻体感染蓝细菌以及噬藻体-蓝细菌相互作用的分子机制。为了更好地认识驱动不同噬藻体与宿主及水生环境相互作用的策略、感染效率及生态学影响,本文不仅对这些与噬藻体感染相关的重要基因研究动态进行综述与讨论,还在了解噬藻体丰富的多样性和复杂性的基础上,提出应用新技术对噬藻体感染相关基因的功能进行广泛研究,以期扩展全球水生病毒数据库,进一步认识噬藻体与宿主的相互作用机理。     

细胞病变型牛病毒性腹泻病毒对宿主细胞自噬作用的研究

细胞自噬(Autophagy)是一种真核生物细胞内损伤的细胞器和长寿命蛋白通过双层膜结构的自噬小泡包裹后,送入溶酶体或液泡中进行降解并得以循环利用的高度保守的分解代谢过程。本研究旨在了解细胞病变型(CEP)牛病毒性腹泻病毒(BVDV NM)对宿主细胞MDBK细胞自噬作用的影响。实验使用BVDV NM株感染宿主细胞MDBK,在不同时间点分别通过透射电镜观察自噬体形成、报告荧光GFP-LC3自噬底物检测以及Western blot方法鉴定细胞自噬标记物LC3-Ⅰ/LC3-Ⅱ和P62的表达等试验方法对自噬进行检测。结果显示,感染BVDV NM株的MDBK细胞出现了明显的细胞病变;透射电镜能观察到细胞中存在大量的双层膜结构的自噬泡;转染GFP-LC3荧光质粒后,在感染病毒的细胞内出现增多的聚集绿色荧光自噬小体;此外,随着BVDV NM株感染MDBK时间的延长可以发现LC3-Ⅰ/Ⅱ蛋白的量逐渐增加以及P62蛋白的降解。试验表明BVDV NM株感染MDBK可以促进细胞自噬的发生。     

Evolutionary dynamics of giant viruses and their virophages

Giant viruses contain large genomes, encode many proteins atypical for viruses, replicate in large viral factories, and tend to infect protists. The giant virus replication factories can in turn be infected by so called virophages, which are smaller viruses that negatively impact giant virus replication. An example is Mimiviruses that infect the protist Acanthamoeba and that are themselves infected by the virophage Sputnik. This study examines the evolutionary dynamics of this system, using mathematical models. While the models suggest that the virophage population will evolve to increasing degrees of giant virus inhibition, it further suggests that this renders the virophage population prone to extinction due to dynamic instabilities over wide parameter ranges. Implications and conditions required to avoid extinction are discussed. Another interesting result is that virophage presence can fundamentally alter the evolutionary course of the giant virus. While the giant virus is predicted to evolve toward increasing its basic reproductive ratio in the absence of the virophage, the opposite is true in its presence. Therefore, virophages can not only benefit the host population directly by inhibiting the giant viruses but also indirectly by causing giant viruses to evolve toward weaker phenotypes. Experimental tests for this model are suggested.     

Broad Spectrum of Mimiviridae Virophage Allows Its Isolation Using a Mimivirus Reporter

The giant virus Mimiviridae family includes 3 groups of viruses: group A (includes Acanthamoeba polyphaga Mimivirus), group B (includes Moumouvirus) and group C (includes Megavirus chilensis). Virophages have been isolated with both group A Mimiviridae (the Mamavirus strain) and the related Cafeteria roenbergensis virus, and they have also been described by bioinformatic analysis of the Phycodnavirus. Here, we found that the first two strains of virophages isolated with group A Mimiviridae can multiply easily in groups B and C and play a role in gene transfer among these virus subgroups. To isolate new virophages and their Mimiviridae host in the environment, we used PCR to identify a sample with a virophage and a group C Mimiviridae that failed to grow on amoeba. Moreover, we showed that virophages reduce the pathogenic effect of Mimivirus (plaque formation), establishing its parasitic role on Mimivirus. We therefore developed a co-culture procedure using Acanthamoeba polyphaga and Mimivirus to recover the detected virophage and then sequenced the virophage''s genome. We present this technique as a novel approach to isolating virophages. We demonstrated that the newly identified virophages replicate in the viral factories of all three groups of Mimiviridae, suggesting that the spectrum of virophages is not limited to their initial host.     

Zamilon,a Novel Virophage with Mimiviridae Host Specificity

Virophages, which are potentially important ecological regulators, have been discovered in association with members of the order Megavirales. Sputnik virophages target the Mimiviridae, Mavirus was identified with the Cafeteria roenbergensis virus, and virophage genomes reconstructed by metagenomic analyses may be associated with the Phycodnaviridae. Despite the fact that the Sputnik virophages were isolated with viruses belonging to group A of the Mimiviridae, they can grow in amoebae infected by Mimiviridae from groups A, B or C. In this study we describe Zamilon, the first virophage isolated with a member of group C of the Mimiviridae family. By co-culturing amoebae with purified Zamilon, we found that the virophage is able to multiply with members of groups B and C of the Mimiviridae family but not with viruses from group A. Zamilon has a 17,276 bp DNA genome that potentially encodes 20 genes. Most of these genes are closely related to genes from the Sputnik virophage, yet two are more related to Megavirus chiliensis genes, a group B Mimiviridae, and one to Moumouvirus monve transpoviron.     

A novel group of diverse Polinton-like viruses discovered by metagenome analysis

Background

The rapidly growing metagenomic databases provide increasing opportunities for computational discovery of new groups of organisms. Identification of new viruses is particularly straightforward given the comparatively small size of viral genomes, although fast evolution of viruses complicates the analysis of novel sequences. Here we report the metagenomic discovery of a distinct group of diverse viruses that are distantly related to the eukaryotic virus-like transposons of the Polinton superfamily.

Results

The sequence of the putative major capsid protein (MCP) of the unusual linear virophage associated with Phaeocystis globosa virus (PgVV) was used as a bait to identify potential related viruses in metagenomic databases. Assembly of the contigs encoding the PgVV MCP homologs followed by comprehensive sequence analysis of the proteins encoded in these contigs resulted in the identification of a large group of Polinton-like viruses (PLV) that resemble Polintons (polintoviruses) and virophages in genome size, and share with them a conserved minimal morphogenetic module that consists of major and minor capsid proteins and the packaging ATPase. With a single exception, the PLV lack the retrovirus-type integrase that is encoded in the genomes of all Polintons and the Mavirus group of virophages. However, some PLV encode a newly identified tyrosine recombinase-integrase that is common in bacteria and bacteriophages and is also found in the Organic Lake virophage group. Although several PLV genomes and individual genes are integrated into algal genomes, it appears likely that most of the PLV are viruses. Given the absence of protease and retrovirus-type integrase, the PLV could resemble the ancestral polintoviruses that evolved from bacterial tectiviruses. Apart from the conserved minimal morphogenetic module, the PLV widely differ in their genome complements but share a gene network with Polintons and virophages, suggestive of multiple gene exchanges within a shared gene pool.

Conclusions

The discovery of PLV substantially expands the emerging class of eukaryotic viruses and transposons that also includes Polintons and virophages. This class of selfish elements is extremely widespread and might have been a hotbed of eukaryotic virus, transposon and plasmid evolution. New families of these elements are expected to be discovered.

     

Impact of external forces on cyanophage–host interactions in aquatic ecosystems

Cyanobacterial (algal) blooms have by convention been attributed to the excessive level of nutrients from pollution and runoff, which promotes the rapid growth and multiplication of cyanobacteria or algae. The cyanophage (virus) is the natural predator of cyanobacteria (the host). The aim of this review is to unveil certain pressures that disrupt cyanophage–host interactions and the formation of cyanobacterial blooms. This review focuses principally on the impact of greenhouse gases, ozone depletion, solar ultraviolet radiation (SUR) and the role of recently discovered virophages, which coexist with and in turn are the natural predator of phages. The key findings are that the increase in SUR, the mutation of cyanophages and cyanobacteria, along with changing nutrient levels, have combined with virophages to impede cyanophage–host interactions and the resultant viral infection and killing of the cyanobacterial cell, which is a necessary step in controlling cyanobacterial blooms. Consider this a ‘call to action’ for researchers interested in corrective action aimed at evolving aquatic ecosystems.     

A bag of genes and surprises: Giant viruses continue to fascinate researchers for their role in eukaryote evolution and ecology

Giant viruses continue to yield fascinating discoveries from ancient eukaryotic immune defenses to viruses’ role in the global carbon cycle. Subject Categories: Ecology, Microbiology, Virology & Host Pathogen Interaction

The identification of the first giant virus shook up the field of virology in 2003 and challenged common ideas about the early evolution of viruses and eukaryotes (La Scola et al, 2003). Since, more giant viruses from different host species have been discovered, along with virophages that are viral parasites of giant viruses. It has also become increasingly clear that giant viruses and their parasites are not just another curiosity from an ecological niche but do play an important role in eukaryotic evolution and also perhaps in global marine carbon cycles. Notwithstanding, the evolution and ecology of giant viruses has become a fascinating field of study in itself.     

Diversity,evolutionary contribution and ecological roles of aquatic viruses

Aquatic viruses include infected viruses in aquatic animals, plants and microorganisms, and free-floating viruses(virioplankton)in water environments. In the last three decades, a huge number of aquatic viruses, especially diverse free-floating viruses,including cyanophages, phycoviruses, archaea viruses, giant viruses, and even virophages, have been identified by virological experiments and metagenomic analyses. Based on a comprehensive introduction of aquatic virus classification and their morphological and genetic diversity, here, we summarize and outline main virus species, their evolutionary contribution to aquatic communities through horizontal gene transfer, and their ecological roles for cyanobacterial bloom termination and global biogeochemical cycling in freshwater and marine ecosystems. Thereby, some novel insights of aquatic viruses and virus-host interactions, especially their evolutionary contribution and ecological rolesin diverse aquatic communities and ecosystems, are highlighted in this review.     

Cytopathogenesis and inhibition of host gene expression by RNA viruses.

Many viruses interfere with host cell function in ways that are harmful or pathological. This often results in changes in cell morphology referred to as cytopathic effects. However, pathogenesis of virus infections also involves inhibition of host cell gene expression. Thus the term "cytopathogenesis," or pathogenesis at the cellular level, is meant to be broader than the term "cytopathic effects" and includes other cellular changes that contribute to viral pathogenesis in addition to those changes that are visible at the microscopic level. The goal of this review is to place recent work on the inhibition of host gene expression by RNA viruses in the context of the pathogenesis of virus infections. Three different RNA virus families, picornaviruses, influenza viruses, and rhabdoviruses, are used to illustrate common principles involved in cytopathogenesis. These examples were chosen because viral gene products responsible for inhibiting host gene expression have been identified, as have some of the molecular targets of the host. The argument is made that the role of the virus-induced inhibition of host gene expression is to inhibit the host antiviral response, such as the response to double-stranded RNA. Viral cytopathogenesis is presented as a balance between the host antiviral response and the ability of viruses to inhibit that response through the overall inhibition of host gene expression. This balance is a major determinant of viral tissue tropism in infections of intact animals.     

Cytopathogenesis and Inhibition of Host Gene Expression by RNA Viruses

Many viruses interfere with host cell function in ways that are harmful or pathological. This often results in changes in cell morphology referred to as cytopathic effects. However, pathogenesis of virus infections also involves inhibition of host cell gene expression. Thus the term “cytopathogenesis,” or pathogenesis at the cellular level, is meant to be broader than the term “cytopathic effects” and includes other cellular changes that contribute to viral pathogenesis in addition to those changes that are visible at the microscopic level. The goal of this review is to place recent work on the inhibition of host gene expression by RNA viruses in the context of the pathogenesis of virus infections. Three different RNA virus families, picornaviruses, influenza viruses, and rhabdoviruses, are used to illustrate common principles involved in cytopathogenesis. These examples were chosen because viral gene products responsible for inhibiting host gene expression have been identified, as have some of the molecular targets of the host. The argument is made that the role of the virus-induced inhibition of host gene expression is to inhibit the host antiviral response, such as the response to double-stranded RNA. Viral cytopathogenesis is presented as a balance between the host antiviral response and the ability of viruses to inhibit that response through the overall inhibition of host gene expression. This balance is a major determinant of viral tissue tropism in infections of intact animals.     

Innate immunity against HIV: a priority target for HIV prevention research

The xenotropic/polytropic subgroup of mouse leukemia viruses (MLVs) all rely on the XPR1 receptor for entry, but these viruses vary in tropism, distribution among wild and laboratory mice, pathogenicity, strategies used for transmission, and sensitivity to host restriction factors. Most, but not all, isolates have typical xenotropic or polytropic host range, and these two MLV tropism types have now been detected in humans as viral sequences or as infectious virus, termed XMRV, or xenotropic murine leukemia virus-related virus. The mouse xenotropic MLVs (X-MLVs) were originally defined by their inability to infect cells of their natural mouse hosts. It is now clear, however, that X-MLVs actually have the broadest host range of the MLVs. Nearly all nonrodent mammals are susceptible to X-MLVs, and all species of wild mice and several common strains of laboratory mice are X-MLV susceptible. The polytropic MLVs, named for their apparent broad host range, show a more limited host range than the X-MLVs in that they fail to infect cells of many mouse species as well as many nonrodent mammals. The co-evolution of these viruses with their receptor and other host factors that affect their replication has produced a heterogeneous group of viruses capable of inducing various diseases, as well as endogenized viral genomes, some of which have been domesticated by their hosts to serve in antiviral defense.