Temperate phages are common and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses infecting mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity, and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages reveals at least five distinct prophage-expressed viral defense systems that interfere with infection of lytic and temperate phages that are either closely-related (homotypic defense) or unrelated (heterotypic defense). Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defense systems include a single-subunit restriction system, a heterotypic exclusion system, and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival, and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, that acts as a highly effective counter-defense system. Prophage-mediated viral defense offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defense promotes phage co-evolution.

The maior immediate-early (IE) gene region mapping at coordinates 0.71 to 0.74 in the genome of human cytomegalovirus (HCMV) gives rise to a series of overlapping spliced IE mRNAs that are all under the transcriptional control of the complex IE68 promoter-enhancer region. We show here that one of the phosphorylated nuclear proteins encoded by this region behaves as a powerful but nonspecific trans-activator of gene expression. In transient chloramphenicol acetyltransferase (CAT) assay experiments with Vero cells all relatively weak heterologous target promoters tested, including those of herpes simplex virus IE175 and delayed-early genes, adenovirus E3, the enhancerless simian virus 40 early gene, and the human beta interferon gene, were stimulated between 30and 800-fold by cotransfection with the HindIII C fragment of HCMV (Towne) DNA. In contrast, expression of the homologous HCMV IE68-CAT gene but not SV2-CAT was specifically repressed. Inactivation mapping studies of the effector DNA, together with dose-response comparisons with subclones from the region, revealed that an intact 7. 1-kilobase sequence encompassing both the IE1 and 1E2 coding regions (exons 1 to 5) in the major IE transcription complex was required for both the nonspecific trans-activation and autoregulatory responses. The IEl coding region alone (exons 1 to 4) was inactive, but both functions were restored by insertion of the IE2 coding region (exon 5) in the correct orientation downstream from the IE1 coding region. Internal deletions or inserted terminator codons in IEI (exon 4) still gave efficient trans-activation and autoregulation, whereas the insertion of terminator codons in IE2 (exon 5) abolished both activities. Finally, IE2 (exon 5) sequences only (under the direct transcriptional control of the strong simian CMV IE94 promoter) were still able to specifically down regulate IE68-CAT expression but failed to exhibit trans-activation properties. Therefore, the IE2 gene product(s) of HCMV appear likely to be key control proteins involved in gene regulation during HCMV infection. All of the major classes of DNA viruses that replicate in mammalian cell nuclei encode immediate-early (IE) gene products that behave as trans-activators of subsequent viral gene expression and are themselves under the control of complex upstream protnoters and regulatory or enhancer regions. The large T antigens of papovaviruses, the ElA gene products of adenoviruses, the IE175 (ICP4) and IE110 (ICPO) proteins of herpes simplex virus (HSV), the E2 proteins of papillomaviruses, and the rep gene products of parvoviruses all appear to fit into this classification. They also all share the characteristic of being hydrophilic nuclear phosphoproteins whose mRNAs are synthesized immediately after infection and in the absence of de novo protein synthesis. Most of these proteins are needed within their own systems for efficient synthesis of subsequent viral genes (usually acting at the transcriptional level), but they may also show various degrees of relaxed specificity...

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copies of a consensus response element commonly referred to as the 29,33,51,63), plus, in some cases, an overlapping consensus octamer element, ATGCTAAT (39; C. apRhys, D. M. Ciufo, E. A. O'Neill, T. J. Kelly, and G. S. Hayward, submitted for publication). In addition, 11 CCCGCCC elements, which appear to be associated with basal expression properties of the IE175-IE68 region, have been shown by DNA footprinting studies to bind to the purified cellular Sp-1 factor (25).During HSV infection, the IE175 gene product is essential for progression of the lytic cycle (8, 50, 60) and for activation of the transcription of the delayed-early (DE) class of viral genes (30,31,46,50). The isolated viral DE and late promoters, whether associated with their own genes (11,55) or as hybrid HSV promoter-driven reporter genes, also respond to virus superinfection in an IE175-dependent fashion, both when in an integrated state in permanent DNAtransfected cell lines (6,9,11,12,35,53) and in transientexpression assays with superinfecting virus (14,40). In DNA cotransfection assays, the isolated IE175 gene encodes a trans-acting factor that stimulates expression of HSV DE promoter targets (13,21,41,52) and inhibits expression from its own promoter in IE175- CAT (9,22,42,43). Although the HSV IE110 gene product was shown to stimulate expression 4307 on July 6, 2020 by guest http://jvi.asm.org/ Downloaded from with polynucleotide kinase and [-y-32P]ATP. The two com-J. VIROL.on July 6, 2020 by guest http://jvi.asm.org/ Downloaded from DNA TARGET SITES FOR IE175 BINDING AND AUTOREGULATION plementary oligonucleotides were annealed by heating to 65°C in 50 mM NaCI-10 mM MgCl2-25 mM Tris hydrochloride (pH 8.0)-100 ,ug of bovine serum albumin per ml-2 mM P-mercaptoethanol followed by slow cooling. For cloning, the double-stranded oligonucleotides were ligated after phosphorylation with polynucleotide kinase to BamHI-plus-BglII-cleaved pGH59 DNA. The resulting plasmids, pGH123a and pGH123b, contained sequences from -8 to

The 82-kDa IE2 protein of human cytomegalovirus (HCMV) acts as both a powerful nonspecific trans activator of heterologous promoters and a negative autoregulator of HCMV immediate-early gene expression in transient assays. We show here that the highly specific down-regulation effect occurs in permissive diploid human fibroblast cells as well as in nonpermissive Vero cells and that the target sequences are conserved within the major immediate-early promoters of both HCMV and simian cytomegalovirus. The response sequences were localized between-67 and +30 in the simian cytomegalovirus IE94 promoter and upstream of position +9 in the HCMV IE68 promoter. Deletion of sequences downstream of-14 in a target IE68-CAT gene abolished the negative phenotype and resulted in a reporter gene that was stimulated instead of inhibited by cotransfection with IE2 effector DNA. Insertion of an oligonucleotide containing sequences from between-17 and +9 into the IE68-CAT deletion construction restored autoregulation in either orientation. Furthermore, this same oligonucleotide transferred the full down-regulation phenotype when inserted at +10 into the nonresponsive IE175 promoter from herpes simplex virus. Therefore, a specific response signal that acts at the DNA level must lie within these boundaries. Additional analysis with inserted oligonucleotides containing deletions or point mutations revealed that essential components of the signal lie between positions-12 and +5. Therefore, negative autoregulation by HCMV IE2 in DNA cotransfection systems resembles that for simian virus 40 large T antigen and herpes simplex virus IE175 by acting through a signal located near the cap site, but the target sequence itself bears no resemblance to those utilized in these other viral systems.

The IE2 region of the human cytomegalovirus (CMV) strain Towne major immediate-early (MIE) gene encodes a transcriptional transactivator that stimulates expression from a variety of heterologous target promoters but specifically down-regulates its own promoter. By immunofluorescence and Western immunoblot analysis with monospecific peptide antisera, we found that human CMV MIE exon 5 encodes four overlapping polypeptides, two present at immediate-early times (80 and 55 kDa) and two others detected only at late times after infection (55 and 40 kDa). However, only the 80-kDa version (579 amino acids), which is derived from the small upstream exons 2 and 3 fused to the intact exon 5 region, was functionally active in both transactivation and autoregulation as assessed by cotransfection experiments. These results confirm the corrected assignment of the coding capacity of the exon 5 region based on amino acid homology with the equivalent IE2 protein from simian CMV (Colburn). In transient DNA transfection assays, IE2 expression plasmids also produced a predominant full-length 80-kDa protein, which was localized in a distinctive reticular pattern in the nucleus. Two short basic nuclear localization signals in IE2 were identified by deletion analysis and by conversion of a test cytoplasmic herpes simplex virus protein into a form that localized in the nucleus after insertion of either of these two human CMV motifs. Functional assays with MIE region plasmids containing deletions or truncations in exon 5 revealed that both transactivation and autoregulation required several distinct domains within the COOH half of the IE2 protein, whereas a region between codons 99 and 194 could be discarded. Three segments at the NH2 end of the protein between codons 1 to 85, 86 to 98, and 195 to 290 were also essential for transactivation but played no role in autoregulation. Finally, in domain swap experiments, GAL4-fusion proteins containing either an NH2-terminal 51-amino-acid domain from exon 3 (codons 25 to 85) or the COOH-terminal 33-amino-acid domain from exon 5 (codons 544 to 579) identified two distinct activator domains from IE2, both of which have acidic characteristics.

The vast bacteriophage population harbors an immense reservoir of genetic information. Almost 2000 phage genomes have been sequenced from phages infecting hosts in the phylum Actinobacteria, and analysis of these genomes reveals substantial diversity, pervasive mosaicism, and novel mechanisms for phage replication and lysogeny. Here, we describe the isolation and genomic characterization of 46 phages from environmental samples at various geographic locations in the U.S. infecting a single Arthrobacter sp. strain. These phages include representatives of all three virion morphologies, and Jasmine is the first sequenced podovirus of an actinobacterial host. The phages also span considerable sequence diversity, and can be grouped into 10 clusters according to their nucleotide diversity, and two singletons each with no close relatives. However, the clusters/singletons appear to be genomically well separated from each other, and relatively few genes are shared between clusters. Genome size varies from among the smallest of siphoviral phages (15,319 bp) to over 70 kbp, and G+C contents range from 45–68%, compared to 63.4% for the host genome. Although temperate phages are common among other actinobacterial hosts, these Arthrobacter phages are primarily lytic, and only the singleton Galaxy is likely temperate.

Bees are important plant pollinators in both natural and agricultural ecosystems. Managed and wild bees have experienced high average annual colony losses, population declines, and local extinctions in many geographic regions. Multiple factors, including virus infections, impact bee health and longevity. The majority of bee-infecting viruses are positive-sense single-stranded RNA viruses. Bee-infecting viruses often cause asymptomatic infections but may also cause paralysis, deformity or death. The severity of infection is governed by bee host immune responses and influenced by additional biotic and abiotic factors. Herein, we highlight studies that have contributed to the current understanding of antiviral defense in bees, including the Western honey bee (Apis mellifera), the Eastern honey bee (Apis cerana) and bumble bee species (Bombus spp.). Bee antiviral defense mechanisms include RNA interference (RNAi), endocytosis, melanization, encapsulation, autophagy and conserved immune pathways including Jak/STAT (Janus kinase/signal transducer and activator of transcription), JNK (c-Jun N-terminal kinase), MAPK (mitogen-activated protein kinases) and the NF-κB mediated Toll and Imd (immune deficiency) pathways. Studies in Dipteran insects, including the model organism Drosophila melanogaster and pathogen-transmitting mosquitos, provide the framework for understanding bee antiviral defense. However, there are notable differences such as the more prominent role of a non-sequence specific, dsRNA-triggered, virus limiting response in honey bees and bumble bees. This virus-limiting response in bees is akin to pathways in a range of organisms including other invertebrates (i.e., oysters, shrimp and sand flies), as well as the mammalian interferon response. Current and future research aimed at elucidating bee antiviral defense mechanisms may lead to development of strategies that mitigate bee losses, while expanding our understanding of insect antiviral defense and the potential evolutionary relationship between sociality and immune function.