病毒工厂：病毒复制的关键场所

多种病毒的复制和组装过程需要在被称为"病毒工厂"的特殊结构内完成。随着研究水平的不断提高,研究者已经在一定程度上揭示了病毒工厂的形成过程及结构。病毒入侵细胞后,能够招募细胞和病毒成分从而形成病毒组装和成熟的场所,细胞膜结构和细胞骨架能够参与该结构的形成,且部分病毒形成的病毒工厂还需线粒体提供能量。除上述特征外,病毒工厂的结构及形态会随病毒复制阶段的不同而不断变化。本文将对病毒工厂的结构、细胞器的招募、病毒工厂结构的变化及大分子物质的运输进行综述。     

Comparison of the effects of Sindbis virus and Sindbis virus replicons on host cell protein synthesis and cytopathogenicity in BHK cells.

Infection of BHK cells by Sindbis virus leads to rapid inhibition of host cell protein synthesis and cytopathic effects (CPE). We have been studying these events to determine whether the expression of a specific viral gene is required and, in the present study, have focused our attention on the role of the structural proteins--the capsid protein and the two membrane glycoproteins. We tested a variety of Sindbis viruses and Sindbis virus replicons (virus particles containing an RNA that is self-replicating but with some or all of the viral structural protein genes deleted) for their abilities to inhibit host cell protein synthesis and cause CPE in infected BHK cells. Our results show that shutoff of host cell protein synthesis occurred in infected BHK cells when no viral structural proteins were synthesized and also under conditions in which the level of the viral subgenomic RNA was too low to be detected. These results support the conclusion that the early steps in viral gene expression are the ones required for the inhibition of host cell protein synthesis in BHK cells. In contrast, the Sindbis viruses and Sindbis virus replicons were clearly distinguished by the time at which CPE became evident. Viruses that synthesized high levels of the two membrane glycoproteins on the surface of the infected cells caused a rapid (12 to 16 h postinfection) appearance of CPE, and those that did not synthesize the glycoprotein spikes showed delayed (30 to 40 h) CPE.     

Fusion peptides and the mechanism of viral fusion

Segments of viral fusion proteins play an important role in viral fusion. They are defined by a number of criteria, including the sensitivity of this region of the viral fusion protein to loss of function as a consequence of mutation. In addition, small model peptides designed to mimic this segment of viral fusion proteins often have some membrane perturbing activity. The properties of viral fusion peptides are quite varied. Many are found at the amino terminus of viral fusion proteins. As isolated peptides, they have been found to form both α-helical as well as β-structure. In addition, some viruses have internal fusion peptides. Just as there are several structural motifs for viral fusion peptides, there are also several mechanisms by which they accelerate the process of membrane fusion. These include the promotion of negative curvature, lowering the rupture tension of the lipid monolayer, acting as an anchor to join the fusion membranes, transmitting a force to the membrane or imparting energy to the system by other means. It is not likely that the fusion peptide can fulfill all of these diverse roles and future studies will elucidate which of these mechanisms is most important for the action of individual viral fusion peptides.     

Deubiquitinating function of adenovirus proteinase

The invasion strategy of many viruses involves the synthesis of viral gene products that mimic the functions of the cellular proteins and thus interfere with the key cellular processes. Here we show that adenovirus infection is accompanied by an increased ubiquitin-cleaving (deubiquitinating) activity in the host cells. Affinity chromatography on ubiquitin aldehyde (Ubal), which was designed to identify the deubiquitinating proteases, revealed the presence of adenovirus L3 23K proteinase (Avp) in the eluate from adenovirus-infected cells. This proteinase is known to be necessary for the processing of viral precursor proteins during virion maturation. We show here that in vivo Avp deubiquitinates a number of cellular proteins. Analysis of the substrate specificity of Avp in vitro demonstrated that the protein deubiquitination by this enzyme could be as efficient as proteolytic processing of viral proteins. The structural model of the Ubal-Avp interaction revealed some similarity between S1-S4 substrate binding sites of Avp and ubiquitin hydrolases. These results may reflect the acquisition of an advantageous property by adenovirus and may indicate the importance of ubiquitin pathways in viral infection.     

Intracellular location of rabbit poxvirus nucleic acid within infected cells as determined by in situ hybridization.

The intracellular location of rabbit poxvirus DNA within cells during the course of infection has been determined by the hybridization in situ of labeled viral DNA probes to uninfected and infected cells under various conditions. Extensive control experiments were performed to demonstrate that DNA could be detected selectively and accurately within the cell. Our results suggest that rabbit poxvirus DNA is located only within the cytoplasm during the reproductive cycle, and we found no evidence that viral DNA enters the cell nucleus. The pattern of hybridization of viral DNA at early times (1 and 2 h postinfection) and in the presence of inhibitors of viral DNA synthesis suggests that there may be an association between the input viral DNA and some structural component of the host cell. A number of observations support the hypothesis that the host cell nucleus is required for a productive poxvirus infection. Our results are discussed in terms of the possible role of the nucleus in the replication of poxviruses.     

Persistence of the cytomegalovirus genome in human cells.

A small percentage of human fibroblast cells survived high-multiplicity infection by cytomegalovirus and were isolated as persistently infected cultures. Approximately 30% of the cells were in the productive phase of infection, since virus-specific structural antigens and virions were associated with these cells. The remaining cells contained neither viral structural antigens nor particles. Nuclear DNA from these nonproductive cells contained approximately 120 genome equivalents of viral DNA per cell as determined by reassociation kinetics. In situ hybridization confirmed that nuclei from nonproductive cells contained a significant amount of viral DNA that was distributed in most of these cells. Early virus-induced proteins and antigens were also detected. Nonproductive cells continued to grow, and there was a slow, spontaneous transition of some of these cells to productive viral replication. The majority of the viral DNA in nonproductive cells persisted with restricted gene expression. When infectious virus production was eliminated by growing the persistently infected cultures in the presence of anticytomegalovirus serum, approximately 45 genome equivalents of the viral DNA persisted per cell. The reassociation reaction approached completion. After removal of the antiserum and subculturing, infectious virus production resumed. Therefore, it was assumed that all sequences of the viral genome remained associated with these cells. Restriction of cytomegalovirus gene expression in persistently infected cell cultures is discussed.     

LearnCoil-VMF: computational evidence for coiled-coil-like motifs in many viral membrane-fusion proteins.

Crystallographic studies have shown that the coiled-coil motif occurs in several viral membrane-fusion proteins, including HIV-1 gp41 and influenza virus hemagglutinin. Here, the LearnCoil-VMF program was designed as a specialized program for identifying coiled-coil-like regions in viral membrane-fusion proteins. Based upon the use of LearnCoil-VMF, as well as other computational tools, we report detailed sequence analyses of coiled-coil-like regions in retrovirus, paramyxovirus and filovirus membrane-fusion proteins. Additionally, sequence analyses of these proteins outside their putative coiled-coil domains illustrate some structural differences between them. Complementing previous crystallographic studies, the coiled-coil-like regions detected by LearnCoil-VMF provide further evidence that the three-stranded coiled coil is a common motif found in many diverse viral membrane-fusion proteins. The abundance and structural conservation of this motif, even in the absence of sequence homology, suggests that it is critical for viral-cellular membrane fusion. The LearnCoil-VMF program is available at http://web.wi.mit.edu/kim Copyright 1999 Academic Press.     

Modulation of signaling pathways by RNA virus capsid proteins

Capsid proteins are structural components of virus particles. They are nucleic acid-binding proteins whose main recognized function is to package viral genomes into protective structures called nucleocapsids. Research over the last 10 years indicates that in addition to their role as genome guardians, viral capsid proteins modulate host cell signaling networks. Disruption or alteration of intracellular signaling pathways by viral capsids may benefit replication of the virus by affecting innate immunity and in some cases, may underlie disease progression. In this review, we describe how the capsid proteins from medically relevant RNA viruses interact with host cell signaling pathways.     

Comparison and functional implications of the 3D architectures of viral tRNA-like structures

RNA viruses co-opt the host cell's biological machinery, and their infection strategies often depend on specific structures in the viral genomic RNA. Examples are tRNA-like structures (TLSs), found at the 3′ end of certain plant viral RNAs, which can use the cell's aminoacyl tRNA-synthetases (AARSs) to drive addition of an amino acid to the 3′ end of the viral RNA. TLSs are multifunctional RNAs involved in processes such as viral replication, translation, and viral RNA stability; these functions depend on their fold. Experimental result-based structural models of TLSs have been published. In this study, we further examine these structures using a combination of biophysical and biochemical approaches to explore the three-dimensional (3D) architectures of TLSs from the turnip yellow mosaic virus (TYMV), tobacco mosaic virus (TMV), and brome mosaic virus (BMV). We find that despite similar function, these RNAs are biophysically diverse: the TYMV TLS adopts a characteristic tRNA-like L shape, the BMV TLS has a large compact globular domain with several helical extensions, and the TMV TLS aggregates in solution. Both the TYMV and BMV TLS RNAs adopt structures with tight backbone packing and also with dynamic structural elements, suggesting complexities and subtleties that cannot be explained by simple tRNA mimicry. These results confirm some aspects of existing models and also indicate how these models can be improved. The biophysical characteristics of these TLSs show how these multifunctional RNAs might regulate various viral processes, including negative strand synthesis, and also allow comparison with other structured RNAs.     

Construction and Characterization of Virus-Like Particles: A Review

Over the last three decades, virus-like particles (VLPs) have evolved to become a widely accepted technology, especially in the field of vaccinology. In fact, some VLP-based vaccines are currently used as commercial medical products, and other VLP-based products are at different stages of clinical study. Several remarkable advantages have been achieved in the development of VLPs as gene therapy tools and new nanomaterials. The analysis of published data reveals that at least 110 VLPs have been constructed from viruses belonging to 35 different families. This review therefore discusses the main principles in the cloning of viral structural genes, the relevant host systems and the purification procedures that have been developed. In addition, the methods that are used to characterize the structural integrity, stability, and components, including the encapsidated nucleic acids, of newly synthesized VLPs are analyzed. Moreover, some of the modifications that are required to construct VLP-based carriers of viral origin with defined properties are discussed, and examples are provided.     

Site-specific glycosylation of SARS-CoV-2: Big challenges in mass spectrometry analysis

Glycosylation of viral proteins is required for the progeny formation and infectivity of virtually all viruses. It is increasingly clear that distinct glycans also play pivotal roles in the virus's ability to shield and evade the host's immune system. Recently, there has been a great advancement in structural identification and quantitation of viral glycosylation, especially spike proteins. Given the ongoing pandemic and the high demand for structure analysis of SARS-CoV-2 densely glycosylated spike protein, mass spectrometry methodologies have been employed to accurately determine glycosylation patterns. There are still many challenges in the determination of site-specific glycosylation of SARS-CoV-2 viral spike protein. This is compounded by some conflicting results regarding glycan site occupancy and glycan structural characterization. These are probably due to differences in the expression systems, form of expressed spike glycoprotein, MS methodologies, and analysis software. In this review, we recap the glycosylation of spike protein and compare among various studies. Also, we describe the most recent advancements in glycosylation analysis in greater detail and we explain some misinterpretation of previously observed data in recent publications. Our study provides a comprehensive view of the spike protein glycosylation and highlights the importance of consistent glycosylation determination.     

Disproportionate synthesis of Semiliki Forest virus 42S and 26S RNAs in polyamine-depleted baby hamster kidney cells

The role of polyamines in viral RNA synthesis has been studied using Semliki Forest virus-infected, polyamine-depleted baby hamster kidney cells as a model system. The synthesis of viral 42S RNA, which corresponds to the viral genome, was markedly inhibited, while the synthesis of viral 26S RNA, which acts as a messenger for viral structural proteins, was reduced much less or not at all. The decreased total viral RNA synthesis and the ratio of 42S to 26S RNA were rapidly returned to normal by adding spermidine to the culture medium. From these results it can be hypothesized that polyamines have a special role in the synthesis of viral RNA, possibly affecting the conformation of the RNA template.     

Comprehensive analysis of ebola virus GP1 in viral entry

Ebola virus infection is initiated by interactions between the viral glycoprotein GP1 and its cognate receptor(s), but little is known about the structure and function of GP1 in viral entry, partly due to the concern about safety when working with the live Ebola virus and the difficulty of manipulating the RNA genome of Ebola virus. In this study, we have used a human immunodeficiency virus-based pseudotyped virus as a surrogate system to dissect the role of Ebola virus GP1 in viral entry. Analysis of more than 100 deletion and amino acid substitution mutants of GP1 with respect to protein expression, processing, viral incorporation, and viral entry has allowed us to map the region of GP1 responsible for viral entry to the N-terminal 150 residues. Furthermore, six amino acids in this region have been identified as critical residues for early events in Ebola virus entry, and among these, three are clustered and are implicated as part of a potential receptor-binding pocket. In addition, substitutions of some 30 residues in GP1 are shown to adversely affect GP1 expression, processing, and viral incorporation, suggesting that these residues are involved in the proper folding and/or overall conformation of GP. Sequence comparison of the GP1 proteins suggests that the majority of the critical residues for GP folding and viral entry identified in Ebola virus GP1 are conserved in Marburg virus. These results provide information for elucidating the structural and functional roles of the filoviral glycoproteins and for developing potential therapeutics to block viral entry.     

Vaccinia viral core inhibits Met-tRNAf·40S initiation complex formation with physiological mRNAs

Vaccinia viral core inhibits protein synthesis in reticulocyte lysates. In partial reactions using micrococcal nuclease treated reticulocyte lysates, the viral core inhibits Met-tRNA_f binding to 40S ribosomes in response to physiological mRNAs such as globin mRNA, cowpea mosaic viral RNA, and brome mosaic viral RNA but not in response to a trinucleotide codon, AUG. The core has also no effect on Met-tRNA_f binding to 40S ribosomes in a partial reaction using partially purified peptide chain initiation factors and AUG codon.The present observation of preferential inhibition by vaccinia viral core of Met-tRNA_f·40S initiation complex formation with physiological mRNAs and not with an artificial mRNA such as AUG codon, suggests that the viral core inhibits some step(s) in peptide chain initiation involved in the recognition of structural feature(s) unique to physiological mRNAs.     

小麦丛矮病毒糖蛋白(G蛋白)的研究

应用SDS-聚丙烯酰胺电泳可以从小麦丛矮病毒中分离出5种结构蛋白。经过碘酸—Schiff′s试剂染色证明,其中分子量为66K的是糖蛋白,是组成病毒外膜突起的G蛋白。应用不同的植物凝集素对完整病毒进行凝集反应试验证实,只有ConA凝集素对病毒有凝集作用,葡萄糖有抑止凝集的作用。G蛋白氨基酸组成分析证明,酸性氨基酸的含量较高。用同位素~(125)I标记的G蛋白和N蛋白的双向图谱表明,植物弹状病毒的结构蛋白之间无共同的肽段。说明植物弹状病毒和动物弹状病毒一样,其蛋白也是由同一病毒基因组的不同片段转录和翻译产生的。     

Viral escape at the molecular level explained by quantitative T-cell receptor/peptide/MHC interactions and the crystal structure of a peptide/MHC complex

Viral escape, first characterized for the lymphocytic choriomeningitis virus (LCMV) in a mouse transgenic for the P14 T cell-receptor (TCR), can be due to mutations in T-cell epitopes. We have measured the affinity between the H-2D(b) containing the wild-type and two of its "viral escape" epitopes, as well as other altered peptide ligands (APL), by using BIACORE analysis, and solved the crystal structure of H-2D(b) in complex with the wild-type peptide at 2.75 A resolution. We show that viral escape is due to a 50 to 100-fold reduction in the level of affinity between the P14 TCR and the binary complexes of the MHC molecule with the different peptides. Structurally, one of the mutations alters a TCR contact residue, while the effect of the other on the binding of the TCR must be indirect through structural rearrangements. The former is a null ligand, while the latter still leads to some central tolerance. This work defines the structural and energetic threshold for viral escape.     

Viral enzymes

Viral genomes show unequalled diversity, ranging from single-stranded DNA to double-stranded RNA. Moreover, viruses can quickly adapt to the host's immune response and drug treatment. Although they tend to make optimal use of the host cell's reservoir of proteins, viruses need to carry some enzymatic functions with them, as they may not be available or accessible in the infected cell. Recently, progress has been made in our structural understanding of viral enzymes involved in all stages of the viral life cycle, which includes entry, hijack, replication and exit stages.