Identification of a novel transcriptional repressor encoded by human cytomegalovirus

UL34 Deletion Restricts Human Cytomegalovirus Capsid Formation and Maturation

Over 50% of the world’s population is infected with Human Cytomegalovirus (HCMV). HCMV is responsible for serious complications in the immuno-compromised and is a leading cause of congenital birth defects. The molecular function of many HCMV proteins remains unknown, and a deeper understanding of the viral effectors that modulate virion maturation is required. In this study, we observed that UL34 is a viral protein expressed with leaky late kinetics that localises to the nucleus during infection. Deletion of UL34 from the HCMV genome (ΔUL34) did not abolish the spread of HCMV. Instead, over >100-fold fewer infectious virions were produced, so we report that UL34 is an augmenting gene. We found that ΔUL34 is dispensable for viral DNA replication, and its absence did not alter the expression of IE1, MCP, gB, UL26, UL83, or UL99 proteins. In addition, ΔUL34 infections were able to progress through the replication cycle to form a viral assembly compartment; however, virion maturation in the cytoplasm was abrogated. Further examination of the nucleus in ΔUL34 infections revealed replication compartments with aberrant morphology, containing significantly less assembled capsids, with almost none undergoing subsequent maturation. Therefore, this work lays the foundation for UL34 to be further investigated in the context of nuclear organization and capsid maturation during HCMV infection.

Mouse Cytomegalovirus M34 Encodes a Non-essential, Nuclear, Early-Late Expressed Protein Required for Efficient Viral Replication

Human cytomegalovirus (HCMV) is a prototypic betaherpesvirus which causes severe manifestations in individuals with impaired or immature immunity. To investigate cytomegalovirus-induced pathogenesis and virus-specific immune responses, mouse cytomegalovirus (MCMV) infections in mice are employed as accepted small animal model. MCMV and HCMV share co-linear genomes and encode several homologous proteins. Due to the size and complexity of CMV genomes, the molecular functions of numerous cytomegaloviral gene products remain to be elucidated. While the essential nature of viral genes highlights their biological relevance, it renders functional studies particularly cumbersome by precluding experiments in the infection context. The HCMV-encoded protein pUL34 binds the HCMV genome and regulates viral gene expression (e.g., of US3). Several groups provided compelling evidence that UL34 is essential for HCMV replication. MCMV encodes the homologous protein pM34 (34% identical and 55% similar). Based on unsuccessful attempts to reconstitute M34-deficient virus from a bacterial artificial chromosome (BAC), M34 was previously classified as essential for MCMV replication. To characterize pM34 during viral infection, we engineered and analyzed an MCMV mutant expressing an HA-epitope-tagged pM34 which was expressed with early-late kinetics and localized in the nucleus. Additionally, we generated an M34-deficient (“ΔM34”) MCMV-BAC by replacing the entire M34 coding sequence by a kanamycin resistance cassette. The deletion of M34 was confirmed by Southern blot and PCR. Unexpectedly, we could reconstitute replicating ΔM34-MCMV upon transfection of the BAC DNA into mouse embryonic fibroblasts. The absence of M34 from the genome of the replicating ΔM34-MCMV was also confirmed. Accordingly, a ΔM34-MCMV, in which the kanamycin cassette was excised by frt/Flp-mediated recombination, was also replication competent. In order to corroborate the absence of pM34 protein, the M34 deletion was recapitulated on the background of M34HA, which yielded replicating virus devoid of detectable pM34HA protein. The replication of MCMVs lacking M34 was found to be 10- to 100-fold reduced as compared to wt-MCMV which might explain previous unsuccessful reconstitution attempts conducted by others. Taken together, our findings reveal that MCMV remains replication competent despite the absence of M34, enabling functional studies in the infection context.

pUL34 binding near the human cytomegalovirus origin of lytic replication enhances DNA replication and viral growth

The human cytomegalovirus (HCMV) UL34 gene encodes sequence-specific DNA-binding proteins (pUL34) which are required for viral replication. Interactions of pUL34 with DNA binding sites represses transcription of two viral immune evasion genes, US3 and US9. 12 additional predicted pUL34-binding sites are present in the HCMV genome (strain AD169) with three binding sites concentrated near the HCMV origin of lytic replication (oriLyt). We used ChIP-seq analysis of pUL34-DNA interactions to confirm that pUL34 binds to the oriLyt region during infection. Mutagenesis of the UL34-binding sites in an oriLyt-containing plasmid significantly reduced viral-mediated oriLyt-dependent DNA replication. Mutagenesis of these sites in the HCMV genome reduced the replication efficiencies of the resulting viruses. Protein-protein interaction analyses demonstrated that pUL34 interacts with the viral proteins IE2, UL44, and UL84, that are essential for viral DNA replication, suggesting that pUL34-DNA interactions in the oriLyt region are involved in the DNA replication cascade.

Quantitative temporal viromics: an approach to investigate host-pathogen interaction

A systematic quantitative analysis of temporal changes in host and viral proteins throughout the course of a productive infection could provide dynamic insights into virus-host interaction. We developed a proteomic technique called “quantitative temporal viromics” (QTV), which employs multiplexed tandem-mass-tag-based mass spectrometry. Human cytomegalovirus (HCMV) is not only an important pathogen but a paradigm of viral immune evasion. QTV detailed how HCMV orchestrates the expression of >8,000 cellular proteins, including 1,200 cell-surface proteins to manipulate signaling pathways and counterintrinsic, innate, and adaptive immune defenses. QTV predicted natural killer and T cell ligands, as well as 29 viral proteins present at the cell surface, potential therapeutic targets. Temporal profiles of >80% of HCMV canonical genes and 14 noncanonical HCMV open reading frames were defined. QTV is a powerful method that can yield important insights into viral infection and is applicable to any virus with a robust in vitro model.

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>8,000 proteins quantified over eight time points, including 1,200 cell-surface proteins

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Temporal profiles of 139/171 canonical HCMV proteins and 14 noncanonical HCMV ORFs

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Multiple families of cell-surface receptors selectively modulated by HCMV

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Multiple signaling pathways modulated during HCMV infection

Human cytomegalovirus UL34 early and late proteins are essential for viral replication

UL34 is one of the ~50 genes of human cytomegalovirus (HCMV) required for replication in cell culture in human fibroblasts. UL34 encodes highly related early (UL34a) and late (UL34b) proteins that are virtually identical, with the early protein containing an additional 21 amino terminal amino acids. The UL34 proteins are sequence-specific DNA‑binding proteins that localize to the nucleus. The HCMV genome contains 14 to 15 UL34 binding sites; two of the UL34 binding sites contribute to transcriptional regulation of two other viral genes, US3 and US9. The roles of the remaining binding sites and the requirement for both UL34 proteins during viral infection remain unknown. We examined the contributions of the early and late UL34 proteins to viral replication by generating HCMV-containing bacterial artificial chromosomes with the initiation codon for the early or the late protein mutated. Neither virus was able to replicate, demonstrating that UL34 expression is required throughout the viral replication cycle. A marked decrease in viral gene expression for each of the mutants suggests that UL34 proteins may contribute generally to transcriptional regulation. Intracellular localization studies demonstrated that UL34 colocalizes with the major immediate early protein, IE2, and the viral DNA polymerase processivity factor, UL44, to viral DNA replication centers. In conclusion, sustained UL34 protein expression is required for viral replication. The sequence-specific DNA binding ability of UL34 proteins, their localization to viral DNA replication centers and their general effects on viral gene expressions suggests that UL34 proteins contribute to the establishment of a nuclear environment necessary for viral gene expression and DNA replication.

Nontraditional localization and retention signals localize human cytomegalovirus pUL34 to the nucleus

The human cytomegalovirus (HCMV) UL34 proteins localize to the nucleus. We identified a 204-amino-acid region, amino acids 40 to 244, as required for nuclear retention. A highly conserved 12-amino-acid section, amino acids 198 to 210, was required for nuclear localization. Although the nuclear localization and retention signals of pUL34 overlap the domain required for DNA-binding activity, the two regions are separable by point mutations. Our results presented here identify the first example of an HCMV protein with separable nuclear localization and retention signals.

Human cytomegalovirus UL34 binds to multiple sites within the viral genome

The human cytomegalovirus UL34 gene encodes a sequence-specific DNA binding protein that downregulates expression of the viral immune evasion gene US3. Analysis of the viral genome identified 14 potential UL34 binding sites. Using mobility shift experiments, UL34 bound to all predicted sites that were assayed (7 of 14). Furthermore, the UL34 binding site present within the regulatory region of the US9 gene downregulates expression in a manner similar to that seen for the US3 gene.

Human CMV transcripts: an overview

The human CMV (HCMV) genome consists of an approximately 230-kb dsDNA and is predicted to contain over 165 open reading frames. Although the entire sequence of the laboratory-adapted AD169 strain of HCMV was first available in 1991, the precise number and nature of viral genes and gene products are still unclear. Fewer than 100 predicted genes have been convincingly elucidated with respect to their expression patterns, transcript structure and transcription characteristics. The high gene number of HCMV creates a crowded genome with many overlapping transcriptional units. 3´- or 5´-coterminal overlapping polycistronic transcripts could use a common promoter element or a poly-A signal. 3´-coterminal monocistronic transcripts could encode 'nested' open reading frames, which possess different initiation but the same termination sites. As a virus with eukaryotic cells as the host, HCMV has the capacity to splice out introns during transcription. Major alternately spliced mRNA species of HCMV originate primarily, but not exclusively, from the immediate early gene regions. Alternate splicing patterns of the mRNAs could encode a number of gene products with different sizes. In recent years, some antisense and noncoding transcripts of HCMV have been reported. These RNAs probably have functions in genomic replication or the regulation of gene expression.

Human cytomegalovirus: host immune modulation by the viral US3 gene

Human cytomegalovirus (HCMV) is a common infection, opportunistically causing disease in people with immune system deficits. HCMV expresses several proteins that contribute to avoidance of the host immune response. The US3 gene is one of the first immune evasion genes expressed following infection. Expression of the US3 gene is highly regulated, with the gene encoding autoregulatory proteins. The largest of the US3 proteins, a 22 kDa resident endoplasmic reticulum protein, binds to MHC class I heavy chain complexes and components of the peptide loading complex, delaying the maturation of the MHC class I complexes and presentation of viral antigen on the surface of infected cells. A smaller US3 protein, a 17 kDa US3 protein, competes with the 22 kDa for protein interactions, counteracting, in part, the effects of the larger protein. The US3 amino acid sequence is highly conserved among clinical isolates and laboratory strains, suggesting an important role for this gene in natural infections in the human host.

Preliminary characterization of murine cytomegaloviruses with insertional and deletional mutations in the M34 open reading frame

A viable virus could not be recovered from a mutant murine cytomegalovirus (MCMV) BAC in which the M34 ORF had been deleted (BACDeltaM34). In contrast, an M34 mutant virus (RcM34), in which the M34 ORF was interrupted by transposon insertion at nt 44,827 of the Smith MCMV BAC, was attenuated in replication both in tissue culture and in SCID mice. Similarly, mutant virus Rc3'DeltaM34, in which the 3'-end was deleted from nt 44,724 to nt 45,647, produced similar replication kinetics in tissue culture to RcM34 while BAC5'DeltaM34, in which the 5'-end from nt 43,083 up to nt 44,896 was deleted, was non-viable like BACDeltaM34. A transcript analysis of wt and RcM34 virus-infected cells showed that a truncated transcript encoding a putative protein of 624 amino acids was produced by RcM34, of which the amino terminal 582 amino acids would be identical to the predicted wt 854 amino acids product. Recent, re-annotations of the MCMV genome have identified three putative M34 overlapping ORFs (m33.1, m34.1, and m34.2) that may be interrupted in the above mutants. All three were transcribed in RcM34 virus-infected cells confirming that the RcM34 virus phenotype was probably due to interruption of the M34 ORF. These results suggest that M34, like human CMV UL34, is an essential gene.

Identification of the functional domains of the essential human cytomegalovirus UL34 proteins

The human cytomegalovirus UL34 gene represses expression of the US3 immune evasion gene and is essential for viral replication in cell culture. Two highly related proteins, an early and a late protein, are synthesized at different times during infection from the UL34 gene. The late protein differs from the early protein only by the omission of 21 amino terminal amino acids. Both UL34 proteins repress expression of the US3 promoter and bind specifically to a DNA element in the US3 gene. We have localized the DNA-binding domain of the UL34 open reading frame to amino acids 22 to 243. Surprisingly, this same region of the UL34 open reading frame was also sufficient for transcriptional repression of US3 expression. The UL34 gene is unusual in encoding proteins that have extensively overlapping DNA-binding and transcriptional regulatory domains.

Characterization of the human cytomegalovirus UL34 gene

UL34 encodes the transcriptional repressor of the human cytomegalovirus immune evasion gene, US3, and is essential for viral replication in tissue culture. Two different monocistronic transcripts originate from UL34 at early and late times postinfection and encode two predominant proteins and a third, minor protein. The UL34 proteins are differentially expressed throughout the viral replication cycle, with both proteins localizing to the nucleus and repressing expression of the US3 gene.

Reevaluation of human cytomegalovirus coding potential

The Bio-Dictionary-based Gene Finder was used to reassess the coding potential of the AD169 laboratory strain of human cytomegalovirus and sequences in the Toledo strain that are missing in the laboratory strain of the virus. The gene-finder algorithm assesses the potential of an ORF to encode a protein based on matches to a database of amino acid patterns derived from a large collection of proteins. The algorithm was used to score all human cytomegalovirus ORFs with the potential to encode polypeptides >/=50 aa in length. As a further test for functionality, the genomes of the chimpanzee, rhesus, and murine cytomegaloviruses were searched for orthologues of the predicted human cytomegalovirus ORFs. The analysis indicates that 37 previously annotated ORFs ought to be discarded, and at least nine previously unrecognized ORFs with relatively strong coding potential should be added. Thus, the human cytomegalovirus genome appears to contain approximately 192 unique ORFs with the potential to encode a protein. Support for several of the predictions of our in silico analysis was obtained by sequencing several domains within a clinical isolate of human cytomegalovirus.

Cellular proteins bind to sequence motifs in the R1 element between the HCMV immune evasion genes

The viral US3 and US6 gene products of human cytomegalovirus (CMV) are sequentially expressed at immediate-early and early times after infection, respectively. They downregulate the surface expression of HLA class I molecules. There are two repeat-containing regulatory regions between the US3 promoter and the US6 transcription unit designated R1 and R2. R2 contains repetitions of the NF-kappa B responsive element and enhances the immediate-early expression of the US3 gene. R1 contains 19 repetitions of a 5'-TRTCG-3' pentanucleotide arranged as everted repeats, inverted repeats, and variably spaced single pentanucleotides. In the context of the viral genome, R1 also enhances immediate-early US3 gene expression by an unknown mechanism (G. C. Bullock, et al., 2001, Virology 288, 164-174). We report a sequence motif within the R1 element that binds a human cell nuclear protein which is antigenically related to the Drosophila boundary element-associated factor (BEAF). The potential role of a 35-kDa cellular protein that binds to sequence motifs within the R1 element in regulating the expression of the CMV US3 immune evasion gene is discussed.

The human cytomegalovirus UL35 gene encodes two proteins with different functions

The human cytomegalovirus (HCMV) virion is a complex structure that contains at least 30 proteins, many of which have been identified. We determined that the HCMV UL35 gene encodes two proteins, including a previously unidentified virion protein. A 22-kDa phosphoprotein (ppUL35(A)) was translated from a 1.2-kb UL35 transcript by 4 h postinfection; a second phosphoprotein of 75 kDa (ppUL35) was translated from a 2.2-kb transcript predominantly late in infection. The 22-kDa protein localized to the nucleus, while the 75-kDa protein localized to the juxtanuclear compartment and was packaged into virion particles. The 22-kDa protein was identical to the COOH-terminal end of the 75-kDa protein but was not found in virions, thus defining the NH(2)-terminal portion of the 75-kDa protein as essential for packaging. Expression of the 22-kDa protein inhibited activation of the major immediate-early promoter by ppUL82 (pp71), suggesting that the UL35 22-kDa protein may modulate expression of the major immediate-early gene.