Open Reading Frame III of Borna Disease Virus Encodes a Nonglycosylated Matrix Protein

The open reading frame III of Borna disease virus (BDV) codes for a protein with a mass of 16 kDa, named p16 or BDV-M. p16 was described as an N-glycosylated protein in several previous publications and therefore was termed gp18, although the amino acid sequence of p16 does not contain any regular consensus sequence for N glycosylation. We examined glycosylation of p16 and studied its membrane topology using antisera raised against peptides, which comprise the N and the C termini. Neither an N- nor a C-terminal peptide is cleaved from p16 during maturation. Neither deglycosylation of p16 by endoglycosidases nor binding of lectin to p16 was detectable. Introduction of typical N-glycosylation sites at the proposed sites of p16 failed in carbohydrate attachment. Flotation experiments with membranes of BDV-infected cells on density gradients revealed that p16 is not an integral membrane protein, since it can be dissociated from membranes. Our experimental data strongly suggest that p16 is a typical nonglycosylated matrix protein associated at the inner surface of the viral membrane, as is true for homologous proteins of other members of the Mononegavirales order.     

The UL2 Open Reading Frame of Bovine Herpesvirus 1 Encodes a Uracil-DNA Glycosylase

Sequence analysis within the unique long segment of the bovine herpesvirus 1 (BHV-1) genome previously identified an open reading frame (ORF), designated UL2, whose deduced polypeptide of 204 amino acids contained a consensus uracil-DNA glycosylase (UDGase) signature sequence. To determine whether the BHV-1 UL2 ORF product has UDGase activity, we positioned the UL2 sequence downstream of the T7 promoter on the vector pET-28b(+) and expressed it in Escherichia coli. Upon induction with isopropyl β-D -thiogalactopyranoside these cells produced a 23-kDa protein, the molecular mass of which was in accordance with the prediction from the nucleotide sequence. A one-step purification procedure using nickel-chelating affinity chromatography resulted in a homogeneous preparation of this protein, which displayed specific UDGase activity in an in vitro enzyme assay. These results provide evidence that the BHV-1 UL2 gene does encode a UDGase.     

Open Reading Frame 33 of a Gammaherpesvirus Encodes a Tegument Protein Essential for Virion Morphogenesis and Egress

Tegument is a unique structure of herpesvirus, which surrounds the capsid and interacts with the envelope. Morphogenesis of gammaherpesvirus is poorly understood due to lack of efficient lytic replication for Epstein-Barr virus and Kaposi''s sarcoma-associated herpesvirus/human herpesvirus 8, which are etiologically associated with several types of human malignancies. Murine gammaherpesvirus 68 (MHV-68) is genetically related to the human gammaherpesviruses and presents an excellent model for studying de novo lytic replication of gammaherpesviruses. MHV-68 open reading frame 33 (ORF33) is conserved among Alpha-, Beta-, and Gammaherpesvirinae subfamilies. However, the specific role of ORF33 in gammaherpesvirus replication has not yet been characterized. We describe here that ORF33 is a true late gene and encodes a tegument protein. By constructing an ORF33-null MHV-68 mutant, we demonstrated that ORF33 is not required for viral DNA replication, early and late gene expression, viral DNA packaging or capsid assembly but is required for virion morphogenesis and egress. Although the ORF33-null virus was deficient in release of infectious virions, partially tegumented capsids produced by the ORF33-null mutant accumulated in the cytoplasm, containing conserved capsid proteins, ORF52 tegument protein, but virtually no ORF45 tegument protein and the 65-kDa glycoprotein B. Finally, we found that the defect of ORF33-null MHV-68 could be rescued by providing ORF33 in trans or in an ORF33-null revertant virus. Taken together, our results indicate that ORF33 is a tegument protein required for viral lytic replication and functions in virion morphogenesis and egress.Gammaherpesviruses are associated with tumorigenesis. Like other herpesviruses, they are characterized as having two distinct stages in their life cycle: lytic replication and latency (15, 16, 18, 21, 54). Latency provides the viruses with advantages to escape host immune surveillance and to establish lifelong persistent infection and contributes to transformation and development of malignancies. However, it is through lytic replication that viruses propagate and transmit among hosts to maintain viral reservoirs. Both viral latency and lytic replication play important roles in tumorigenesis. The gammaherpesvirus subfamily includes Epstein-Barr virus (EBV), Kaposi''s sarcoma-associated herpesvirus (KSHV)/human herpesvirus 8 and murine gammaherpesvirus 68 (MHV-68), among others. EBV is associated with Burkitt''s lymphoma, nasopharyngeal carcinoma, Hodgkin''s disease, and lymphoproliferative diseases in immunodeficient patients (28). KSHV is etiologically linked with Kaposi''s sarcoma, primary effusion lymphoma, and multicentric Castleman''s disease (11-13, 22, 52). Neither in vivo nor in vitro studies of EBV and KSHV are convenient due to their propensity to establish latency in cell culture and their limited host ranges.MHV-68 is genetically related to these two human gammaherpesviruses, especially to KSHV, based on the alignment of their genomic sequences and other biological properties (55). As a natural pathogen of wild rodents, MHV-68 also infects laboratory mice (6, 40, 46) and replicates to a high titer in a variety of fibroblast and epithelial cell lines. These advantages make MHV-68 an excellent model for studying the lytic replication of gammaherpesviruses in vitro and certain aspects of virus-host interactions in vivo. In addition, the MHV-68 genome has been cloned as a bacterial artificial chromosome (BAC) that can propagate in Escherichia coli (1, 2, 36, 51), making it convenient to study the function of each open reading frame (ORF) by genetic methods. Exploring the functions of MHV-68 ORFs will likely shed light on the functions of their homologues in human gammaherpesviruses.Gammaherpesviral particles have a characteristic multilayered architecture. An infectious virion contains a double-stranded DNA genome, an icosahedral capsid shell, a thick, proteinaceous tegument compartment, and a lipid bilayer envelope spiked with glycoproteins (14, 30, 47, 49). As a unique structure of herpesviruses, the tegument plays important roles in multiple aspects of the viral life cycle, including virion assembly and egress (38, 48, 53), translocation of nucleocapsids into the nucleus, transactivation of viral immediate-early genes, and modulation of host cell gene expression, innate immunity, and signal transduction (9, 10, 23, 60). Some components of MHV-68 tegument have been identified by a mass spectrometric study (8), and the functions of some tegument proteins have been revealed, such as ORF45, ORF52, and ORF75c (7, 24, 29).MHV-68 ORF33 is conserved among Alpha-, Beta-, and Gammaherpesvirinae subfamilies. Its homologues include human herpes simplex virus type 1 (HSV-1) UL16, human herpes simplex virus type 2 (HSV-2) UL16, human cytomegalovirus (HCMV) UL94, EBV BGLF2, KSHV ORF33, and rhesus monkey rhadinovirus (RRV) ORF33. HSV-1 UL16 has been identified as a tegument protein and may function in viral DNA packaging, virion assembly, budding, and egress (5, 32, 35, 41, 44). HCMV UL94 is a virion associated protein and might function in virion assembly and budding (31, 57). EBV BGLF2, KSHV ORF33, and RRV ORF33 are also virion-associated proteins, but their functions are not clear (26, 43, 59). The mass spectrometric study of MHV-68 did not identify ORF33 as a virion component (8), although ORF33 is found to be essential for viral lytic replication by transposon mutagenesis of the MHV-68 genome cloned as a BAC (51). However, insertion of the 1.2-kbp Mu transposon in that study may influence the expression of ORFs approximate to ORF33. Consequently, the role ORF33 plays in viral replication needs to be confirmed, preferably through site-directed mutagenesis. Whether ORF33 is a tegument protein and the exact viral replication stage in which it functions also need to be investigated.We determined that MHV-68 ORF33 encodes a tegument protein and is expressed with true late kinetics. To explore the function of ORF33 in viral lytic phase, we used site-directed mutagenesis and generated an ORF33-null mutant, taking advantage of the MHV-68 BAC system. We showed that the ORF33-null mutant is capable of viral DNA replication, early and late gene expression, capsid assembly, and DNA packaging, but incapable of virion release. The defect of ORF33-null mutant can be rescued in trans by an ORF33 expression plasmid.     

An Upstream Open Reading Frame in Phosphatase and Tensin Homolog Encodes a Circuit Breaker of Lactate Metabolism

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Human Herpesvirus 6 Open Reading Frame U12 Encodes a Functional β-Chemokine Receptor

Human herpesvirus 6 (HHV-6), which belongs to the betaherpesvirus subfamily and infects mainly T cells in vitro, causes acute and latent infections. HHV-6 contains two genes (U12 and U51) that encode putative homologs of cellular G-protein-coupled receptors (GCR), while three other betaherpesviruses, human cytomegalovirus, murine cytomegalovirus, and human herpesvirus 7, have three, one, and two GCR-homologous genes, respectively. The U12 gene is expressed late in infection from a spliced mRNA. The U12 gene was cloned, and the protein was expressed in cells and analyzed for its biological characteristics. U12 functionally encoded a calcium-mobilizing receptor for β-chemokines such as regulated upon activation, normal T expressed and secreted (RANTES), macrophage inflammatory proteins 1α and 1β (MIP-1α and MIP-1β) and monocyte chemoattractant protein 1 but not for the α-chemokine interleukin-8, suggesting that the chemokine selectivity of the U12 product was distinct from that of the known mammalian chemokine receptors. These findings suggested that the product of U12 may play an important role in the pathogenesis of HHV-6 through transmembrane signaling by binding with β-chemokines.     

Reverse Genetics Identifies the Product of Open Reading Frame 4 as an Essential Particle Assembly Factor of Nyamanini Virus

We established a reverse genetics system for Nyamanini virus (NYMV) and recovered green fluorescent protein (GFP)-expressing virus from full-length cDNA. Using this technology, we assessed the functions of two poorly characterized viral genes. NYMV lacking open reading frame 2 (ORF2) could not be rescued, whereas virus lacking ORF4 was replication competent. ORF4-deficient NYMV readily established a persisting noncytolytic infection but failed to produce infectious viral particles, supporting the view that ORF4 represents an essential factor for NYMV particle assembly.     

Evolutionary Conservation of the PA-X Open Reading Frame in Segment 3 of Influenza A Virus

PA-X is a fusion protein of influenza A virus encoded in part from a +1 frameshifted X open reading frame (X-ORF) in segment 3. We show that the X-ORFs of diverse influenza A viruses can be divided into two groups that differ in selection pressure and likely function, reflected in the presence of an internal stop codon and a change in synonymous diversity. Notably, truncated forms of PA-X evolved convergently in swine and dogs, suggesting a strong species-specific effect.     

Frog Virus 3 Open Reading Frame 97R Localizes to the Endoplasmic Reticulum and Induces Nuclear Invaginations

Frog virus 3 (FV3) is the type species of the genus Ranavirus, family Iridoviridae. The genome of FV3 is 105,903 bases in length and encodes 97 open reading frames (ORFs). The FV3 ORF 97R contains a B-cell lymphoma 2 (Bcl-2) homology 1 (BH1) domain and has sequence similarity to the myeloid cell leukemia-1 (Mcl-1) protein, suggesting a potential role in apoptosis. To begin to understand the role of 97R, we characterized 97R through immunofluorescence and mutagenesis. Here we demonstrated that 97R localized to the endoplasmic reticulum (ER) at 24 h posttransfection. However, at 35 h posttransfection, 97R localized to the ER but also began to form concentrated pockets continuous with the nuclear membrane. After 48 h posttransfection, 97R was still localized to the ER, but we began to observe the ER and the outer nuclear membrane invaginating into the nucleus. To further explore 97R targeting to the ER, we created a series of C-terminal transmembrane domain deletion mutants. We found that deletion of 29 amino acids from the C terminus of 97R abolished localization to the ER. In contrast, deletion of 12 amino acids from the C terminus of 97R did not affect 97R localization to the ER. In addition, a hybrid protein containing the 97R C-terminal 33 amino acids was similarly targeted to the ER. These data indicate that the C-terminal 33 amino acids of 97R are necessary and sufficient for ER targeting.     

The Hepatitis E Virus Open Reading Frame 3 Product Interacts with Microtubules and Interferes with Their Dynamics

Hepatitis E virus (HEV) is the causative agent of hepatitis E, a major form of viral hepatitis in developing countries. The open reading frame 3 (ORF3) of HEV encodes a phosphoprotein with a molecular mass of approximately 13 kDa (hereinafter called vp13). vp13 is essential for establishing HEV infections in animals, yet its exact functions are still obscure. Our current study found evidence showing interaction between vp13 and microtubules. Live-cell confocal fluorescence microscopy revealed both filamentous and punctate distribution patterns of vp13 in cells transfected with recombinant ORF3 reporter plasmids. The filamentous pattern of vp13 was altered by a microtubule-destabilizing drug. The vp13 expression led to elevation of acetylated α-tubulin, indicating increased microtubule stability. Its association with microtubules was further supported by its presence in microtubule-containing pellets in microtubule isolation assays. Exposure of these pellets to a high-salt buffer caused release of the vp13 to the supernatant, suggesting an electrostatic interaction. Inclusion of ATP and GTP in the lysis buffer during microtubule isolation also disrupted the interaction, indicating its sensitivity to the nucleotides. Further assays showed that motor proteins are needed for the vp13 association with the microtubules because disruption of dynein function abolished the vp13 filamentous pattern. Analysis of ORF3 deletion constructs found that both of the N-terminal hydrophobic domains of vp13 are needed for the interaction. Thus, our findings suggest that the vp13 interaction with microtubules might be needed for establishment of an HEV infection.The hepatitis E virus (HEV), the sole member of the genus Hepevirus, is a single-strand positive-sense RNA virus that is the causative agent in endemics and epidemics of acute human hepatitis in many parts of the world (5). Transmitted mainly from contaminated water through the fecal-oral route, HEV infection causes a fulminant form of hepatitis that has a mortality rate of up to 20% in pregnant women (28). HEV infection is considered zoonotic. Swine and chicken HEV strains have been found in the United States (11, 23). A swine strain can infect chimpanzees under experimental conditions, and a human strain that is genetically similar to the swine strain can experimentally infect pigs (22). Direct evidence of the zoonotic nature of HEV infection has been provided in reports of a series of cases of HEV infection in people who ate undercooked deer meat 6 to 7 weeks before the onset of the disease (19, 33, 39). HEV RNA recovered from the leftover deer meat was found to be identical in nucleotide sequence to the HEV RNA recovered from the individuals who became ill (31).The HEV genome is approximately 7.2 kb in length and consists of three open reading frames (ORFs) (32). ORF1 encodes a nonstructural polyprotein that includes the RNA-dependent RNA polymerase. ORF2 encodes the capsid protein, the major structural protein in virion. ORF3 encodes a phosphoprotein that was found to be essential for establishing an HEV infection in macaques and pigs under experimental conditions (9, 12). It has been reported that ORF3 translation initiates at the third in-frame AUG codon, which lies 23 bases downstream of the ORF1 termination codon (10, 12). Propagation of HEV and studies of virus replication still rely upon nonhuman primates due to the lack of an effective cell culture system. As a result, functional study of the ORF3 product in HEV biology and infection is limited.The phosphoprotein encoded by HEV ORF3 has a molecular mass of approximately 13 kDa (hereinafter called vp13) (32). The exact functions of vp13 in HEV infection remain unknown although the findings of a number of studies have shown that it plays a role in cellular signaling pathways (13, 17, 24, 34-36, 40). During subcellular fractionation of COS-7 cells transfected with a vp13-expressing plasmid, vp13 was found to partition with the cytoskeletal fraction (40). Deletion of the N-terminal hydrophobic domain of vp13 abolished the association with the cytoskeleton fraction. The vp13-binding proteins in the cytoskeleton and the nature of this interaction are not known.In this study, we found that the HEV ORF3 product localizes to microtubules and interferes with their dynamics. The filamentous pattern of vp13 distribution in the cell was abolished by a microtubule-destabilizing drug. vp13 led to elevation of acetylated α-tubulin. These results suggested that vp13 interaction with the microtubules might facilitate HEV infection. We further studied the nature of the vp13-microtubule interaction.     

Enumeration of an Extremely High Particle-to-PFU Ratio for Varicella-Zoster Virus

Varicella-zoster virus (VZV) is renowned for its low titers. Yet investigations to explore the low infectivity are hampered by the fact that the VZV particle-to-PFU ratio has never been determined with precision. Herein, we accomplish that task by applying newer imaging technology. More than 300 images were taken of VZV-infected cells on 4 different samples at high magnification. We enumerated the total number of viral particles within 25 cm² of the infected monolayer at 415 million. Based on these numbers, the VZV particle:PFU ratio was approximately 40,000:1 for a cell-free inoculum.A precise ratio of particles to PFU of varicella-zoster virus (VZV) has never been determined, even though VZV was first isolated in cell culture by the Nobel laureate T. H. Weller in 1952 (21). His group determined that VZV replicated in a few embryonic tissues and in amnion cells. Subsequently, Taylor-Robinson and Caunt found that VZV replication was restricted to a small number of mainly embryonic cells by testing more than 20 primary and continuous cell lines (19). A decade later, VZV was propagated in melanoma cell lines, which are derived from the neural crest (8). In all of these cultured cells, the titer was found to be low, particularly when compared with that of the closely related herpes simplex type 1 virus (HSV-1). Again, in sharp contrast with HSV-1, the virus remained strongly cell associated.The term particle/PFU ratio refers to the number of viral particles required to form one plaque in a plaque assay. It is a measure of the efficiency by which a virus infects cultured cells. Early in the 1960s, investigators began using negative staining electron microscopy to count viral particles in inoculum material and compare those counts to the measured titer, thereby measuring ratios for a few animal viruses (6). For example, the ratio for HSV-1 is around 10:1 (10, 20). Due to the strong cell association of VZV infection of cultured cells, no precise VZV particle/PFU ratio has ever been determined. The lack of any widely accepted VZV ratio severely limits our ability to assess whether mutated or recombinant viruses produce more or fewer complete infectious particles in cultured cells (4, 5, 15, 17). In other words, if an attenuated virus has a lower titer, we do not know whether fewer viral particles are produced per square centimeter of cellular monolayer (without a change in the particle/PFU ratio) or alternatively fewer infectious viral particles are produced overall (with a higher particle/PFU ratio).In this report, we successfully define a VZV particle/PFU ratio by imaging viral particles with advanced scanning electron microscopic (SEM) technology not available during our earlier investigations of viral structure (12). We demonstrate that the VZV ratio is much higher than that for other common human viruses grown in cultured cells and remarkably higher than that for HSV. Finally, this report documents evidence of an ever-widening difference between HSV and VZV replication and assembly in cultured cells (7, 13, 18).     

The Mycobacteriophage D29 Gene 65 Encodes an Early-Expressed Protein That Functions as a Structure-Specific Nuclease

The genomes of mycobacteriophages of the L5 family, which includes the lytic phage D29, contain several genes putatively linked to DNA synthesis. One such gene is 65, which encodes a protein belonging to the RecA/DnaB helicase superfamily. In this study a recombinant version of the mycobacteriophage D29 gp65 was functionally characterized. The results indicated that it is not a helicase as predicted but an exonuclease that removes 3′ arms from forked structures in an ATP-dependent manner. The gp65 exonuclease acts progressively from the 3′ end, until the fork junction is reached. As it goes past, its progress is stalled over a stretch of seven to eight nucleotides immediately downstream of the junction. It efficiently acts on forked structures with single stranded arms. It also acts upon 5′ and 3′ flaps, though with somewhat relaxed specificity, but not on double-stranded forks. Sequence comparison revealed the presence of a KNRXG motif in the C-terminal half of the protein. This is a conserved element found in the RadA/Sms family of DNA repair proteins. A mutation (R203G) in this motif led to complete loss of nuclease activity. This indicated that KNRXG plays an important role in the nuclease function of not only gp65, but possibly other RadA/Sms family proteins as well. This is the first characterization of a bacteriophage-derived RadA/Sms class protein. Given its mode of action, it is very likely that gp65 is involved in processing branched replication intermediates formed during the replication of phage DNA.Fork structures are intricately associated with DNA replication. Such structures result due to unwinding of the DNA ahead of the replicating machinery. The unwound single strands are then used as templates for the synthesis of the new strands, either continuously (leading strand) or discontinuously (lagging strand). Repair of stalled forks involve complex mechanisms which may vary from one organism to another (5). However, in most cases the process requires nucleases that recognize stalled fork structures and cleave them specifically. Such nucleases are generally referred to as structure-specific nucleases (25). One such nuclease named FEN1 found in eukaryotes has been studied fairly extensively, and it is believed that this nuclease is involved in the removal of 5′ flaps from Okazaki fragments (11, 23). FEN1 belongs to a larger family of structure-specific nucleases, which includes human XPG (17), an endonuclease related to the disease xeroderma pigmentosa. Although the XPG family is associated with the removal of 5′ flaps the XPF type proteins are needed for removing the 3′ flaps (3). Similar proteins have been found in several Archaea (28). In Escherichia coli, the Holliday junction resolving enzyme system RuvABC is believed to be involved in resolving stalled forks by creating double-stranded breaks, which may be repaired through homologous recombination (29). Studies in E. coli have revealed that there are multiple redundant pathways that are capable of repairing stalled forks. One such pathway involves a protein named RadA/Sms, the absence of which results in partial increase in sensitivity to radiation in E. coli (2). Genes encoding RadA/Sms family proteins are present in many bacteria, including mycobacteria. Most of these members carry a conserved element KNRFG. It is believed (2) that RadA/Sms family of proteins may generate double-stranded breaks at fork junctions, although this has not been specifically demonstrated.Mycobacteriophages of the L5 family, which includes D29, BxB1, may be either temperate or potentially temperate (D29) (14, 15, 27). Despite their temperate character these phages share a strong resemblance with lytic phages. An important feature shared by lytic phages in general is their ability to synthesize DNA using phage-encoded DNA polymerases (13). They also possess many genes linked to nucleotide metabolism. It appears that as far as DNA replication is concerned, lytic phages prefer to be self-sufficient. This is apparently an important issue since lytic phages inactivate their host and therefore host-specific functions cannot be used to support phage growth.Following the availability of the genome sequence, many interesting aspects of mycobacteriophages have come to light. The central region of mycobacteriophage L5/D29 genome has been predicted to harbor several genes whose products may contribute directly or indirectly toward synthesis of new DNA strands. In a recent investigation from this laboratory it has been demonstrated (4) that at least some of the genes in this region are involved in the production of deoxyribonucleotide precursors which are probably needed at increased levels during phage replication. Apart from these genes there are several others which probably encode DNA polymerization related functions. One such gene that drew our interest was gene 65, which appears to encode a RecA/DnaB helicase superclass protein (22). The N-terminal region of this protein contains the Walker motifs A and B, which are characteristically present in the members of the RecA/DnaB superfamily. Walker motifs A and B (30) are found in proteins that hydrolyze ATP for executing their respective functions. To investigate the possible function of gp65, its gene was overexpressed in E. coli, and the recombinant protein was purified. Assays performed with the recombinant gp65 revealed that it is a structure-specific nuclease that acts exonucleolytically on fork structures, resulting in truncated forms lacking the 3′ arm. This function was demonstrated to require a particular motif KNRXG that is omnipresent in the RadA/Sms family of proteins (2). This characterization of D29 gp65 could give us better insight into how mycobacteriophages replicate their DNA within their hosts.     

Long Open Reading Frame Transcripts Escape Nonsense-Mediated mRNA Decay in Yeast

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