Construction of a chimeric Theiler's murine encephalomyelitis virus containing the leader gene of foot-and-mouth disease virus

Interaction between FMDV Lpro and transcription factor ADNP is required for optimal viral replication

The foot-and-mouth disease virus (FMDV) leader protease (L^pro) inhibits host translation and transcription affecting the expression of several factors involved in innate immunity. In this study, we have identified the host transcription factor ADNP (activity dependent neuroprotective protein) as an L^pro interacting protein by mass spectrometry. We show that L^pro can bind to ADNP in vitro and in cell culture. RNAi of ADNP negatively affected virus replication and higher levels of interferon (IFN) and IFN-stimulated gene expression were detected. Importantly, infection with FMDV wild type but not with a virus lacking Lpro (leaderless), induced recruitment of ADNP to IFN-α promoter sites early during infection. Furthermore, we found that L^pro and ADNP are in a protein complex with the ubiquitous chromatin remodeling factor Brg-1. Our results uncover a novel role of FMDV L^pro in targeting ADNP and modulation of its transcription repressive function to decrease the expression of IFN and ISGs.

Enhancing the Tumor Selectivity of a Picornavirus Virotherapy Promotes Tumor Regression and the Accumulation of Infiltrating CD8+ T Cells

Picornaviruses have emerged as promising cancer therapies due to their ability to drive cytotoxic cellular immune responses and for promoting oncolysis. These properties include preferential replication in tumor cells, the induction of strong innate and adaptive immune responses, and the ease with which their genomes can be manipulated. We have developed Theiler's murine encephalomyelitis virus (TMEV) as an immunotherapy vector that promotes strong adaptive immune responses to tumor antigens embedded within its genome. To further explore its usefulness as cancer therapy, we investigated whether direct intratumoral delivery of TMEV could promote tumor regression. We generated several picornavirus hybrids using substrains of TMEV that have unique immunopathologic characteristics, despite their extensive sequence homology. These hybrids exhibit a unique propensity to infect and replicate in melanoma. We have identified GD7-KS1, a virus that is particularly effective at replicating and infecting B16 melanoma in vitro and provides benefit as an oncolytic therapy in vivo after intratumoral injection. In addition, this virus promotes the mobilization and accumulation of CD8(+) T cells within treated tumors. Altogether, these findings demonstrate that picornavirus substrains can be used to rationally design virus hybrids that promote antitumor responses and add to the known strategies identified by us and others to further enhance the therapeutic potential of vectors used to treat cancer.

Toward genetics-based virus taxonomy: comparative analysis of a genetics-based classification and the taxonomy of picornaviruses

Virus taxonomy has received little attention from the research community despite its broad relevance. In an accompanying paper (C. Lauber and A. E. Gorbalenya, J. Virol. 86:3890-3904, 2012), we have introduced a quantitative approach to hierarchically classify viruses of a family using pairwise evolutionary distances (PEDs) as a measure of genetic divergence. When applied to the six most conserved proteins of the Picornaviridae, it clustered 1,234 genome sequences in groups at three hierarchical levels (to which we refer as the "GENETIC classification"). In this study, we compare the GENETIC classification with the expert-based picornavirus taxonomy and outline differences in the underlying frameworks regarding the relation of virus groups and genetic diversity that represent, respectively, the structure and content of a classification. To facilitate the analysis, we introduce two novel diagrams. The first connects the genetic diversity of taxa to both the PED distribution and the phylogeny of picornaviruses. The second depicts a classification and the accommodated genetic diversity in a standardized manner. Generally, we found striking agreement between the two classifications on species and genus taxa. A few disagreements concern the species Human rhinovirus A and Human rhinovirus C and the genus Aphthovirus, which were split in the GENETIC classification. Furthermore, we propose a new supergenus level and universal, level-specific PED thresholds, not reached yet by many taxa. Since the species threshold is approached mostly by taxa with large sampling sizes and those infecting multiple hosts, it may represent an upper limit on divergence, beyond which homologous recombination in the six most conserved genes between two picornaviruses might not give viable progeny.

Viral security proteins: counteracting host defences

Viral reproduction involves not only replication but also interactions with host defences. Although various viral proteins can take part in counteracting innate and adaptive immunity, many viruses possess a subset of proteins that are specifically dedicated to counter-defensive activities. These proteins are sometimes referred to as 'virulence factors', but here we argue that the term 'security proteins' is preferable, for several reasons.

The concept of security proteins of RNA-containing viruses can be considered using the leader (L and L^*) and 2A proteins of picornaviruses as examples. The picornaviruses are a large group of human and animal viruses that include important pathogens such as poliovirus, hepatitis A virus and foot-and-mouth disease virus. The genomes of different picornaviruses have a similar organization, in which the genes for L and 2A occupy fixed positions upstream and downstream of the capsid genes, respectively.

Both L and 2A are extremely heterogeneous with respect to size, sequence and biochemical properties. The similarly named proteins can be completely unrelated to each other in different viral genera, and the variation can be striking even among members of the same genus. A subset of picornaviruses lacks L altogether.

The properties and functions of L and 2A of many picornaviruses are unknown, but in those viruses that have been investigated sufficiently it has been found that these proteins can switch off various aspects of host macromolecular synthesis and specifically suppress mechanisms involved in innate immunity. Thus, notwithstanding their unrelatedness, the security proteins carry out similar biological functions. It is proposed that other picornavirus L and 2A proteins that have not yet been investigated should also be primarily involved in security activities.

The L, L^* and 2A proteins are dispensable for viral reproduction, but their elimination or inactivation usually renders the viruses less pathogenic. The phenotypic changes associated with inactivation of security proteins are much less pronounced in cells or organisms that have innate immunity deficiencies. In several examples, the decreased fitness of a virus in which a security protein has been inactivated could be rescued by the experimental introduction of an unrelated security protein.

It can be argued that L and 2A were acquired by different picornaviruses independently, and possibly by exploiting different mechanisms, late in the evolution of this viral family.

It is proposed that the concept of security proteins is of general relevance and can be applied to viruses other than picornaviruses. The hallmarks of security proteins are: structural and biochemical unrelatedness in related viruses or even absence in some of them; dispensability of the entire protein or its functional domains for viral viability; and, for mutated versions of the proteins, fewer detrimental effects on viral reproduction in immune-compromised hosts than in immune-competent hosts.

Viral security proteins are structurally and biochemically unrelated proteins that function to counteract host defences. Here, Agol and Gmyl consider the impact of the picornavirus security proteins on viral reproduction, pathogenicity and evolution.

Interactions with host defences are key aspects of viral infection. Various viral proteins perform counter-defensive functions, but a distinct class, called security proteins, is dedicated specifically to counteracting host defences. Here, the properties of the picornavirus security proteins L and 2A are discussed. These proteins have well-defined positions in the viral polyprotein, flanking the capsid precursor, but they are structurally and biochemically unrelated. Here, we consider the impact of these two proteins, as well as that of a third security protein, L^*, on viral reproduction, pathogenicity and evolution. The concept of security proteins could serve as a paradigm for the dedicated counter-defensive proteins of other viruses.

Differential IFN-alpha/beta production suppressing capacities of the leader proteins of mengovirus and foot-and-mouth disease virus

Picornaviruses encompass a large family of RNA viruses. Some picornaviruses possess a leader (L) protein at the N-terminus of their polyprotein. The L proteins of encephalomyocarditis virus, a cardiovirus, and foot-and-mouth disease virus (FMDV), an aphthovirus, are both dispensable for replication and their major function seems to be the suppression of antiviral host cell responses. Previously, we showed that the L protein of mengovirus, a strain of encephalomyocarditis virus, inhibits antiviral responses by inhibiting type I interferon (IFN-alpha/beta) gene transcription. The L protein of the FMDV is a protease (L(pro)) that cleaves cellular factors to reduce cytokine and chemokine mRNA production and to inhibit cap-dependent cellular host mRNA translation, thereby limiting the production of proteins with antiviral activity. In this study, we constructed a viable chimeric mengovirus that expresses FMDV L(pro) in place of the authentic L protein in order to compare the efficiency of the immune evasion mechanisms mediated by L and L(pro) respectively. We show that in this mengovirus background the L protein is more potent than FMDV L(pro) in suppressing IFN-alpha/beta responses. Yet, FMDV L(pro) is important to antagonize infection-limiting responses both in vitro and in vivo.

A conserved domain in the leader proteinase of foot-and-mouth disease virus is required for proper subcellular localization and function

The leader proteinase (L(pro)) of foot-and-mouth disease virus (FMDV) is involved in antagonizing the innate immune response by blocking the expression of interferon (IFN) and by reducing the immediate-early induction of IFN-beta mRNA and IFN-stimulated genes. In addition to its role in shutting off cap-dependent host mRNA translation, L(pro) is associated with the degradation of the p65/RelA subunit of nuclear factor kappaB (NF-kappaB). Bioinformatics analysis suggests that L(pro) contains a SAP (for SAF-A/B, Acinus, and PIAS) domain, a protein structure associated in some cases with the nuclear retention of molecules involved in transcriptional control. We have introduced a single or a double mutation in conserved amino acid residues contained within this domain of L(pro). Although three stable mutant viruses were obtained, only the double mutant displayed an attenuated phenotype in cell culture. Indirect immunofluorescence analysis showed that L(pro) subcellular distribution is altered in cells infected with the double mutant virus. Interestingly, nuclear p65/RelA staining disappeared from wild-type (WT) FMDV-infected cells but not from double mutant virus-infected cells. Consistent with these results, NF-kappaB-dependent transcription was not inhibited in cells infected with double mutant virus in contrast to cells infected with WT virus. However, degradation of the translation initiation factor eIF-4G was very similar for both the WT and the double mutant viruses. Since L(pro) catalytic activity was demonstrated to be a requirement for p65/RelA degradation, our results indicate that mutation of the SAP domain reveals a novel separation-of-function activity for FMDV L(pro).

Degradation of nuclear factor kappa B during foot-and-mouth disease virus infection

We have previously shown that the leader proteinase (L(pro)) of foot-and-mouth disease virus (FMDV) interferes with the innate immune response by blocking the translation of interferon (IFN) protein and by reducing the immediate-early induction of beta IFN mRNA and IFN-stimulated genes. Here, we report that L(pro) regulates the activity of nuclear factor kappaB (NF-kappaB). Analysis of NF-kappaB-dependent reporter gene expression in BHK-21 cells demonstrated that infection with wild-type (WT) virus has an inhibitory effect compared to infection with a genetically engineered mutant lacking the leader coding region. The expression of endogenous NF-kappaB-dependent genes tumor necrosis factor alpha and RANTES is also reduced in WT virus-infected primary porcine cells. This inhibitory effect is neither the result of a decrease in the level of the mRNA of p65/RelA, a subunit of NF-kappaB, nor a block on the nuclear translocation of p65/RelA, but instead appears to be a consequence of the degradation of accumulated p65/RelA. Viral L(pro) is localized to the nucleus of infected cells, and there is a correlation between the translocation of L(pro) and the decrease in the amount of nuclear p65/RelA. By using a recombinant cardiovirus expressing L(pro), we demonstrate that the disappearance of p65/RelA takes place in the absence of any other FMDV product. The observation that L(pro) disrupts the integrity of NF-kappaB suggests a global mechanism by which FMDV antagonizes the cellular innate immune and inflammatory responses to viral infection.

Studies on hybrid comoviruses reveal the importance of three-dimensional structure for processing of the viral coat proteins and show that the specificity of cleavage is greater in trans than in cis

A series of cowpea mosaic virus (CPMV)-based hybrid comoviral RNA-2 molecules have been constructed. In these, the region encoding both the large (L) and small (S) viral coat proteins was replaced by the equivalent region from bean pod mottle virus (BPMV). The hybrid RNA-2 molecules were able to replicate in cowpea protoplasts in the presence of CPMV RNA-1. Though processing of the hybrid polyproteins by the CPMV-specific 24K proteinase at the site between the 58/48K and L proteins could readily be achieved, no processing at the site between the L and S coat proteins could be obtained even when the sequence of amino acids between the two coat proteins was made CPMV-like. As a result, none of the hybrids was able to form functional virus particles, and they could not infect cowpea plants. Comparison with the processing of the L-S site in cis in reticulocyte lysates demonstrated that the requirements for processing are more stringent in trans than in cis. The results suggest that the L-S cleavage site is defined by more than just a linear sequence of amino acids and probably involves interactions between the L-S loop and the beta barrels of the viral coat proteins.