Studies on the role of the 2'-5'-oligoadenylate synthetase-RNase L pathway in beta interferon-mediated inhibition of encephalomyocarditis virus replication

Evidence of a dysregulated vitamin D endocrine system in SARS-CoV-2 infected patient's lung cells

Although a defective vitamin D endocrine system has been widely suspected to be associated in SARS-CoV-2 pathobiology, the status of the vitamin D endocrine system and vitamin D-modulated genes in lung cells of patients infected with SARS-CoV-2 remains unknown. To understand the significance of the vitamin D endocrine system in SARS-CoV-2 pathobiology, computational approaches were applied to transcriptomic datasets from bronchoalveolar lavage fluid (BALF) cells of such patients or healthy individuals. Levels of vitamin D receptor, retinoid X receptor, and CYP27A1 in BALF cells of patients infected with SARS-CoV-2 were found to be reduced. Additionally, 107 differentially expressed, predominantly downregulated genes, as potentially modulated by vitamin D endocrine system, were identified in transcriptomic datasets from patient's cells. Further analysis of differentially expressed genes provided eight novel genes with a conserved motif with vitamin D-responsive elements, implying the role of both direct and indirect mechanisms of gene expression by the dysregulated vitamin D endocrine system in SARS-CoV-2-infected cells. Protein-protein interaction network of differentially expressed vitamin D-modulated genes were enriched in the immune system, NF-κB/cytokine signaling, and cell cycle regulation as top predicted pathways that might be affected in the cells of such patients. In brief, the results presented here povide computational evidence to implicate a dysregulated vitamin D endocrine system in the pathobiology of SARS-CoV-2 infection.

Collateral Lethal Effects of Complementary Oncolytic Viruses

Virus-infected cells release type 1 interferons, which induce an antiviral state in neighboring cells. Naturally occurring viruses are therefore equipped with stealth replication strategies to limit virus sensing and/or with combat strategies to prevent or reverse the antiviral state. Here we show that oncolytic viruses with simple RNA genomes whose spread was suppressed in tumor cells pretreated with interferon were able to replicate efficiently when the cells were coinfected with a poxvirus known to encode a diversity of innate immune combat proteins. In vivo the poxvirus was shown to reverse the intratumoral antiviral state, rescuing RNA virus replication in an otherwise restrictive syngeneic mouse tumor model leading to antitumor efficacy. Pairing of complementary oncolytic viruses is a promising strategy to enhance the antitumor activity of this novel class of anticancer drugs.

Wanderings in biochemistry

My Ph.D. thesis in the laboratory of Severo Ochoa at New York University School of Medicine in 1962 included the determination of the nucleotide compositions of codons specifying amino acids. The experiments were based on the use of random copolyribonucleotides (synthesized by polynucleotide phosphorylase) as messenger RNA in a cell-free protein-synthesizing system. At Yale University, where I joined the faculty, my co-workers and I first studied the mechanisms of protein synthesis. Thereafter, we explored the interferons (IFNs), which were discovered as antiviral defense agents but were revealed to be components of a highly complex multifunctional system. We isolated pure IFNs and characterized IFN-activated genes, the proteins they encode, and their functions. We concentrated on a cluster of IFN-activated genes, the p200 cluster, which arose by repeated gene duplications and which encodes a large family of highly multifunctional proteins. For example, the murine protein p204 can be activated in numerous tissues by distinct transcription factors. It modulates cell proliferation and the differentiation of a variety of tissues by binding to many proteins. p204 also inhibits the activities of wild-type Ras proteins and Ras oncoproteins.

Intrinsic cellular defenses against virus infection by antiviral type I interferon

Intrinsic cellular defenses are non-specific antiviral activities by recognizing pathogen-associated molecular patterns (PAMPs). Toll-like receptors (TLRs), one of the pathogen recognize receptor (PRR), sense various microbial ligands. Especially, TLR2, TLR3, TLR4, TLR7, TLR8 and TLR9 recognize viral ligands such as glycoprotein, single- or double-stranded RNA and CpG nucleotides. The binding of viral ligands to TLRs transmits its signal to Toll/interleukin-1 receptor (TIR) to activate transcription factors via signal transduction pathway. Through activation of transcription factors, such as interferon regulatory factor-3, 5, and 7 (IRF-3, 5, 7) or nuclear factor-kappaB (NF-kappaB), type I interferons are induced, and antiviral proteins such as myxovirus-resistance protein (Mx) GTPase, RNA-dependent Protein Kinase (PKR), ribonuclease L (RNase L), Oligo-adenylate Synthetase (OAS) and Interferon Stimulated Gene (ISG) are further expressed. These antiviral proteins play an important role of antiviral resistancy against several viral pathogens in infected cells and further activate innate immune responses.

RNase L downmodulation of the RNA-binding protein, HuR, and cellular growth

Ribonuclease L (RNase L) is an intracellular enzyme that is vital in innate immunity, but also is a tumor suppressor candidate. Here, we show that overexpression of RNase L decreases cellular growth and downmodulates the RNA-binding protein, HuR, a regulator of cell-cycle progression and tumorigenesis. The effect is temporal, occurring in specific cell-cycle phases and correlated with the cytoplasmic localization of RNase L. Both cellular growth and HuR were increased in RNASEL-null mouse fibroblast lines when compared to wild-type cells. Moreover, the stability of HuR mRNA was enhanced in RNASEL-null cells. The HuR 3' untranslated region (UTR), which harbors U-rich and adenylate-uridylate-rich elements, was potently responsive to RNase L when compared to control 3' UTR. Our results may offer a new explanation to the tumor suppressor function of RNase L.

Double-stranded RNA-binding protein E3 controls translation of viral intermediate RNA, marking an essential step in the life cycle of modified vaccinia virus Ankara

Infection of human cells with modified vaccinia virus Ankara (MVA) activates the typical cascade-like pattern of viral early-, intermediate- and late-gene expression. In contrast, infection of human HeLa cells with MVA deleted of the E3L gene (MVA-DeltaE3L) results in high-level synthesis of intermediate RNA, but lacks viral late transcription. The viral E3 protein is thought to bind double-stranded RNA (dsRNA) and to act as an inhibitor of dsRNA-activated 2'-5'-oligoadenylate synthetase (2'-5'OA synthetase)/RNase L and protein kinase (PKR). Here, it is demonstrated that viral intermediate RNA can form RNase A/T1-resistant dsRNA, suggestive of activating both the 2'-5'OA synthetase/RNase L pathway and PKR in various human cell lines. Western blot analysis revealed that failure of late transcription in the absence of E3L function resulted from the deficiency to produce essential viral intermediate proteins, as demonstrated for vaccinia late transcription factor 2 (VLTF 2). Substantial host cell-specific differences were found in the level of activation of either RNase L or PKR. However, both rRNA degradation and phosphorylation of eukaryotic translation initiation factor-2alpha (eIF2alpha) inhibited the synthesis of VLTF 2 in human cells. Moreover, intermediate VLTF 2 and late-protein production were restored in MVA-DeltaE3L-infected mouse embryonic fibroblasts from Pkr(0/0) mice. Thus, both host-response pathways may be involved, but activity of PKR is sufficient to block the MVA molecular life cycle. These data imply that an essential function of vaccinia virus E3L is to secure translation of intermediate RNA and, thereby, expression of other viral genes.

Role of viral factor E3L in modified vaccinia virus ankara infection of human HeLa Cells: regulation of the virus life cycle and identification of differentially expressed host genes

Modified vaccinia virus Ankara (MVA) is a highly attenuated virus strain being developed as a vaccine for delivery of viral and recombinant antigens. The MVA genome lacks functional copies of numerous genes interfering with host response to infection. The interferon resistance gene E3L encodes one important viral immune defense factor still made by MVA. Here we demonstrate an essential role of E3L to allow for completion of the MVA molecular life cycle upon infection of human HeLa cells. A deletion mutant virus, MVA-DeltaE3L, was found defective in late protein synthesis, viral late transcription, and viral DNA replication in infected HeLa cells. Moreover, we detected viral early and continuing intermediate transcription associated with degradation of rRNA, indicating rapid activation of 2'-5'-oligoadenylate synthetase/RNase L in the absence of E3L. Further molecular monitoring of E3L function by microarray analysis of host cell transcription in MVA- or MVA-DeltaE3L-infected HeLa cells revealed an overall significant down regulation of more than 50% of cellular transcripts expressed under mock conditions already at 5 h after infection, with a more prominent shutoff following MVA-DeltaE3L infection. Interestingly, a cluster of genes up regulated exclusively in MVA-DeltaE3L-infected cells could be identified, including transcripts for interleukin 6, growth arrest and DNA damage-inducible protein beta, and dual-specificity protein phosphatases. Our data indicate that lack of E3L inhibits MVA antigen production in human HeLa cells at the level of viral late gene expression and suggest that E3L can prevent activation of additional host factors possibly affecting the MVA molecular life cycle.

Differential action of natural selection on the N and C-terminal domains of 2'-5' oligoadenylate synthetases and the potential nuclease function of the C-terminal domain

2'-5' Oligoadenylate synthetases (OAS) are a family of enzymes, which are best known for their important role in interferon-dependent antiviral mechanisms, but are also involved in the regulation of apoptosis, cell growth and differentiation in vertebrates. These enzymes bind double-stranded RNA and catalyze the synthesis of 2'-5' oligoadenylates from ATP. Several 2'-5' oligoadenylate synthetase-like proteins, which lack the ability to synthesize 2'-5' A, have been recently identified in humans and mice; the functions of these inactivated OAS derivatives remain unknown. Examination of phylogenetic trees shows that OAS inactivation in mammals occurred on several independent occasions. Comparative sequence analysis of OAS, poly(A)-polymerases, TRF4/sigma-family polymerases, archaeal CCA-adding enzymes and uridilyltransferases from trypanosomes resulted in the identification of a C-terminal domain, which is conserved in all these enzymes and is distinct from the nucleotidyltransferase domain. Secondary structure prediction shows that this domain has a four-helix core, which is most closely related to the ATP-cone domain, a regulatory nucleotide-binding domain present in ribonucleotide reductases and several other enzymes and transcription regulators. These observations, taken together with the experimental evidence of nuclease activity in the TRF4/sigma-family of polymerases, suggest that the C-terminal domain of OAS and their homologs might have nuclease activity. The putative nuclease domain is preferentially conserved in OAS derivatives that lack an active nucleotidyltransferase domain and, as indicated by the analysis of the ratio of synonymous to non-synonymous substitutions, appears to be subject to purifying selection in these proteins. In contrast, phylogenetic analysis provided evidence of episodic positive selection in the mouse OAS-like proteins with inactivated nucleotidyltransferase domains, which suggests that some of these proteins might have distinct antiviral functions.

Relationship between 24-hour rhythm in antiviral effect of interferon-beta and interferon-alpha/beta receptor expression in mice

The influence of interferon-beta (IFN-beta) dosing time on antiviral activity was investigated in ICR male mice under light-dark cycle conditions (lights on at 07:00, off at 19:00) with food and water available ad libitum. There was a significant dosing time-dependent change in 2',5'-oligoadenylate synthetase (2',5'-OAS) activities, as an index of antiviral activity, in liver at 12 h after IFN-beta (15 MIU/kg, i.v.) injection. IFN-beta-induced 2',5'-OAS activity was more potent after the drug injection during the late dark phase. The higher antiviral effect of IFN-beta was observed when the interferon-alpha/beta receptor (IFNAR) expression in the liver increased, and the lower effect was observed when its expression decreased. IFN-beta-induced fever was more serious after IFN-beta injection from the late dark phase to the early light phase. A significant dosing time-dependent change was demonstrated for plasma IFN-beta concentrations, which showed a higher level during the light phase and a lower level during the dark phase. The dosing time-dependent change of plasma IFN-beta concentrations was not associated with that of the antiviral effect or fever induced by IFN-beta. These results suggest that selecting the most suitable dosing time of IFN-beta, associated with the 24-h rhythm of IFNAR expression in the liver, may be important to increase effectively the antiviral activity of the drug in experimental and clinical situations.

Genomic structure of the mouse 2',5'-oligoadenylate synthetase gene family

2',5'-Oligoadenylate synthetase (2-5OAS) is one of the interferon (IFN)-induced proteins and mediates the antiviral action of IFN. In human, three classes of 2-5OAS genes (OAS1, OAS2, and OAS3) and one OAS-like gene (OASL) are reported. In mice, however, OAS genes corresponding to human OAS2 and OAS3 have not been identified. In this report, we identified six novel OAS family genes in mice by screening mouse genomic library and expressed sequence tag (EST) database. These genes include three homologs of the human OAS1 and each homologous gene of the human OAS2, OAS3, and OASL, respectively. Each gene displays 52%-65% amino acid identity to the corresponding human homologs. Nine 2-5OAS genes, except for two OASL genes, locate within the 210-kb genomic region and form a cluster. Each novel 2-5OAS gene showed a characteristic expression pattern among different tissues, and all of them were induced by polyinosinic-polycytidylic acid. Biochemical analyses using recombinant proteins produced in Escherichia coli showed that all the novel mouse 2-5OAS molecules have double-stranded RNA (dsRNA) binding ability, but they do not have 2-5OAS activity except for the OAS2 and OAS3 mouse homologs. These results show that there are at least 11 OAS genes, which are classified into four groups, in the mouse.

Biological assays for interferons

Interferons (IFN) are potent biologically active proteins synthesised and secreted by somatic cells of all mammalian species. They have been well characterised, especially those of human origin, with respect to structure, biological activities, and clinical therapeutic effects. While structural differences are known to exist among the IFN species that constitute the "IFN family" and despite the existence of different receptors for type I and type II IFN, all species have been shown to exert a similar spectrum of in vitro biological activities in responsive cells. Principal among the biological activities induced by IFN is antiviral activity, the activity used to originally define IFN. Antiviral activity of IFN is mediated via cell receptors and is dependent on the activation of signalling pathways, the expression of specific gene products, and the development of antiviral mechanisms. Sensitivity of cells to IFN-mediated antiviral activity is variable, and depends on a number of factors including cell type, expression of IFN receptors and downstream effector response elements, effectiveness of antiviral mechanisms, and the type of virus used to infect cells. Nevertheless, by the judicious use of sensitive cell lines in combination with appropriate cytopathic viruses, effective assays to measure the antiviral activity have been developed. Historically, "antiviral assays" (AVA) were the first type of biological assays that were developed to measure the relative activity or potency of IFN preparations. However, the subsequent discoveries of several other biological activities of IFN has opened the way to the development of assays based on one or other of these activities. The latter include inhibition of cell proliferation, regulation of functional cellular activities, regulation of cellular differentiation and immunomodulation. More recently, the cloning of IFN responsive genes has led to the development of "reporter gene assays". In this case, the promoter region of IFN responsive genes is linked with a heterologous reporter gene, for example, firefly luciferase or alkaline phosphatase, and transfected into an IFN-sensitive cell line. Stably transfected cell lines exposed to IFN increase expression of the reporter gene product in direct relation to the dose of IFN, the readout being a measure of this product's enzymic action. The current review aims to give a critical overview of the development, specificity, standardisation and present use of the various biological assay methods now available for the quantification of IFN activity.

Role and fate of PML nuclear bodies in response to interferon and viral infections

Interferons (IFNs) are a family of secreted proteins with antiviral, antiproliferative and immunomodulatory activities. The different biological actions of IFN are believed to be mediated by the products of specifically induced cellular genes in the target cells. The promyelocytic leukaemia (PML) protein localizes both in the nucleoplasm and in matrix-associated multi-protein complexes known as nuclear bodies (NBs). PML is essential for the proper formation and the integrity of the NBs. Modification of PML by the Small Ubiquitin MOdifier (SUMO) was shown to be required for its localization in NBs. The number and the intensity of PML NBs increase in response to interferon (IFN). Inactivation of the IFN-induced PML gene by its fusion to retinoic acid receptor alpha alters the normal localization of PML from the punctuate nuclear patterns of NBs to micro-dispersed tiny dots and results in uncontrolled growth in Acute Promyelocytic Leukaemia. The NBs-associated proteins, PML, Sp100, Sp140, Sp110, ISG20 and PA28 are induced by IFN suggesting that nuclear bodies could play a role in IFN response. Although the function of PML NBs is still unclear, some results indicate that they may represent preferential targets for viral infections and that PML could play a role in the mechanism of the antiviral action of IFNs. Viruses, which require the cellular machinery for their replication, have evolved different ways to counteract the action of IFN by inhibiting IFN signalling, by blocking the activities of specific antiviral mediators or by altering PML expression and/or localization on nuclear bodies.

Expansion and molecular evolution of the interferon-induced 2'-5' oligoadenylate synthetase gene family

The mammalian 2'-5' oligoadenylate synthetases (2'-5'OASs) are enzymes that are crucial in the interferon-induced antiviral response. They catalyze the polymerization of ATP into 2'-5'-linked oligoadenylates which activate a constitutively expressed latent endonuclease, RNaseL, to block viral replication at the level of mRNA degradation. A molecular evolutionary analysis of available OAS sequences suggests that the vertebrate genes are members of a multigene family with its roots in the early history of tetrapods. The modern mammalian 2'-5'OAS genes underwent successive gene duplication events resulting in three size classes of enzymes, containing one, two, or three homologous domains. Expansion of the OAS gene family occurred by whole-gene duplications to increase gene content and by domain couplings to produce the multidomain genes. Evolutionary analyses show that the 2'-5'OAS genes in rodents underwent gene duplications as recently as 11 MYA and predict the existence of additional undiscovered OAS genes in mammals.

Evidence for IRF-1-dependent gene expression deficiency in interferon unresponsive HepG2 cells

Induction of the antiproliferative and antiviral state by IFNs (type I and II) is dramatically impaired in HepG2 cells. We show here that RNase L, IDO, GBP-2 and iNOS genes normally expressed as a secondary response to IFN are no longer inducible in HepG2 cells, while induction of primary response genes (IRF-1, PKR, p48-ISGF3gamma, 2-5AS, 6-16 and p56-(trp)tRNA) are unaffected. On the basis of previous data implicating transcription factor IRF-1 in the induction of some IFN-induced genes, we tested the effects of transfecting an IRF-1 oligonucleotide antisense in HeLa cells and found specifically impaired IFN induction of secondary response genes (RNase L, IDO and GBP-2). This raised the possibility that IRF-1 was defective in HepG2 cells. However, some molecular and biochemical analyses reveal that IRF-1 is induced normally by IFNs and retains its normal size, cellular location, phosphorylation status and ability to bind the IDO promoter in vitro. Therefore, we conclude that although the primary response pathway is fully functional, some aspects of the secondary pathway involving IRF-1 (but not IRF-1 itself) are defective in HepG2 cells. It may be possible that the promoter region of these deficient HepG2-genes requires an unidentified transcription factor in addition to de novo IRF-1, which could be elicited by a cooperative activator.

Transcriptional induction of the p69 isoform of 2',5'-oligoadenylate synthetase by interferon-beta and interferon-gamma involves three regulatory elements and interferon-stimulated gene factor 3

The 2',5'-oligoadenylate synthetases are key enzymes that mediate antiviral actions of interferon (IFN). The mRNAs for the intermediate isoforms (p69) of human 2',5'-oligoadenylate synthetase are rapidly induced 10- to 20-fold in HT1080 glioma cells by IFN-beta and induced 3-fold at 24 h by IFN-gamma. Induction is mediated by three regulatory elements, an IFN-stimulated response element and two identical sites resembling interferon response factor binding sites that are located within 300 bp of the transcriptional start site. Maximal induction requires all three elements, yet mutation in the most distal IRF-1-like site diminishes transcription only slightly. Mutation in the ISRE substantially decreases constitutive expression but does not abrogate the response to IFNs. Simultaneous mutation in all three elements abolishes responsiveness to both IFN-beta and IFN-gamma. Both constitutive and IFN-beta-induced expression from the p69 promoter is blocked in mutant cell lines deficient in components of the transcription factor, interferon-stimulated gene factor 3, suggesting that it is the primary factor controlling IFN-beta induced expression of this gene.

Role of the vaccinia virus E3L and K3L gene products in rescue of VSV and EMCV from the effects of IFN-alpha

Vaccinia virus (VV) has been shown to be relatively resistant to the antiviral effects of interferon-alpha (IFN-alpha) and to rescue replication of IFN-sensitive viruses, such as encephalomyocarditis virus (EMCV) and vesicular stomatitis virus (VSV), from the antiviral effects of IFN. The E3L and K3L gene products have been implicated in the IFN resistance of VV. We have investigated the role that these VV-encoded functions play in the rescue of VSV and EMCV from the effects of IFN. Transient expression of the E3L open reading frame (ORF) was sufficient to rescue VSV but not EMCV from the IFN-induced antiviral state. Rescue of VSV by mutants of E3L correlated with the ability of the mutated E3L gene products to bind dsRNA. Conversely, transient expression of the K3L ORF was sufficient to partially rescue EMCV but not VSV from the effects of IFN. Results with VV deleted of either the K3L or E3L ORFs were consistent with results obtained by transient expression of these genes. These results demonstrate that the VV E3L gene products are likely responsible for the VV-mediated rescue of VSV from the effects of IFN and the K3L gene product is likely at least partly responsible for rescue of EMCV.

RNase L mediates the antiviral effect of interferon through a selective reduction in viral RNA during encephalomyocarditis virus infection

The 2',5'-oligoadenylate (2-5A) system is an RNA degradation pathway which plays an important role in the antipicornavirus effects of interferon (IFN). RNase L, the terminal component of the 2-5A system, is thought to mediate this antiviral activity through the degradation of viral RNA; however, the capacity of RNase L to selectively target viral RNA has not been carefully examined in intact cells. Therefore, the mechanism of RNase L-mediated antiviral activity was investigated following encephalomyocarditis virus (EMCV) infection of cell lines in which expression of transfected RNase L was induced or endogenous RNase L activity was inhibited. RNase L induction markedly enhanced the anti-EMCV activity of IFN via a reduction in EMCV RNA. Inhibition of endogenous RNase L activity inhibited this reduction in viral RNA. RNase L had no effect on IFN-mediated protection from vesicular stomatitis virus. RNase L induction reduced the rate of EMCV RNA synthesis, suggesting that RNase L may target viral RNAs involved in replication early in the virus life cycle. The RNase L-mediated reduction in viral RNA occurred in the absence of detectable effects on specific cellular mRNAs and without any global alteration in the cellular RNA profile. Extensive rRNA cleavage, indicative of high levels of 2-5A, was not observed in RNase L-induced, EMCV-infected cells; however, transfection of 2-5A into cells resulted in widespread degradation of cellular RNAs. These findings provide the first demonstration of the selective capacity of RNase L in intact cells and link this selective activity to cellular levels of 2-5A.

Interferons Alpha, Beta, and Omega

Interferon alpha (IFN-α) is a mixture of closely related proteins, termed “subtypes,” expressed from distinct chromosomal genes. Interferon β (IFN-β) is a single protein species and is molecularly related to IFN-α subtypes, although it is antigenically distinct from them. IFN omega (IFN-ω) is antigenically distinct from IFN-α and IFN-β but is molecularly related to both. The genes of three IFN subtypes are tandemly arranged on the short arm of chromosome 9. They are transiently expressed following induction by various exogenous stimuli, including viruses. They are synthesized from their respective mRNAs for relatively short periods following gene activation and are secreted to act, via specific cell surface receptors, on other cells. IFN-α subtypes are secreted proteins and as such are transcribed from mRNAs as precursor proteins, pre-IFN-α, containing N-terminal signal polypeptides of 23 hydrophobic amino acids (aa) mainly. Pre-IFN-β contains 187 aa, of which 21 comprise the N-terminal signal polypeptide and 166 comprise the mature IFN-β protein. IFN-ω contains 195 aa—the N-terminal 23 comprising the signal sequence and the remaining 172, the mature IFN-ω protein. At the C-terminus, the aa sequence of IFN-ω is six residues longer than that of IFN-α or IFN-β proteins. IFN-α, as a mixture of subtypes, and IFN-ω may be produced together following viral infection of null lymphocytes or monocytes/macrophages. The biological activities of IFNs are mostly dependent upon protein synthesis with selective subsets of proteins mediating individual activities. IFNs can also stimulate indirect antiviral and antitumor mechanisms, depending upon cellular differentiation and the induction of cytotoxic activity.

To kill or to cure: options in host defense against viral infection

It is generally thought that viral clearance is mediated primarily by antigen-specific T cell responses that destroy infected cells. This assumption may not be true for all viruses. Recent studies using a transgenic mouse model of hepatitis B virus infection have shown that adoptively transferred, virus-specific cytotoxic T cells can abolish hepatitis B virus gene expression and replication in the liver without killing the hepatocytes. This effect is mediated by interferon-gamma and tumor necrosis factor-alpha, which are secreted by the cytotoxic T lymphocytes following antigen recognition. Similar noncytopathic cytokine-dependent 'curative' processes also occur in this model during an unrelated infection of the liver. Intracellular viral inactivation mechanisms such as these could greatly amplify the protective effects of the immune response. Research has also been carried out to clarify the relevance of curative versus destructive mechanisms of viral clearance in other models of viral infection.

Viral cross talk: intracellular inactivation of the hepatitis B virus during an unrelated viral infection of the liver

Hepatitis B virus (HBV) infection is thought to be controlled by virus-specific cytotoxic T lymphocytes (CTL). We have recently shown that HBV-specific CTL can abolish HBV replication noncytopathically in the liver of transgenic mice by secreting tumor necrosis factor alpha (TNF-alpha) and interferon gamma (IFN-gamma) after antigen recognition. We now demonstrate that hepatocellular HBV replication is also abolished noncytopathically during lymphocytic choriomeningitis virus (LCMV) infection, and we show that this process is mediated by TNF-alpha and IFN-alpha/beta produced by LCMV-infected hepatic macrophages. These results confirm the ability of these inflammatory cytokines to abolish HBV replication; they elucidate the mechanism likely to be responsible for clearance of HBV in chronically infected patients who become superinfected by other hepatotropic viruses; they suggest that pharmacological activation of intrahepatic macrophages may have therapeutic value in chronic HBV infection; and they raise the possibility that conceptually similar events may be operative in other viral infections as well.

Molecular cloning of a new interferon-induced factor that represses human immunodeficiency virus type 1 long terminal repeat expression

Transcriptional induction of genes is an essential part of the cellular response to interferons. To isolate yet unidentified IFN-regulated genes we have performed a differential screening on a cDNA library prepared from human lymphoblastoid Daudi cells treated for 16 h with human alpha/beta interferon (Hu-alpha/beta IFN). In the course of these studies we have isolated a human cDNA which codes for a protein sharing homology with the mouse Rpt-1 gene; it will be referred as Staf-50 for Stimulated Trans-Acting Factor of 50 kDa. Amino acid sequence analysis revealed that Staf-50 is a member of the Ring finger family and contains all the features of a transcriptional regulator able to initiate a second cascade of gene induction (secondary response). Staf-50 is induced by both type I and type II IFN in various cell lines and down-regulates the transcription directed by the long terminal repeat promoter region of human immunodeficiency virus type 1 in transfected cells. These data are consistent with a role of Staf-50 in the mechanism of transduction of the IFN antiviral action.

Effect of interferon and 2',5'-oligoadenylates on rotavirus RNA synthesis

Based on the antiviral effect of interferon on rotavirus replication the inhibitory effect of 2',5'-oligoadenylates on MRNA and double-stranded RNA synthesis was studied using an in vitro assay. The chemically synthesized oligonucleotides were used to determine several characteristics of the inhibitory effect, such as chain length, presence of phosphate residues at the 5'-end, and the 2',5'-phosphodiester bond itself. In vitro transcription was inhibited by oligos with 5 or more adenine residues at a final concentration of 100 microM or greater. This result makes rotavirus transcriptase different from other viruses in which the inhibitory effects are associated with dinucleotides and trinucleotides. The inhibitory effect was increased when the oligo contained a phosphate residue at the 5'-end; in this case, inhibition was also seen at lower oligo concentrations as well as at shorter oligo chain length. The study of the kinetics of inhibition showed that the inhibition by p(A2'p5')(3)3A was competitive with a Ki value of 256 microM. The effect of the oligonucleotides on the in vitro viral RNA replication showed that the 2',5'-oligoadenylates were not able to significantly inhibit the in vitro rotavirus RNA synthesis. The lack of inhibition in the in vitro assay was very peculiar since RNA transcription and replication involves the viral RNA polymerase, VP1.

Mechanisms of viral inhibition by interferons

Interferons (IFNs) are a family of related proteins grouped in four species (alpha, beta, gamma and omega) according to their cellular origin, inducing agents and antigenic and functional properties. Their binding to specific receptors leads to the activation of signal transduction pathways that stimulate a defined set of genes, whose products are eventually responsible for the IFN antiviral effects. Their action against viruses is a complex phenomenon. It has been reported that IFNs restrict virus growth at the levels of penetration, uncoating, synthesis of mRNA, protein synthesis and assembly. This review will attempt to evaluate evidence of the involvement of the IFN-inducible proteins in the expression of the antiviral state against RNA or DNA viruses.

Fascination with 2-5A-dependent RNase: a unique enzyme that functions in interferon action

Interferon (IFN) treatment of cells results in the induction of 2-5A-synthetases, double-stranded RNA-activated enzymes that produce unusual 5'-phosphorylated 2',5'-linked oligoadenylates known as 2-5A. 2.5A activates a unique IFN-induced endoribonuclease, the 2-5A-dependent RNase (RNase L), that is capable of degrading both viral and cellular RNA. The expression cloning of 2-5A-dependent RNase is leading to meaningful analysis of the physiological functions of the 2-5A system. For example, expression in mouse cells of a dominant-negative mutant form of 2-5A-dependent RNase suppressed both the antiencephalomyocarditis virus and anticellular activities of IFN. Future investigations into this intriguing ribonuclease pathway promise to provide an intricate view into a molecular pathway of IFN action.

Interleukin-2 and alpha/beta interferon down-regulate hepatitis B virus gene expression in vivo by tumor necrosis factor-dependent and -independent pathways

We have recently reported that administration of recombinant tumor necrosis factor alpha (TNF-alpha) to hepatitis B virus (HBV) transgenic mice reduces the hepatic steady-state content of HBV-specific mRNA by up to 80% in the absence of liver cell injury. In the current study, we analyzed the regulatory effects of several other inflammatory cytokines in the same transgenic model system. Hepatic HBV mRNA content was reduced by up to 90% following administration of a single noncytopathic dose (100,000 U) of interleukin 2 (IL-2). Comparable effects were produced by administration of alpha and beta interferons (IFN-alpha and IFN-beta), but only after multiple injections of at least 500,000 U per mouse. Importantly, the regulatory effect of IL-2 was completely blocked by the prior administration of antibodies to tumor necrosis factor alpha (TNF-alpha), which did not block the effect of IFN-alpha or IFN-beta. In contrast to these observations, recombinant IFN-gamma, IL-1, IL-3, IL-6, TNF-beta, transforming growth factor beta, and granulocyte-monocyte colony-stimulating factor were inactive in this system. These results suggest that selected inflammatory cytokines can down-regulate HBV gene expression in vivo by at least two pathways, one that is dependent on TNF-alpha and another that is not. These results imply that antigen-nonspecific products of the intrahepatic HBV-specific inflammatory response may contribute to viral clearance or persistence during HBV infection.

Picornavirus inhibitors

Picornaviruses are among the best understood animal viruses in molecular terms. A number of important human and animal pathogens are members of the Picornaviridae family. The genome organization, the different steps of picornavirus growth and numerous compounds that have been reported as inhibitors of picornavirus functions are reviewed. The picornavirus particles and several agents that interact with them have been solved at atomic resolution, leading to computer-assisted drug design. Picornavirus inhibitors are useful in aiding a better understanding of picornavirus biology. In addition, some of them are promising therapeutic agents. Clinical efficacy of agents that bind to picornavirus particles has already been demonstrated.

Replication of lymphocytic choriomeningitis virus is restricted in terminally differentiated neurons

We have investigated the replication of lymphocytic choriomeningitis virus (LCMV) before and after the nerve growth factor (NGF)-induced transdifferentiation of PC12 cells from the chromaffin to the neuron-like phenotype. Untreated and NGF-treated cells were equally susceptible to LCMV infection; however, the viral yield was found to be 1,000-fold lower in NGF-differentiated PC12 cells. The reduced viral yield correlated with restricted LCMV replication and transcription within the infected cell, which was not caused by the lack of cell proliferation in the NGF-treated cells but rather was related to the induction or changes in expression levels of specific gene product(s) associated with the cell commitment to a neuronal phenotype. The return to the chromaffin phenotype after withdrawal of NGF restored normal LCMV yields as well as levels of viral replication and transcription. The finding of reduced viral replication in terminally differentiated neuronal cells has important implications for understanding the mechanism by which neurotropic viruses, such as LCMV, are able to establish a long-term persistent infection in the central nervous system in the absence of severe pathological changes.

A dominant negative mutant of 2-5A-dependent RNase suppresses antiproliferative and antiviral effects of interferon

2-5A-dependent RNase is the terminal factor in the interferon-regulated 2-5A system thought to function in both the molecular mechanism of interferon action and in the general control of RNA stability. However, direct evidence for specific functions of 2-5A-dependent RNase has been generally lacking. Therefore, we developed a strategy to block the 2-5A system using a truncated form of 2-5A-dependent RNase which retains 2-5A binding activity while lacking RNase activity. When the truncated RNase was stably expressed to high levels in murine cells, it prevented specific rRNA cleavage in response to 2-5A transfection and the cells were unresponsive to the antiviral activity of interferon alpha/beta for encephalomyocarditis virus. Remarkably, cells expressing the truncated RNase were also resistant to the antiproliferative activity of interferon. The truncated RNase is a dominant negative mutant that binds 2-5A and that may interfere with normal protein-protein interactions through nine ankyrin-like repeats.

Interferon alpha induces the expression of retinoblastoma gene product in human Burkitt lymphoma Daudi cells: role in growth regulation

Interferon alpha (IFN-alpha) is a regulatory secretory protein with distinctive biological effects such as antiproliferative actions against many tumor cell lines, including human Burkitt lymphoma Daudi cells. The mechanism underlying growth inhibition by IFN-alpha is not well established. The growth of many mammalian cell types is also regulated by tumor suppressor retinoblastoma (RB) gene product, the RB protein. In the studies presented here, we explored the possible involvement of RB protein in the growth inhibitory action of IFN-alpha in the Daudi cell model system. We observed that IFN-alpha induces a 3- to 10-fold increased expression of RB protein in growth-sensitive Daudi cells but not in the growth-resistant variant of Daudi cells. IFN-alpha-mediated induction of RB protein was an early event that preceded the period of growth inhibition of Daudi cells. IFN-alpha-induced RB protein predominantly exists as the underphosphorylated form. Addition of antibody against IFN-alpha to Daudi cells resulted in the inhibition of constitutive expression of RB protein and stimulation of [3H]thymidine incorporation. These results demonstrate that the induction of RB protein expression in IFN-alpha-treated Daudi cells could constitute an important mechanism of IFN-alpha-mediated growth regulation.

Interferon action: binding of viral RNA to the 40-kilodalton 2'-5'-oligoadenylate synthetase in interferon-treated HeLa cells infected with encephalomyocarditis virus

The 40-kDa 2'-5'-oligoadenylate [(2'-5') (A)n] synthetase isoenzyme was proven to be a mediator of the inhibition of encephalomyocarditis virus (EMCV) replication by interferon (IFN). When activated by double-stranded RNA, this enzyme converts ATP into 2'-5'-oligoadenylate [(2'-5') (A)n], and (2'-5') (A)n was found to accumulate in IFN-treated, EMCV-infected cells. The only known function of (2'-5') (A)n is the activation of RNase L, a latent RNase, and this was also implicated in the inhibition of EMCV replication. Intermediates or side products in EMCV RNA replication, presumed to be partially double stranded, were shown to activate (2'-5') (A)n synthetase in vitro. These findings served as the basis of the long-standing hypothesis that the activator of (2'-5') (A)n synthetase in IFN-treated, EMCV-infected cells is the viral RNA. To test this hypothesis, we have generated a polyclonal rabbit antiserum to the human 40-kDa (2'-5') (A)n synthetase. The antiserum immunoprecipitated, from IFN-treated HeLa cells that had been infected with EMCV, the 40-kDa (2'-5') (A)n synthetase protein in complex with both strands of EMCV RNA. The immunoprecipitate was active in (2'-5') (A)n synthesis even without addition of double-stranded RNA, whereas the immunoprecipitate from IFN-treated, uninfected cells was not. These and other results demonstrate that in IFN-treated, EMCV-infected cells, viral RNA is bound to the (2'-5') (A)n synthetase and suggest that the agent activating the (2'-5') (A)n synthetase is the bound viral RNA.

Detection of (2'-5')oligoadenylate binding proteins by nondenaturing polyacrylamide gel electrophoresis and affinity blotting onto nitrocellulose

A latent endoribonuclease, RNase L, binds to and is activated by (2'-5')oligoadenylates ((2'-5')(A)n, n = 2-15). Binding to a labeled derivative of (2'-5')(A)n, [32P](2'-5')(A)3pCp, is detected as a protein-ligand complex observed following nondenaturing polyacrylamide gel electrophoresis. One major binding complex and two minor binding complexes are readily seen in cytoplasmic extracts from Ehrlich ascites tumor cells, murine tissue extracts and rabbit liver tissue extracts. At least one of the more rapidly migrating complexes appears to be a proteolytic degradation product of the larger [32P](2'-5')(A)3pCp binding protein. Cell and tissue extracts containing [32P](2'-5')(A)3pCp binding activity can be immobilized onto nitrocellulose filters and [32P](2'-5')(A)3pCp binding activity detected using a simple, rapid, economical affinity blot assay. Detection of [32P](2'-5')(A)3pCp binding proteins following electrophoresis on nondenaturing polyacrylamide gels and the affinity blot assay significantly improve and simplify the analysis of (2'-5')(A)n binding proteins.

Transforming growth factor beta 1 enhances expression of 50 kDa protein related to 2'-5' oligoadenylate synthetase in human sperm cells

Human cellular polypeptide factors, namely interferon-alpha, interferon-gamma transforming growth factor (TGF)-alpha, and TGF-beta 1, were analyzed for their effect on motility of human sperm cells. Both interferons caused an inhibition of sperm cell motility due to direct cytotoxic effects without inducing 2'-5' oligoadenylate [2-5(A)]synthetase activity. TGF-alpha affected neither motility nor the levels of 2-5(A) synthetase in sperm cells. TGF-beta 1 had no affect on sperm motility, yet it caused an induction of 2-5(A)synthetase activity. Western immunoblot analysis of TGF-beta 1-treated sperm indicated an enhancement of a 50 kDa protein. Metabolic labeling of sperm cells revealed biosynthesis of one major protein of 50 kDa and at least five minor proteins in the range of 30-92 kDa; the level of 50 kDa protein increased after treatment with TGF-beta 1. The treatment of sperm cells with TGF-beta 1 did not affect their penetration in zona-free hamster eggs (SPA). These results indicate that TGF-beta 1 enhances expression of a 50 kDa protein related to 2-5(A) synthetase in human sperm cells along with other minor proteins, and this increase does not affect sperm motility and SPA.

Selective inhibition of hepatitis B virus and human immunodeficiency virus sequence-promoted gene expression by cotransfected poly(I):poly(C)

The transient expression of hepatitis B virus (HBV) surface and "eJ" antigens caused by transfection of human hepatoblastoma HepG2 cells with HBV DNA was markedly inhibited by cotransfection with poly(I):poly(C). Cotransfection with poly(I):poly(C) also inhibited the expression of bacterial chloramphenicol acetyltransferase (CAT) gene which was under the control of either the HBV core promoter or the human immunodeficiency virus (HIV-1) long terminal repeat. This inhibition was much more pronounced on the expression of HBV-promoted CAT than HIV-promoted CAT. The uptake of reporter plasmid was not affected by cotransfected poly(I):poly(C). The inhibition was found to be at the steady-state CAT mRNA level and appeared to be specific for HBV and HIV regulatory sequences since CAT expression directed by other viral and cellular regulatory sequences was not inhibited. Cotransfection with a mixture of equal amounts of poly(I) and poly(C) had similar inhibitory effects whereas cotransfection with poly(l) or poly(C) alone, or other double-stranded ribo- or deoxyribonucleotides, did not have such strong effects. The addition of poly(l):poly(C) to the culture medium of cells transfected with these reporter plasmids caused little inhibition. Transfection with poly(l):poly(C) induced a minimal amount of intracellular interferon-alpha in HepG2 cells which may be involved in selective inhibition of HBV-and HIV-1-directed gene expression. 2-Aminopurine, an inhibitor of double-stranded RNA activated protein kinase known to block interferon gene induction by poly(l):poly(C), partially reversed the poly(l):poly(C)-induced inhibitory effect on HBV-CAT expression.

2',5'-Oligoadenylate synthetase gene expression in revertants of ras-transformed NIH3T3 fibroblasts

Persistent revertant (PR) cells of Ha-ras-transformed NIH3T3 fibroblasts, isolated after prolonged treatment with interferon (IFN), have been previously described. PR cells remain nontumorigenic even after IFN withdrawal. To investigate the mechanisms responsible for the stable phenotypic reversion, we have now examined the potential involvement of an endogenous IFN and the 2',5'-oligoadenylate (2-5A) synthetase pathway. Northern blot analysis revealed an increased level of 2-5A synthetase transcripts in PR cells compared to parental Ha-ras-transformed cultures. Although inducible on treatment with exogenous IFN alpha/beta, this mRNA was not detectable in untreated NIH3T3 cells. 2-5A synthetase expression following IFN treatment was also significantly higher in PRs than in the normal or ras-transformed NIH3T3. The increased levels of synthetase mRNA correlated with a similarly elevated enzymatic activity in cell extracts from PR cells. This increased expression was biologically functional, since the revertant cells were more resistant to the cytolytic action of mengovirus than normal or ras-transformed NIH3T3 fibroblasts. Another class of IFN-induced genes, H-2 class I antigens, showed enhanced expression in PRs. Antibodies directed against mouse IFN alpha/beta did not reduce the constitutive expression of 2-5A synthetase in PR cells. Furthermore, conditioned medium from PR cultures or cocultivation with PRs failed to induce the enzyme message in NIH3T3 cells. Finally, there was no detectable elevation in the mRNA specific for IFN beta in the PR cultures, as determined using a sensitive polymerase chain reaction amplification protocol. These results show that the Ha-ras revertants constitutively produce a functional 2-5A synthetase, which appears to be independent of the production of an endogenous interferon alpha or beta.

A full-length murine 2-5A synthetase cDNA transfected in NIH-3T3 cells impairs EMCV but not VSV replication

Treatment of cells with interferons (IFNs) induces resistance to virus infection. The 2'-5'oligo A (2-5A) synthetase/RNase L is one of the pathways leading to translation inhibition induced by IFN treatment. A murine cDNA encoding the 43-kDa 2-5A synthetase was cloned and sequenced. NIH-3T3 cell clones transfected with this cDNA expressed the enzymatic activity to various extents and exhibited resistance to encephalomyocarditis virus (EMCV) but not to vesicular stomatitis virus replication. The specific resistance to EMCV can be attributed to 2-5A synthetase.

Effect of 2',5'-oligoadenylate on herpes simplex virus-infected cells and preventive action of 2',5'-oligoadenylate on the lethal effect of HSV-2

Antiviral effects of ppp(A2'p)nA, (2-5A) on herpes simplex virus type 1 or type 2 (HSV-1 or HSV-2)-infected baby hamster kidney fibroblasts (BHK cells) and HSV-2-infected female guinea pigs were examined. 2-5A was introduced into BHK cells in the form of a calcium phosphate precipitate and as an ointment of polyethylene glycol (PEG) into guinea pig vagina. Under optimum conditions, 2-5A trimer and other 2-5A derivatives inhibited over 90% of HSV-1 syncytia formation and over 50% of HSV-2 plaque formation. The growth of uninfected cells was only slightly and transiently inhibited under these conditions. Northern analysis of viral immediate early mRNAs and cellular mRNAs showed that all transcripts determined were reduced in amount by the 2-5A trimer treatment. The reduction in level of viral mRNAs (ICP4, ICP22, and ICP47) by 2-5A trimer was significantly more than that of cellular mRNAs (represented by beta-actin). HSV-2 (strain 186) inoculation into the vagina of female guinea pigs causes severe symptoms in the genital area and high mortality. Topically applied 2-5A trimer almost completely prevented the lethal effect of HSV-2. These data are discussed from the viewpoint of mechanism of interferon action.

Regulation of 2',5'-oligoadenylate synthetase gene expression by interferons and platelet-derived growth factor

In murine BALB/c 3T3 cell cultures, either beta interferon or platelet-derived growth factor (PDGF) enhanced expression of the 2',5'-oligoadenylate synthetase mRNA and protein. The time course of induction in response to beta interferon was similar to that in response to PDGF. Of several growth factors known to be present in clotted blood serum (i.e., epidermal growth factor, transforming growth factor beta, and PDGF), only PDGF enhanced expression of 2',5'-oligoadenylate synthetase. The linkage of an interferon response element-containing segment from the 5'-flanking region of a human or murine 2',-5'-oligoadenylate synthetase gene made a heterologous gene responsive to interferon. The expression of such a gene construct in transfected cells was also induced by PDGF. Induction by PDGF was inhibited by mono- or polyclonal antibodies to murine interferon, which suggested that induction by PDGF requires interferon. Both PDGF and interferon induced nuclear factors that bound to this interferon response element-containing segment in vitro.

Regulation of 2',5'-oligoadenylate synthetase gene expression by interferons and platelet-derived growth factor

In murine BALB/c 3T3 cell cultures, either beta interferon or platelet-derived growth factor (PDGF) enhanced expression of the 2',5'-oligoadenylate synthetase mRNA and protein. The time course of induction in response to beta interferon was similar to that in response to PDGF. Of several growth factors known to be present in clotted blood serum (i.e., epidermal growth factor, transforming growth factor beta, and PDGF), only PDGF enhanced expression of 2',5'-oligoadenylate synthetase. The linkage of an interferon response element-containing segment from the 5'-flanking region of a human or murine 2',-5'-oligoadenylate synthetase gene made a heterologous gene responsive to interferon. The expression of such a gene construct in transfected cells was also induced by PDGF. Induction by PDGF was inhibited by mono- or polyclonal antibodies to murine interferon, which suggested that induction by PDGF requires interferon. Both PDGF and interferon induced nuclear factors that bound to this interferon response element-containing segment in vitro.

Differential modulating effects of retinoic acid on interferon antiviral activity

The effect of retinoic acid (RA) on the antiviral activity of interferons (IFNs) alpha and beta in the U937 and WISH cells was examined to ascertain whether or not RA could reduce the effectiveness of IFN-induced resistance to viral infection. Our results indicate that in the U937 cells, RA (0.1-1.0 microM) had neither enhancing nor suppressive effect on the antiviral activity of IFN-alpha or beta against the Semliki Forest virus (SFV). However, in the WISH cells, RA had different effects on IFNs alpha and beta. Thus, while RA (0.1-50 microM) invariably suppressed the activity of IFN-alpha, it enhanced the action of IFN-beta at low dose (0.1-1.0 microM) but became suppressive at higher concentrations (greater than or equal to 10 microM). Furthermore, higher antiviral activity was consistently obtained when RA (0.1-10 microM) was added prior to either IFN-alpha or IFN-beta comparing to cultures with IFN alone. In addition, direct correlation between antiviral activity and the amplitude of 2-5 oligoadenylate (A) synthetase activity was not observed. These results suggest that modulation of IFN antiviral activity by RA varies with different systems and is dependent on the sequence of treatment.