The viral protein NS4B is also important for the formation of the membranous web, possibly by inducing membrane curvature not shown. The white arrowhead indicates a DENV-induced vesicle in the ER with an opening towards the nuclear envelope; the black arrowhead points to a virus particle in a cisterna close to a Golgi stack.
The arrow indicates a putative virus budding site, and red spheres represent virus particles. Parts b,c are reproduced, with permission, from Ref. In addition, coronaviruses induce the formation of interconnected double-membraned vesicles DMVs 89 by exploiting a regulatory pathway that controls ER-associated protein degradation ERAD It has been hypothesized that the accumulation of MHV replication proteins in edemosomes, which are decorated with LC3-I non-lipidated microtubule-associated proteins 1A and 1B light chain 3A; a homologue of yeast Atg8, a ubiquitin-like protein that is required for the formation of autophagosomal membranes , transforms these structures into permanent DMVs The actual function of DMVs has not been fully defined, but they could be the sites of viral replication and virion assembly.
The viral content could be released from DMVs by fusion with other membranes or by disintegration of the DMV membranes. Part c is reproduced from Ref. The role of lipids in VRC assembly. Another major group of host factors that affects VRC assembly is involved in regulating the lipid composition of selected intracellular membranes.
Membrane lipids can serve as scaffolds for the assembly of VRCs or can provide crucial lipid cofactors to regulate the function of the viral replicase.
DENV also increases the amount of free fatty acids derived from lipid droplets in mammalian cells by inducing autophagy These differences could be explained by the different cell types or hosts infected by these viruses HCV infects liver cells in humans, whereas DENV not only infects humans and non-human primates but also persists in the mosquito vector , which could dictate the available lipid synthesis pathways.
The generation of new membrane surfaces via fatty acid biosynthesis also has a major effect on Drosophila C virus replication in Drosophila melanogaster cells: depletion of host HLH, a protein that regulates fatty acid metabolism, blocks the formation of Drosophila C virus-induced vesicular compartments In addition, in S. This results in reduced efficiency of VRC assembly and a low level of replication. Lipids also seem to affect tombusvirus replication. Electron microscopy images of plant cells infected with tombusviruses show extensive remodelling of membranes and indicate that active lipid biosynthesis occurs 52 , 80 , Moreover, genome-wide screens in S.
Detailed studies with Erg25, an important enzyme in the sterol biosynthesis pathway in S. Sterols are ubiquitous and essential membrane components in all eukaryotes, affecting membrane rigidity, fluidity and permeability by interacting with other membrane lipids and proteins 95 , For example, infection of mammalian cells with WNV leads to redistribution of cholesterol from the plasma membrane to the sites of viral replication and also results in reduced antiviral responses For example, reducing phospholipid levels in S.
Interestingly, genes involved in the production of phosphatidylcholine in D. Membrane-shaping proteins. Indeed, dynamic remodelling and deforming of membranes to give rise to unique spherule structures seem to require host proteins.
For example, tombusviruses recruit ESCRT endosomal sorting complexes required for transport proteins 24 , which have a major role in sorting cargo proteins from the endosomes to multivesicular bodies by membrane invagination and vesicle formation , , , This is followed by the recruitment of ESCRT-III proteins Snf7 and Vps24 , which could assist optimal assembly of the VRC, facilitate colocalization of the viral replication proteins p33 and p92 within selected areas in the membrane, and promote the formation of viral spherules by deforming the membranes or stabilizing the 'neck' structure the narrow opening in the spherules that faces the cytosol Fig.
Tombusvirus such as tomato bushy stunt virus TBSV RNA translation and replication, and the host proteins that affect these processes in a Saccharomyces cerevisiae model host. Anther group of membrane-shaping proteins, the reticulon homology proteins Rhps , are involved in assembly of the spherule-like structures during BMV replication in S. Roles of host chaperones. Cellular chaperones are also involved in VRC assembly. For example, the tombusvirus replicase was completely inactive when assembled in vitro using an S.
In addition, Hsp70 seems to be important for the insertion of tombusvirus replication proteins into intracellular membranes 75 and for the folding and stability of the tombusvirus VRC Several of the RBPs that are co-opted by different viruses probably have mechanistically similar functions during viral replication, as discussed below. In addition, the sequestration of these proteins for WNV replication might inhibit the formation of stress granules and P-bodies , thus potentially blocking mRNA degradation Regulation of asymmetric RNA synthesis by host factors.
GAPDH, which is present in the tombusvirus VRC , is a highly conserved, abundant and ubiquitous protein that is a key component of cytosolic energy production Other host factors that affect RNA synthesis.
For example, Pmr1, an S. Many of the identified host factors are conserved in eukaryotes, suggesting that these viruses selectively target highly conserved host functions.
However, although the co-opted host proteins are diverse, they might fulfil similar or related functions during viral RNA replication. Further application of proteomics and genome-wide studies will expand this area of research. Importantly, functional and mechanistic studies based on biochemical approaches such as the use of cell-free extracts and single-molecule techniques in combination with live-cell imaging will be needed to test all the candidate proteins identified.
In vitro reconstitution of VRCs would be extremely useful for the dissection of unknown functions of the host proteins that are co-opted for viral replication. In addition, proteomics can be used to study the possible roles of post-translational modifications of viral replication proteins. The use of Saccharomyces cerevisiae as a model organism to study host—virus interactions has several advantages.
Plants and most animals have large genomes with extensive genetic redundancy functional duplications in various functions, whereas S. The small genome size also means that there is a reduced level of redundancy. Moreover, toolboxes and gene libraries are available for the controlled expression of selected genes.
One advantage to performing genome-wide screens in S. Gene libraries with fluorescent tags or affinity tags for identification of the subcellular localization of proteins and for protein purification, respectively, are also available Microarray chips with DNA oligonucleotides for most S. Finally, the databanks for S. For example, a global analysis of protein localization has been carried out, and detailed protein—protein interaction networks and genetic interaction maps have been constructed , Ahlquist, P.
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Fernandez-Garcia, M. Pathogenesis of flavivirus infections: using and abusing the host cell. Heaton, N. Note: The entire life cycle occurs in the cytoplasm. There is no division into early and late gene expression. Examples of non-segmented negative strand RNA viruses are:. Rhabdoviruses figure 6. These include rabies virus, vesicular stomatitis virus, Mokola virus, Duvenhage virus Paramyxoviruses figure These includes Newcastle disease virus, parainfluenza viruses , mumps virus , measles virus , respiratory syncytial virus.
Figure 7b Rabies virus budding from an inclusion Negri body into the endoplasmic reticulum in a nerve cell. Negri body. Notice the abundant RNP in the inclusion. Budding rabies virus. Example: Rabies virus. The most intensively studied member is vesicular stomatitis virus. Attachment, penetration and uncoating The virus adsorbs to cell surface. G Glycoprotein is the attachment protein figure 7 which binds to a receptor on the host cell surface.
The attached virus is taken up by endocytosis. The membrane of the virus fuses with the endosome membrane the acid pH of endosome is important because the G protein needs to be exposed to acid pH before it can facilitate fusion.
As a result of fusion of the viral membrane with the endosome membrane, the nucleocapsid is released into cytoplasm.
Transcription 'Transcription' is used in this context to refer to synthesis of mRNAs. Complete uncoating of the nucleocapsid is not necessary for transcription - the virion RNA polymerase can copy virion RNA when it is in the nucleocapsid form. This is an advantage in that genomic RNA is therefore somewhat protected from ribonucleases.
There is one monocistronic mRNA for each of the five virally coded proteins figure 8. The mRNAs are capped, methylated, and polyadenylated. Since this is a cytoplasmic, negative-sense RNA virus, the enzymes for mRNA synthesis and modification are packaged in the virion.
Messenger RNAs are translated on host ribosomes and all five viral proteins made at the same time. There is no distinction between early and late functions. The full length plus strand is coated with nucleocapsid protein as it is made mRNAs are not coated with this protein, which would interfere with the host protein translation machinery. The new positive strand is copied into full length minus strand, which is also coated with nucleocapsid protein as it is made.
Note: since the viral RNA polymerase synthesizes mRNAs transcription and full-length RNA replication , it is also sometimes called a transcriptase or a replicase, such names just focus on the different aspects of the polymerase activity. Figure 9 Transport of glycoproteins from the endoplasmic reticulum to the plasma membrane Assembly.
The virus consists of two "modules" - the envelope and the nucleocapsid:. Envelope Transmembrane proteins are made on ribosomes bound to the endoplasmic reticulum.
They are inserted into the endoplasmic reticulum membrane as they are made, glycosylated in the endoplasmic reticulum and pass through the Golgi body where substantial modification of the carbohydrate chains occurs. They are then transported, in vesicles, to the appropriate cell membrane; in the case of vesicular stomatitis virus, this is the plasma membrane figure 9. Figure 10 Rhabdovirus assembly Nucleocapsid Synthesis of the nucleocapsid was described above.
The viral RNA polymerase complex associates with the nucleocapsids as they are formed. Nucleocapsids bud out through modified areas of membrane which contain G and M proteins figure The M matrix protein is involved in assembly - it interacts with patches of G in the membrane and with nucleocapsids.
Note: The entire life cycle occurs in the cytoplasm RNA polymerase and RNA modification enzymes are virally-coded and present in the virus particle virion. They have negative-sense, non-segmented RNA and a helical nucleocapsid figure They are enveloped, that is they are surrounded by a membrane derived from a host cell. The envelope contains two virally coded glycoproteins: The F protein and the attachment protein. The F protein has fusion activity The attachment protein binds to receptors on the host cell This protein may have: Hemagglutinating activity and neuraminidase activity HN protein or hemagglutinating activity alone H protein or neither G protein.
Hemagglutination is easy to test for in the clinical laboratory and is used in diagnosis. Hemagglutination involves the agglutination of red blood cells and relies on the ability of a virus to bind to receptors on red blood cells. Since viruses have multiple attachment proteins per virion, they can bind to more than one red blood cell and so they can serve to link red blood cells into a network.
Inactivated virus can still hemagglutinate as long as its attachment proteins are intact. If someone has antibodies to a viral hemagglutinin, the antibodies will binds to the attachment protein and prevent its binding to the red blood cells. The serum of that person will inhibit the agglutination reaction by the virus to which they have antibodies - but not by other hemagglutinating viruses. This can be used to determine which hemagglutinating virus a person has been exposed to. During infection, the viral attachment protein will be inserted into the plasma membrane of the infected cell.
If the viral attachment protein can bind to red blood cells, the infected cell will bind red blood cells because it has the viral attachment protein on its surface - this is called hemadsorption. In the clinical laboratory, this may enable virally-infected cells to be detected at an early stage in infection, and may allow detection of viruses which do not visibly damage the cell.
Figure 13 Attachment and endocytosis of paramyxoviruses Adsorption and penetration. The F protein facilitates fusion between membranes at physiological pH, so although paramyxoviruses can be taken up by endocytosis, they also often enter the cell by direct fusion with the plasma membrane figure Because the F protein functions at physiological pH, this can result in syncytia being formed in paramyxovirus infections see discussion of consequences of fusion at physiological pH under DNA virus replication strategies — herpesviruses.
Events inside the cell are very similar to rhabdoviruses figure 14 :. Viral multiplication occurs in the cytoplasm. The viral RNA polymerase uses the nucleocapsid as a template. The RNA polymerase does not need a fully uncoated nucleocapsid.
Viral mRNAs are transcribed; these are capped, methylated and polyadenylated. The viral mRNAs are translated to give viral proteins. There is no distinction between early and late functions in gene expression. Viral RNA replication involves full length plus strand synthesis. This is used as a template for full length minus strand. Both full length strands are coated with nucleocapsid protein as they are made figure New full length minus strands may serve as templates for replication, or templates for transcription, or they may be packaged into new virions.
Figure 15 Activation of the fusion protein by proteolytic cleavage. Both viral glycoproteins i. M matrix protein enables nucleocapsids to interact with the regions of the plasma membrane which have the glycoproteins inserted. The virus buds out through membrane. In those paramyxoviruses which have it, the neuraminidase may facilitate release.
In these viruses, sialic acid appears to be an important part of the receptor. The neuraminidase removes sialic acid neuraminic acid from the cell surface. Thus, since sialic acid will have been largely removed from the cell surface and the progeny virions, neither will have functional receptors, so progeny virions will not stick to each other or to the cell they have just budded out from or any other infected cell.
They will therefore be able to diffuse away until they meet an uninfected cell. The neuraminidase may also help during infection since, if the virus binds to sialic acid residues in mucus, it would not be able to bind to a receptor on a cell and infect that cell. The difference may be because in general only lipophagy, but not autophagy, was blocked when AUP1 was knocked out Zhang J. It remains to be seen whether AUP1's main role in DENV infection is primarily involved in E-protein modification and stability or in relation to lipophagy, or both.
Compared to mock-infected cells, the number of LDs dropped and fluorescently labeled long-chain FAs were firstly found to be incorporated into LDs but later at poliovirus replication sites Viktorova et al. Two lipases are recruited and enriched at LDs to release free FAs: hormone sensitive lipase HSL , which is translocated from its primary location of perinuclear areas, and adipocyte triglyceride lipase ATGL Viktorova et al.
With emerging novel technologies such as fluorescent probes for lipid detection and mass spectrometry-based lipidomics , lipids have been demonstrated to play key roles in almost every stage of the viral life cycle. As summarized in Table 1 , different viruses may require the same lipid class for their efficient viral genomic RNA replication.
For instance, PC and sterols are required for the replication of multiple viruses from different families, implying that pathways involved in PC and sterol accumulation at the replication membranes are potential targets to develop broad-spectrum antiviral drugs. Many research groups have identified some specific lipid species that are required for the replication of corresponding viruses Figure 2 and Table 1. However, caution should be taken when generalizing results between virus classes and host organisms as the specific lipids may only be one part of a complex system with many factors and alternative solutions.
There are different lipid biosynthesis pathways that are present, absent, or predominate in different cell-types and organisms. The composition of membranes varies among yeast, plant, insect and mammalian cell types, and one should consider that there may be multiple combinations of specific lipids that allow for efficient viral replication.
FHV provides an interesting example, as its replication complexes can be re-targeted to different intracellular membranes e. This suggests some promiscuity in viral requirements for membrane composition. Another example is that some viruses can form VRCs of different morphology by varying the expression levels of replication proteins Schwartz et al.
Currently, the majority of reports hypothesize the potential roles of lipids in the assembly of VRCs. However, how lipids are organized in VRCs and their roles in the assembly and maintenance of VRCs still needs to be further investigated. Fluorescent imaging has been used to observe lipids in relation to other cellular components and viral replication sites.
However, conventional fluorescent microscopy techniques, such as confocal microscopy, pose limitations due to low spatial resolution, and the inability to image subcellular components in full detail. In addition, super-resolution microscopy has the potential to be used in live-cells, providing insight into the formation of VRCs upon viral infection.
In conclusion, despite the complexity of lipid metabolism and virus-host interactions, knowledge of how viruses modulate host lipid synthesis pathways and remodel cellular membranes to facilitate replication, will undoubtedly unmask many new directions in cell biology, and accelerate the process of developing antiviral strategies.
ZZ made all figures. BK is a Towsley Research Scholar. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. We apologize to all colleagues whose work could not be cited due to space limitations.
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