1
|
High-throughput analysis of human cytomegalovirus genome diversity highlights the widespread occurrence of gene-disrupting mutations and pervasive recombination. J Virol 2015; 89:7673-7695. [PMID: 25972543 DOI: 10.1128/jvi.00578-15] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Human cytomegalovirus is a widespread pathogen of major medical importance. It causes significant morbidity and mortality in the immunocompromised and congenital infections can result in severe disabilities or stillbirth. Development of a vaccine is prioritized, but no candidate is close to release. Although correlations of viral genetic variability with pathogenicity are suspected, knowledge about strain diversity of the 235kb genome is still limited. In this study, 96 full-length human cytomegalovirus genomes from clinical isolates were characterized, quadrupling the available information for full-genome analysis. These data provide the first high-resolution map of human cytomegalovirus interhost diversity and evolution. We show that cytomegalovirus is significantly more divergent than all other human herpesviruses and highlight hotspots of diversity in the genome. Importantly, 75% of strains are not genetically intact, but contain disruptive mutations in a diverse set of 26 genes, including immunomodulative genes UL40 and UL111A. These mutants are independent from culture passaging artifacts and circulate in natural populations. Pervasive recombination, which is linked to the widespread occurrence of multiple infections, was found throughout the genome. Recombination density was significantly higher than in other human herpesviruses and correlated with strain diversity. While the overall effects of strong purifying selection on virus evolution are apparent, evidence of diversifying selection was found in several genes encoding proteins that interact with the host immune system, including UL18, UL40, UL142 and UL147. These residues may present phylogenetic signatures of past and ongoing virus-host interactions. IMPORTANCE Human cytomegalovirus has the largest genome of all viruses that infect humans. Currently, there is a great interest in establishing associations between genetic variants and strain pathogenicity of this herpesvirus. Since the number of publicly available full-genome sequences is limited, knowledge about strain diversity is highly fragmented and biased towards a small set of loci. Combined with our previous work, we have now contributed 101 complete genome sequences. We have used these data to conduct the first high-resolution analysis of interhost genome diversity, providing an unbiased and comprehensive overview of cytomegalovirus variability. These data are of major value to the development of novel antivirals and a vaccine and to identify potential targets for genotype-phenotype experiments. Furthermore, they have enabled a thorough study of the evolutionary processes that have shaped cytomegalovirus diversity.
Collapse
|
2
|
Van Damme E, Van Loock M. Functional annotation of human cytomegalovirus gene products: an update. Front Microbiol 2014; 5:218. [PMID: 24904534 PMCID: PMC4032930 DOI: 10.3389/fmicb.2014.00218] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 04/25/2014] [Indexed: 01/31/2023] Open
Abstract
Human cytomegalovirus is an opportunistic double-stranded DNA virus with one of the largest viral genomes known. The 235 kB genome is divided in a unique long (UL) and a unique short (US) region which are flanked by terminal and internal repeats. The expression of HCMV genes is highly complex and involves the production of protein coding transcripts, polyadenylated long non-coding RNAs, polyadenylated anti-sense transcripts and a variety of non-polyadenylated RNAs such as microRNAs. Although the function of many of these transcripts is unknown, they are suggested to play a direct or regulatory role in the delicately orchestrated processes that ensure HCMV replication and life-long persistence. This review focuses on annotating the complete viral genome based on three sources of information. First, previous reviews were used as a template for the functional keywords to ensure continuity; second, the Uniprot database was used to further enrich the functional database; and finally, the literature was manually curated for novel functions of HCMV gene products. Novel discoveries were discussed in light of the viral life cycle. This functional annotation highlights still poorly understood regions of the genome but more importantly it can give insight in functional clusters and/or may be helpful in the analysis of future transcriptomics and proteomics studies.
Collapse
Affiliation(s)
- Ellen Van Damme
- Janssen Infectious Diseases BVBA, Therapeutic Area of Infectious Diseases Beerse, Belgium
| | - Marnix Van Loock
- Janssen Infectious Diseases BVBA, Therapeutic Area of Infectious Diseases Beerse, Belgium
| |
Collapse
|
3
|
Ma Y, Wang N, Li M, Gao S, Wang L, Zheng B, Qi Y, Ruan Q. Human CMV transcripts: an overview. Future Microbiol 2012; 7:577-93. [PMID: 22568714 DOI: 10.2217/fmb.12.32] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Yanping Ma
- Virus Laboratory, the Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning of PR China, China
| | | | | | | | | | | | | | | |
Collapse
|
4
|
Puchhammer-Stöckl E, Görzer I. Human cytomegalovirus: an enormous variety of strains and their possible clinical significance in the human host. Future Virol 2011. [DOI: 10.2217/fvl.10.87] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human cytomegalovirus (HCMV) does not exist as one defined virus genotype, but as a variety of different strains. Several studies have investigated the significance of specific viral genotypes for the clinical course of HCMV infection. Upon reinfection, patients may acquire additional HCMV strains, and infections with a mixture of HCMV strains appear to be quite common. The analysis of such mixed infections has become increasingly important, not only for investigating the clinical implications of mixed-genotype infections, but also for understanding the pathogenesis of subsequent reinfections with HCMV strains, and this is also of importance for HCMV vaccine development. This article summarizes the clinical implications of infection with individual HCMV genotypes and focuses on infection with mixed populations of HCMV strains.
Collapse
Affiliation(s)
| | - Irene Görzer
- Department of Virology, Medical University Vienna, Kinderspitalgasse 15, A-1095 Vienna, Austria
| |
Collapse
|
5
|
Williamson CD, Colberg-Poley AM. Access of viral proteins to mitochondria via mitochondria-associated membranes. Rev Med Virol 2009; 19:147-64. [PMID: 19367604 DOI: 10.1002/rmv.611] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
By exploiting host cell machineries, viruses provide powerful tools for gaining insight into cellular pathways. Proteins from two unrelated viruses, human CMV (HCMV) and HCV, are documented to traffic sequentially from the ER into mitochondria, probably through the mitochondria-associated membrane (MAM) compartment. The MAM are sites of ER-mitochondrial contact enabling the direct transfer of membrane bound lipids and the generation of high calcium (Ca2+) microdomains for mitochondria signalling and responses to cellular stress. Both HCV core protein and HCMV UL37 proteins are associated with Ca2+ regulation and apoptotic signals. Trafficking of viral proteins to the MAM may allow viruses to manipulate a variety of fundamental cellular processes, which converge at the MAM, including Ca2+ signalling, lipid synthesis and transfer, bioenergetics, metabolic flow, and apoptosis. Because of their distinct topologies and targeted MAM sub-domains, mitochondrial trafficking (albeit it through the MAM) of the HCMV and HCV proteins predictably involves alternative pathways and, hence, distinct targeting signals. Indeed, we found that multiple cellular and viral proteins, which target the MAM, showed no apparent consensus primary targeting sequences. Nonetheless, these viral proteins provide us with valuable tools to access the poorly characterised MAM compartment, to define its cellular constituents and describe how virus infection alters these to its own end. Furthermore, because proper trafficking of viral proteins is necessary for their function, discovering the requirements for MAM to mitochondrial trafficking of essential viral proteins may provide novel targets for the rational design of anti-viral drugs.
Collapse
Affiliation(s)
- Chad D Williamson
- Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, 111 Michigan Ave, NW, Washington, DC 20010, USA.
| | | |
Collapse
|
6
|
Mavinakere MS, Williamson CD, Goldmacher VS, Colberg-Poley AM. Processing of human cytomegalovirus UL37 mutant glycoproteins in the endoplasmic reticulum lumen prior to mitochondrial importation. J Virol 2006; 80:6771-83. [PMID: 16809283 PMCID: PMC1489043 DOI: 10.1128/jvi.00492-06] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human cytomegalovirus (HCMV) UL37 glycoprotein (gpUL37) is internally cleaved and its products divergently traffic to mitochondria or are retained in the secretory pathway. To define the requirements for gpUL37 cleavage, residues -1 and -3 of the consensus endoplasmic reticulum (ER) signal peptidase I site within exon 3 (UL37x3) were replaced by bulky tyrosines (gpUL37 cleavage site mutant I). Internal cleavage of this UL37x3 mutant was inhibited, verifying usage of the consensus site at amino acids (aa) 193/194. The full-length mitochondrial species of gpUL37 cleavage site mutant I was N glycosylated and endoglycosidase H sensitive, indicating that ER translocation and processing took place prior to its mitochondrial importation. Moreover, these results suggest that internal cleavage of gpUL37 is not necessary for its N glycosylation. Partial deletion or disruption of the UL37 hydrophobic core immediately upstream of the cleavage site resulted in decreased protein abundance, suggesting that the UL37x3 hydrophobic alpha-helix contributes to either correct folding or stability of gpUL37. Insertion of the UL37x3 hydrophobic core and cleavage site into pUL37(M), a splice variant of gpUL37 which lacks these sequences and is neither proteolytically cleaved nor N glycosylated, resulted in its internal cleavage and N glycosylation. Its NH(2)-terminal fragment, pUL37(M-NH2), was detected more abundantly in mitochondria, while its N-glycosylated C-terminal fragment, gpUL37(M-COOH), was detected predominantly in the ER in a manner analogous to that of gpUL37 cleavage products. These results indicate that UL37x3 aa 178 to 205 are prerequisite for gpUL37 internal cleavage and alter UL37 protein topology allowing N glycosylation of its C-terminal sequences. In contrast, the NH(2)-terminal UL37x1 hydrophobic leader, present in pUL37x1, pUL37(M), and gpUL37, is not cleaved from mature UL37 protein, retaining a membrane anchor for UL37 isoforms during trafficking. Taken together, these results suggest that HCMV gpUL37 undergoes sequential trafficking, during which it is ER translocated, processed, and then mitochondrially imported.
Collapse
Affiliation(s)
- Manohara S Mavinakere
- Center for Cancer and Immunology Research, Children's Research Institute, Room 5720, Children's National Medical Center, 111 Michigan Ave. NW, Washington, DC 20010, USA
| | | | | | | |
Collapse
|
7
|
Pignatelli S, Dal Monte P, Rossini G, Landini MP. Genetic polymorphisms among human cytomegalovirus (HCMV) wild-type strains. Rev Med Virol 2005; 14:383-410. [PMID: 15386592 DOI: 10.1002/rmv.438] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Human cytomegalovirus (HCMV) clinical isolates display genetic polymorphisms in multiple genes. Some authors have suggested that those polymorphisms may be implicated in HCMV-induced immunopathogenesis, as well as in strain-specific behaviours, such as tissue-tropism and ability to establish persistent or latent infections. This review summarises the features of the main clustered HCMV polymorphic open reading frames and also briefly cites other variable loci within the viral genome. The implications of gene polymorphisms are discussed in terms of potentially advantageous higher fitness obtained by the strain, but also taking into account that the published data are often speculative. The last section of this review summarises and critically analyses the main literature reports about the linkage of strain specific genotypes with clinical manifestations of HCMV disease in different patient populations affected by severe cytomegalovirus infections, namely immunocompromised subjects and congenitally infected newborns.
Collapse
Affiliation(s)
- Sara Pignatelli
- Department of Clinical and Experimental Medicine, Division of Microbiology-St Orsola General Hospital, University of Bologna, Italy.
| | | | | | | |
Collapse
|
8
|
Adair R, Liebisch GW, Su Y, Colberg-Poley AM. Alteration of cellular RNA splicing and polyadenylation machineries during productive human cytomegalovirus infection. J Gen Virol 2004; 85:3541-3553. [PMID: 15557227 DOI: 10.1099/vir.0.80450-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Alternative processing of human cytomegalovirus (HCMV) UL37 pre-mRNA predominantly produces the unspliced UL37 exon 1 (UL37x1) RNA and multiple, lower abundance, alternatively spliced UL37 RNAs. The relative abundance of UL37x1 unspliced RNA is surprising because it requires the favoured use of a polyadenylation signal within UL37 intron 1, just upstream of the UL37 exon 2 (UL37x2) acceptor. Here, it was shown that a downstream element (DSE) in UL37x2 strongly enhanced processing at the UL37x1 polyadenylation site, but did not influence UL37x1-x2 splicing. There was a potential binding site (UCUU) for polypyrimidine tract-binding protein (PTB) at the UL37x1 polyadenylation/cleavage site and its mutation to UGGG reduced both polyadenylation and splicing of UL37x1-x2 minigene pre-mRNA, suggesting a role in both RNA processing events. To determine whether lytic HCMV infection altered the balance of RNA processing factors, which bind to UL37 pre-mRNA cis elements, these were investigated in permissively infected primary and immortalized human diploid fibroblasts (HFFs) and epithelial cells. Induction of polyadenylation factors in HCMV-infected, serum-starved (G(0)) HFFs was also investigated. Permissive HCMV infection consistently increased, albeit with different kinetics, the abundance of cleavage stimulation factor 64 (CstF-64) and PTB, and altered hypo-phosphorylated SF2 in different cell types. Moreover, the preponderance of UL37x1 RNA increased during infection and correlated with CstF-64 induction, whereas the complexity of the lower abundance UL37 spliced RNAs transiently increased following reduction of hypo-phosphorylated SF2. Collectively, multiple UL37 RNA polyadenylation cis elements and induced cellular factors in HCMV-infected cells strongly favoured the production of UL37x1 unspliced RNA.
Collapse
Affiliation(s)
- Richard Adair
- Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, Room 5720, 111 Michigan Avenue NW, Washington, DC 20010, USA
| | - Gregory W Liebisch
- Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, Room 5720, 111 Michigan Avenue NW, Washington, DC 20010, USA
| | - Yan Su
- Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, Room 5720, 111 Michigan Avenue NW, Washington, DC 20010, USA
| | - Anamaris M Colberg-Poley
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC 20010, USA
- Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, Room 5720, 111 Michigan Avenue NW, Washington, DC 20010, USA
| |
Collapse
|
9
|
Mavinakere MS, Colberg-Poley AM. Internal cleavage of the human cytomegalovirus UL37 immediate-early glycoprotein and divergent trafficking of its proteolytic fragments. J Gen Virol 2004; 85:1989-1994. [PMID: 15218184 DOI: 10.1099/vir.0.80094-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human cytomegalovirus UL37 gene encodes at least three isoforms, which share N-terminal UL37 exon 1 (UL37x1) sequences. UL37 proteins traffic dually into the endoplasmic reticulum (ER) and to mitochondria. Trafficking of the UL37 glycoprotein (gpUL37) in relation to its post-translational processing was investigated. gpUL37 is internally cleaved in the ER and its products traffic differentially. Its C-terminal fragment (UL37(COOH)) is ER-localized and N-glycosylated. Unlike conventional ER signal sequences, its N-terminal fragment is stable and traffics to mitochondria. Inhibition of N-glycosylation did not block pUL37 cleavage and dramatically decreased the levels of but not of UL37(COOH). pUL37(M), which differs from gpUL37 by the lack of residues 178-262 and hence the UL37x3 consensus signal peptidase cleavage site, traffics into the ER and mitochondria, but is neither cleaved nor N-glycosylated. This finding of a relationship between ER processing and mitochondrial importation of UL37 proteins is unique for herpesvirus proteins.
Collapse
Affiliation(s)
- Manohara S Mavinakere
- Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, George Washington University, School of Medicine and Health Sciences, 111 Michigan Avenue NW, Washington, DC 20010, USA
| | - Anamaris M Colberg-Poley
- Department of Pediatrics, George Washington University, School of Medicine and Health Sciences, 111 Michigan Avenue NW, Washington, DC 20010, USA
- Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, George Washington University, School of Medicine and Health Sciences, 111 Michigan Avenue NW, Washington, DC 20010, USA
| |
Collapse
|
10
|
Mavinakere MS, Colberg-Poley AM. Dual targeting of the human cytomegalovirus UL37 exon 1 protein during permissive infection. J Gen Virol 2004; 85:323-329. [PMID: 14769889 DOI: 10.1099/vir.0.19589-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human cytomegalovirus (HCMV) UL37 immediate-early (IE) gene minimally encodes three protein isoforms that share NH(2)-terminal sequences. The predominant UL37 isoform detected during HCMV infection was the UL37 exon 1 protein (pUL37x1), which was produced from IE and, more abundantly, through late times of infection. pUL37x1 was localized in both the endoplasmic reticulum (ER) and mitochondria in infected cells. To determine which UL37x1 NH(2)-terminal residues serve as ER and mitochondrial targeting signals, we examined the subcellular localization of two deletion mutants. pUL37x1Delta2-23, which lacks the hydrophobic leader, is neither translocated into the ER nor imported mitochondrially; conversely, pUL37x1Delta23-34, lacking the juxtaposed basic residues, was translocated into the ER but only imported weakly into mitochondria. These studies show for the first time the temporal production and localization of pUL37x1 during HCMV infection. The trafficking patterns of mutants suggest that the pUL37x1 targeting signal to ER and mitochondria is bipartite.
Collapse
Affiliation(s)
- Manohara S Mavinakere
- Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, 111 Michigan Avenue NW, Washington, DC 20010, USA
| | - Anamaris M Colberg-Poley
- Department of Pediatrics, George Washington University, School of Medicine and Health Sciences, 111 Michigan Avenue NW, Washington, DC 20010, USA
- Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, 111 Michigan Avenue NW, Washington, DC 20010, USA
| |
Collapse
|
11
|
Adair R, Liebisch GW, Colberg-Poley AM. Complex alternative processing of human cytomegalovirus UL37 pre-mRNA. J Gen Virol 2004; 84:3353-3358. [PMID: 14645916 DOI: 10.1099/vir.0.19404-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Differentially processed human cytomegalovirus (HCMV) UL37 RNAs encode biologically significant proteins. Due to the recent discovery of alternative UL37 exon 3 (UL37x3) splice donors, permissively infected cells were thoroughly examined for additional alternatively spliced UL37 RNAs. Newly described donors within UL37 exon 1 (nt 52520) and intron 1 (nt 52209) as well as UL37x3 di (nt 50770) and dii (nt 50782) were differentially spliced to known downstream UL37 acceptors. The alternatively spliced UL37(S), UL37(L), UL37(di) and UL37d(ii) RNAs predictably encode proteins of 83, 163, 217 and 213 residues, respectively, which share UL37x1 N-terminal sequences but differ downstream in their C termini. Moreover, temporal expression of the alternatively spliced UL37 RNAs differs during HCMV infection. The complexity of UL37 pre-mRNA processing is evidenced by the detection of 11 UL37 spliced and unspliced UL37x1 RNAs in HCMV-infected cells. Based upon these data, a revised HCMV UL37 gene map is presented, which incorporates all RNA species detected during permissive infection.
Collapse
Affiliation(s)
- Richard Adair
- Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, George Washington University School of Medicine and Health Sciences, 111 Michigan Avenue, NW, Washington, DC 20010, USA
| | - Gregory W Liebisch
- Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, George Washington University School of Medicine and Health Sciences, 111 Michigan Avenue, NW, Washington, DC 20010, USA
| | - Anamaris M Colberg-Poley
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, 111 Michigan Avenue, NW, Washington, DC 20010, USA
- Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, George Washington University School of Medicine and Health Sciences, 111 Michigan Avenue, NW, Washington, DC 20010, USA
| |
Collapse
|
12
|
McCormick AL, Skaletskaya A, Barry PA, Mocarski ES, Goldmacher VS. Differential function and expression of the viral inhibitor of caspase 8-induced apoptosis (vICA) and the viral mitochondria-localized inhibitor of apoptosis (vMIA) cell death suppressors conserved in primate and rodent cytomegaloviruses. Virology 2004; 316:221-33. [PMID: 14644605 DOI: 10.1016/j.virol.2003.07.003] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Human cytomegalovirus (CMV) genes UL36 and UL37 encode viral inhibitor of caspase-8-induced apoptosis (vICA) and viral mitochondria inhibitor of apoptosis (vMIA), respectively. Rhesus macaque CMV homologues, denoted Rh-vICA and Rh-vMIA, were identified and found to suppress apoptosis. One of these functions was conserved in MCMV, encoded by the M36 gene and denoted M-vICA. Conserved regions were compared to domains important to vICA- and vMIA-mediated cell death suppression. The conserved sequences of primate CMV vMIA homologues overlapped with the two known functional domains, providing further evidence supporting a crucial role of vMIA in cell death suppression. RNA blot analyses revealed that expression of murine and rhesus macaque CMV UL36 and UL37 homologues started early and continued through late times of infection. Murine CMV homologues were expressed with alpha (immediate early) kinetics, like human CMV UL36 and UL37, whereas rhesus macaque CMV homologues exhibited beta (delayed early) kinetics. Despite differences in organization and transcriptional regulation, this region appears to carry out a conserved role in cell death suppression. When viewed in light of sequence conservation, a functional vMIA homologue appears to be encoded by every primate CMV, whereas a functional vICA homologue appears to be encoded by all cytomegaloviruses for which sequence data are available.
Collapse
Affiliation(s)
- A Louise McCormick
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | | | | | | |
Collapse
|
13
|
Su Y, Adair R, Davis CN, DiFronzo NL, Colberg-Poley AM. Convergence of RNA cis elements and cellular polyadenylation factors in the regulation of human cytomegalovirus UL37 exon 1 unspliced RNA production. J Virol 2004; 77:12729-41. [PMID: 14610195 PMCID: PMC262569 DOI: 10.1128/jvi.77.23.12729-12741.2003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The human cytomegalovirus (HCMV) UL36-38 immediate early (IE) locus encodes proteins required for its growth. The UL37 promoter drives production of an unspliced and several alternatively spliced RNAs. The UL37 exon 1 (UL37x1) unspliced RNA is abundant from IE to late times of HCMV infection, whereas the UL37 spliced RNAs are markedly less abundant. Production of the UL37x1 unspliced RNA requires polyadenylation (PA) at nucleotide 50998, which lies within intron 1, upstream of the UL37 exon 2 (UL37x2) acceptor. The physical proximity of its cis elements suggests steric hindrance between PA and splicing machineries for UL37 pre-mRNA. To test this possibility, we generated site-specific mutants in Target 1 PA and RNA splicing cis elements and compared the PA and splicing efficiencies of mutant RNAs with those of wild-type RNA. The mutually exclusive processing events of UL37x1 PA and UL37x1-UL37x2 splicing have been accurately recapitulated in transfected permissive human fibroblasts (HFFs) expressing a Target 1 minigene RNA, which contains the required splicing and PA cis elements. Two mutants in the invariant PA signal dramatically decreased UL37x1 PA as expected and, concomitantly, increased the efficiency of UL37x1-UL37x2 RNA splicing. Consistent with these results, changes to consensus UL37x1 donor and UL37x2 acceptor sites increased the efficiency of UL37x1-UL37x2 RNA splicing but decreased the efficiency of UL37x1 PA. Moreover, HCMV infection of HFFs increased the abundance of the PA cleavage stimulatory factor CstF-64, the potent splicing suppressor PTB, and the hypophosphorylated form of the splicing factor SF2 at 4 h postinfection. Induction of these factors further favors production of the UL37x1 unspliced RNA over that of the spliced RNAs. Taken together, these results suggest that there is a convergence in UL37 RNA regulation by cis elements and cellular proteins which favors production of the UL37x1 unspliced RNA during HCMV infection at the posttranscriptional level.
Collapse
Affiliation(s)
- Yan Su
- Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, Washington, D.C. 20010, USA
| | | | | | | | | |
Collapse
|
14
|
McCormick AL, Smith VL, Chow D, Mocarski ES. Disruption of mitochondrial networks by the human cytomegalovirus UL37 gene product viral mitochondrion-localized inhibitor of apoptosis. J Virol 2003; 77:631-41. [PMID: 12477866 PMCID: PMC140587 DOI: 10.1128/jvi.77.1.631-641.2003] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
By 24 h after infection with human cytomegalovirus, the reticular mitochondrial network characteristic of uninfected fibroblasts was disrupted as mitochondria became punctate and dispersed. These alterations were associated with expression of the immediate-early (alpha) antiapoptotic UL37x1 gene product viral mitochondrion-localized inhibitor of apoptosis (vMIA). Similar alterations in mitochondrial morphology were induced directly by vMIA in transfected cells. A 68-amino-acid antiapoptotic derivative of vMIA containing the mitochondrial localization and antiapoptotic domains also induced disruption, whereas a mutant lacking the antiapoptotic domain failed to cause disruption. These data suggest that the fission and/or fusion process that normally controls mitochondrial networks is altered by vMIA. Mitochondrial fission has been implicated in the induction of apoptosis and vMIA-mediated inhibition of apoptosis may occur subsequent to this event.
Collapse
Affiliation(s)
- A Louise McCormick
- Department of Microbiology and Immunology, Stanford University School of Medicine, California 94305-5124, USA
| | | | | | | |
Collapse
|
15
|
Su Y, Testaverde JR, Davis CN, Hayajneh WA, Adair R, Colberg-Poley AM. Human cytomegalovirus UL37 immediate early target minigene RNAs are accurately spliced and polyadenylated. J Gen Virol 2003; 84:29-39. [PMID: 12533698 DOI: 10.1099/vir.0.18700-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human cytomegalovirus (HCMV) UL36-38 immediate early (IE) locus encodes proteins required for virus growth. The UL37 IE promoter drives production of differentially spliced and unspliced RNAs. To study their post-transcriptional processing, we generated target minigenes encoding each UL37 RNA splicing substrate. Target 1 RNA, spanning UL37 exon 1 (x1) donor and 2 (x2) acceptor as well as adjacent intronic sequences, but not the UL38 gene, accurately reproduced UL37 x1/x2 RNA splicing in transfected permissive cells. Surprisingly, deletion of distal intronic sequences nt -82 to -143 from the UL37x2 acceptor resulted in aberrant splicing to an upstream non-consensus exonic donor. Target 1 RNAs carry the UL37x1 polyadenylation (PA) signal and site as well as a downstream SV40 early PA signal. Both the UL37x1 and SV40 PA signals are used in wild-type target 1 RNAs but inhibited in UL37x1 PA signal mutants. Alternative RNA splicing of UL37 exons 2 to 3 or 3A as well as exons 3 to 4, observed in HCMV mature UL37 and UL36 spliced RNAs, is accurately reproduced with target minigene RNAs carrying the corresponding UL37 exonic and intronic sequences. Moreover, alternative splicing using two novel UL37 exon 3 consensus splice donors (di and dii) was found in target and in HCMV-infected cell RNA. These results demonstrate that: (i) target minigene RNAs accurately recapitulate the processing of UL37 IE RNAs in the HCMV-infected cell; (ii) precise UL37x1 donor selection is modulated by 3'-distal UL37 intronic sequences; and (iii) UL37 exon 3 contains multiple alternative consensus splice donors.
Collapse
Affiliation(s)
- Yan Su
- Center for Cancer and Immunology Research, Room 5720, Children's Research Institute, George Washington University School of Medicine and Health Sciences, 111 Michigan Avenue, NW, Washington, DC 20010, USA
| | - James R Testaverde
- Center for Cancer and Immunology Research, Room 5720, Children's Research Institute, George Washington University School of Medicine and Health Sciences, 111 Michigan Avenue, NW, Washington, DC 20010, USA
| | - Candice N Davis
- Center for Cancer and Immunology Research, Room 5720, Children's Research Institute, George Washington University School of Medicine and Health Sciences, 111 Michigan Avenue, NW, Washington, DC 20010, USA
| | - Wail A Hayajneh
- Department of Infectious Diseases, Children's National Medical Center, George Washington University School of Medicine and Health Sciences, 111 Michigan Avenue, NW, Washington, DC 20010, USA
- Center for Cancer and Immunology Research, Room 5720, Children's Research Institute, George Washington University School of Medicine and Health Sciences, 111 Michigan Avenue, NW, Washington, DC 20010, USA
| | - Richard Adair
- Center for Cancer and Immunology Research, Room 5720, Children's Research Institute, George Washington University School of Medicine and Health Sciences, 111 Michigan Avenue, NW, Washington, DC 20010, USA
| | - Anamaris M Colberg-Poley
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, 111 Michigan Avenue, NW, Washington, DC 20010, USA
- Center for Cancer and Immunology Research, Room 5720, Children's Research Institute, George Washington University School of Medicine and Health Sciences, 111 Michigan Avenue, NW, Washington, DC 20010, USA
| |
Collapse
|
16
|
Abstract
Evolutionary studies have a large theoretical component and will not directly provide therapies for herpesvirus infections. However, they do provide a conceptual framework within which we can evaluate the origins of the various systems that contribute to viral lifestyle. An evolutionary context allows ancient systems that are fundamental to the replication of all herpesviruses to be distinguished from those that have developed relatively recently in order to tailor viruses to particular biological niches. Both categories are in principle accessible to intervention, either to prevent basic replicative capabilities or to reduce the advantages that the virus has in its interactions with the host. Phylogenetic data provide estimates of evolutionary rate for herpesviruses that are only between one and two orders of magnitude greater than those of their hosts. However, it is becoming apparent that certain genes have evolved much faster under selection pressures and by mechanisms that are not well understood. Nonetheless, the mutation rates of even the most highly conserved genes are sufficient to permit herpesviruses to escape from antiviral therapy. Greater understanding of the origins and functions of herpesvirus genes may lead to new insights into the determinants of pathogenesis and hence to new diagnostic and therapeutic targets.
Collapse
Affiliation(s)
- Andrew J Davison
- MRC Virology Unit, Institute of Virology, Church Street, Glasgow G11 5JR, UK.
| | | | | |
Collapse
|
17
|
Wang HW, Sharp TV, Koumi A, Koentges G, Boshoff C. Characterization of an anti-apoptotic glycoprotein encoded by Kaposi's sarcoma-associated herpesvirus which resembles a spliced variant of human survivin. EMBO J 2002; 21:2602-15. [PMID: 12032073 PMCID: PMC126038 DOI: 10.1093/emboj/21.11.2602] [Citation(s) in RCA: 129] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We have investigated the expression and function of a novel protein encoded by open reading frame (ORF) K7 of Kaposi's sarcoma-associated herpesvirus (KSHV). Computational analyses revealed that K7 is structurally related to survivin-DeltaEx3, a splice variant of human survivin that protects cells from apoptosis by an undefined mechanism. Both K7 and survivin-DeltaEx3 contain a mitochondrial-targeting sequence, an N-terminal region of a BIR (baculovirus IAP repeat) domain and a putative BH2 (Bcl-2 homology)-like domain. These suggested that K7 is a new viral anti-apoptotic protein and survivin-DeltaEx3 is its likely cellular homologue. We show that K7 is a glycoprotein, which can inhibit apoptosis and anchor to intracellular membranes where Bcl-2 resides. K7 does not associate with Bax, but does bind to Bcl-2 via its putative BH2 domain. In addition, K7 binds to active caspase-3 via its BIR domain and thus inhibits the activity of caspase-3. The BH2 domain of K7 is crucial for the inhibition of caspase-3 activity and is therefore essential for its anti-apoptotic function. Furthermore, K7 bridges Bcl-2 and activated caspase-3 into a protein complex. K7 therefore appears to be an adaptor protein and part of an anti-apoptotic complex that presents effector caspases to Bcl-2, enabling Bcl-2 to inhibit caspase activity. These data also suggest that survivin-DeltaEx3 might function by a similar mechanism to that of K7. We denote K7 as vIAP (viral inhibitor-of-apoptosis protein).
Collapse
MESH Headings
- Alternative Splicing
- Amino Acid Sequence
- Apoptosis
- Blotting, Northern
- Caspase 3
- Caspases/metabolism
- Cell Line
- Chromosomal Proteins, Non-Histone/chemistry
- Cloning, Molecular
- DNA, Complementary/metabolism
- Endoplasmic Reticulum/metabolism
- Glutathione Transferase/metabolism
- Glycoproteins/metabolism
- Herpesvirus 8, Human/genetics
- Herpesvirus 8, Human/metabolism
- Humans
- Inhibitor of Apoptosis Proteins
- Microscopy, Fluorescence
- Microtubule-Associated Proteins
- Mitochondria/metabolism
- Models, Biological
- Models, Molecular
- Molecular Sequence Data
- Mutation
- Neoplasm Proteins
- Oligonucleotide Array Sequence Analysis
- Open Reading Frames
- Phylogeny
- Protein Binding
- Protein Structure, Tertiary
- Proto-Oncogene Proteins c-bcl-2/metabolism
- Sequence Homology, Amino Acid
- Software
- Subcellular Fractions/metabolism
- Survivin
- Transfection
Collapse
Affiliation(s)
| | | | | | | | - Chris Boshoff
- The Cancer Research UK Viral Oncology Group, Wolfson Institute for Biomedical Research, Cruciform Building, University College London, London WC1E 6BT, UK
Corresponding author e-mail:
| |
Collapse
|
18
|
Abstract
Human cytomegalovirus encodes a powerful cell death suppressor vMIA (viral mitochondria-localized inhibitor of apoptosis), also known as pUL37x1. vMIA, a product of the immediate early gene UL37 exon 1, is predominantly localized in mitochondria, where it appears to form a complex with adenine nucleotide translocator, believed to be a component of the mitochondrial transition pore complex. vMIA suppresses apoptosis by blocking permeabilization of the mitochondrial outer membrane. Expression of vMIA protects cells against apoptosis triggered by diverse stimuli, including ligation of death receptors, exposure to certain cytotoxic drugs, and infection with an adenovirus mutant deficient in E1B19K. Deletion mutagenesis of vMIA revealed two domains that are necessary and, together, sufficient for its anti-apoptotic activity. The first domain contains a mitochondrial targeting signal. The function of the second domain is still unknown. vMIA does not share any significant amino acid sequence homology with Bcl-2, and, unlike Bcl-2 or Bcl-x(L), it does not bind BAX or VDAC. These structural and functional differences between vMIA and Bcl-2 suggest that vMIA represents a separate class of cell death suppressors. Experiments with vMIA-deficient CMV (human cytomegalovirus) mutants provide strong evidence that the anti-apoptotic function of vMIA is required to prevent CMV-induced apoptosis, and is necessary for viral replication. In addition to vMIA, UL37 encodes two longer splice-variant proteins, gpUL37 and GP37(M). Biological functions of these proteins have not yet been identified, and may be unrelated to their anti-apoptotic activity. The identification of vMIA and the finding that its anti-apoptotic function is required for CMV replication provides a rationale for the development of anti-CMV pharmaceuticals that would inactivate vMIA and thus restore apoptosis in cells infected with CMV.
Collapse
|