Proteomics of Herpes Simplex Virus Type 1 Nuclear Capsids.

Herpes simplex virus replicates in the nucleus, where new capsids are assembled. It produces procapsids devoid of nucleic acid but containing the preVP22a scaffold protein. These thermo-unstable particles then mature into A-, B- or C-nuclear icosahedral capsids, depending on their ability to shed the proteolytically processed scaffold and incorporation of the viral genome. To study how these viral capsids differ, we performed proteomics studies of highly enriched HSV-1 A-, B- and C-nuclear capsids, relying in part on a novel and powerful flow virometry approach to purify C-capsids. We found that the viral particles contained the expected capsid components and identified several tegument proteins in the C-capsid fraction (pUL21, pUL36, pUL46, pUL48, pUL49, pUL50, pUL51 and pUS10). Moreover, numerous ribosomal, hnRNPs and other host proteins, absent from the uninfected controls, were detected on the capsids with some of them seemingly specific to C-capsids (glycogen synthase, four different keratin-related proteins, fibronectin 1 and PCBP1). A subsequent proteomics analysis was performed to rule out the presence of protein complexes that may share similar density as the viral capsids but do not otherwise interact with them. Using pUL25 or VP5 mutant viruses incapable of assembling C-nuclear or all nuclear capsids, respectively, we confirmed the bulk of our initial findings. Naturally, it will next be important to address the functional relevance of these proteins.IMPORTANCE Much is known about the biology of herpesviruses. This includes their unique ability to traverse the two nuclear envelopes by sequential budding and fusion steps. For HSV-1, this implies the pUL31/pUL34 and pUL17/pUL25 complexes that may favor C-capsid egress. However, this selection process is not clear, nor are all the differences that distinguish A-, B- and C-capsids. The present study probes what proteins compose these capsids, including host proteins. This should open up new research avenues to clarify the biology of this most interesting family of viruses. It also reiterates the use of flow virometry as an innovative tool to purify viral particles.

Quantitative Evaluation of Protein Heterogeneity within Herpes Simplex Virus 1 Particles.

Several virulence genes have been identified thus far in the herpes simplex virus 1 genome. It is also generally accepted that protein heterogeneity among virions further impacts viral fitness. However, linking this variability directly with infectivity has been challenging at the individual viral particle level. To address this issue, we resorted to flow cytometry (flow virometry), a powerful approach we recently employed to analyze individual viral particles, to identify which tegument proteins vary and directly address if such variability is biologically relevant. We found that the stoichiometry of the UL37, ICP0, and VP11/12 tegument proteins in virions is more stable than the VP16 and VP22 tegument proteins, which varied significantly among viral particles. Most interestingly, viruses sorted for their high VP16 or VP22 content yielded modest but reproducible increases in infectivity compared to their corresponding counterparts containing low VP16 or VP22 content. These findings were corroborated for VP16 in short interfering RNA experiments but proved intriguingly more complex for VP22. An analysis by quantitative Western blotting revealed substantial alterations of virion composition upon manipulation of individual tegument proteins and suggests that VP22 protein levels acted indirectly on viral fitness. These findings reaffirm the interdependence of the virion components and corroborate that viral fitness is influenced not only by the genome of viruses but also by the stoichiometry of proteins within each virion.IMPORTANCE The ability of viruses to spread in animals has been mapped to several viral genes, but other factors are clearly involved, including virion heterogeneity. To directly probe whether the latter influences viral fitness, we analyzed the protein content of individual herpes simplex virus 1 particles using an innovative flow cytometry approach. The data confirm that some viral proteins are incorporated in more controlled amounts, while others vary substantially. Interestingly, this correlates with the VP16 trans-activating viral protein and indirectly with VP22, a second virion component whose modulation profoundly alters virion composition. This reaffirms that not only the presence but also the amount of specific tegument proteins is an important determinant of viral fitness.

The ATP-Dependent RNA Helicase DDX3X Modulates Herpes Simplex Virus 1 Gene Expression.

The human protein DDX3X is a DEAD box ATP-dependent RNA helicase that regulates transcription, mRNA maturation, and mRNA export and translation. DDX3X concomitantly modulates the replication of several RNA viruses and promotes innate immunity. We previously showed that herpes simplex virus 1 (HSV-1), a human DNA virus, incorporates DDX3X into its mature particles and that DDX3X is required for optimal HSV-1 infectivity. Here, we show that viral gene expression, replication, and propagation depend on optimal DDX3X protein levels. Surprisingly, DDX3X from incoming viral particles was not required for the early stages of the HSV-1 infection, but, rather, the protein controlled the assembly of new viral particles. This was independent of the previously reported ability of DDX3X to stimulate interferon type I production. Instead, both the lack and overexpression of DDX3X disturbed viral gene transcription and thus subsequent genome replication. This suggests that in addition to its effect on RNA viruses, DDX3X impacts DNA viruses such as HSV-1 by an interferon-independent pathway.IMPORTANCE Viruses interact with a variety of cellular proteins to complete their life cycle. Among them is DDX3X, an RNA helicase that participates in most aspects of RNA biology, including transcription, splicing, nuclear export, and translation. Several RNA viruses and a limited number of DNA viruses are known to manipulate DDX3X for their own benefit. In contrast, DDX3X is also known to promote interferon production to limit viral propagation. Here, we show that DDX3X, which we previously identified in mature HSV-1 virions, stimulates HSV-1 gene expression and, consequently, virion assembly by a process that is independent of its ability to promote the interferon pathway.

Seronegative hepatitis C virus infection in a child infected via mother-to-child transmission.

Hepatitis C virus (HCV) infection typically leads to antibody response within weeks after primary infection. Here, we describe the case of a child infected with HCV by mother-to-child transmission who remained persistently seronegative despite the presence of high levels of circulating HCV RNA.

Analysis of herpes simplex virus type I nuclear particles by flow cytometry.

Flow cytometry has been instrumental to characterize cell populations and examine their inner molecules and processes. In most instances, whole cells are analyzed, and hence, particle size is not an issue. Viruses are 2-3 orders of magnitude smaller than cells so flow cytometry has typically been used to study viral markers within whole infected cells. However, the ability to separate and purify viral particles representing different maturation stages within a viral life cycle would be a useful tool to analyze them in details and characterize the host proteins they associate with. Herpes simplex virus Type 1 is a 250 nm enveloped DNA virus that replicates in the nucleus where it assembles new viral particles called capsids. These capsids eventually travel to the cell surface and are modified along the way, producing several intermediate particles. In the nucleus, three types of stable nonenveloped 125 nm nuclear capsids exist that differ in protein composition and genome content. This includes so-called nuclear C-capsids that are the precursors of mature extracellular virions. We report that we can apply flow cytometry to sort these nuclear C-capsid intermediates by labeling the viral genome with Syto 13, a fluorescent marker that binds to nucleic acids. This is the first time flow cytometry has been used not only to detect but also to purify an intracellular viral maturation intermediate. This opens new research avenues in virology to study capsid assembly, maturation and egress, analyze mutant phenotypes, and define host factors associated with specific viral intermediates.

Analysis and Sorting of Individual HSV-1 Particles by Flow Virometry.

Flow cytometry has been instrumental in characterizing normal and infected cells. However, until recently, it was not possible to use such an approach to analyze small entities such as bacteria, let alone viruses, owing to the 0.5 µm resolution of most instruments. To circumvent this limitation, some laboratories decorate pathogens with antibodies or nanoparticles. Our laboratory instead exploits an alternative approach that relies on the staining of internal viral constituents with permeable SYTO dyes or the fluorescent tagging of individual viral proteinaceous components, whether capsid, tegument or glycoproteins. This opens up a range of new research avenues and, for example, enabled us to characterize individual herpes simplex virus type 1 particles, discern their different subpopulations, measure the heterogeneity of mature virions in terms of protein content, sort these viral particles with >90% purity and, for the first time, directly address the impact of this heterogeneity on viral fitness. This approach, coined flow virometry or nanoscale flow cytometry, allows for the study of a wide variety of pathogens with high statistical significance and the potential discovery of novel virulence factors.