The Cytomegalovirus DNA Polymerase Subunit UL44 Forms a C Clamp-Shaped Dimer

Appleton, B.A.; Loregian, Arianna; Filman, David J.; Coen, Donald M.; Hogle, James M.

doi:10.1016/j.molcel.2004.06.018

Cited by 97 publications

(203 citation statements)

References 47 publications

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“…The functional consequences of these variants have not been characterized although alterations of fidelity are a possibility. Furthermore, extrinsic or accessory factors can alter polymerase fidelity (74,75), and the interaction of HSV and HCMV polymerases with their cognate accessory proteins, UL42 and UL44, respectively, has been shown to differ at the molecular level (76) as have the quaternary structures of the accessory proteins (77). Lastly, the role of host factors, such as proteins of the DNA damage response (78,79), in altering mutation rates of viral replication cannot be excluded, particularly because herpesviruses are potent inducers of host DNA damage responses (79).…”

Section: Discussionmentioning

confidence: 99%

Limits and patterns of cytomegalovirus genomic diversity in humans

Renzette

Pokalyuk

Gibson

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

113

129

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Human cytomegalovirus (HCMV) exhibits surprisingly high genomic diversity during natural infection although little is known about the limits or patterns of HCMV diversity among humans. To address this deficiency, we analyzed genomic diversity among congenitally infected infants. We show that there is an upper limit to HCMV genomic diversity in these patient samples, with ∼25% of the genome being devoid of polymorphisms. These low diversity regions were distributed across 26 loci that were preferentially located in DNA-processing genes. Furthermore, by developing, to our knowledge, the first genome-wide mutation and recombination rate maps for HCMV, we show that genomic diversity is positively correlated with these two rates. In contrast, median levels of viral genomic diversity did not vary between putatively single or mixed strain infections. We also provide evidence that HCMV populations isolated from vascular compartments of hosts from different continents are genetically similar and that polymorphisms in glycoproteins and regulatory proteins are enriched in these viral populations. This analysis provides the most highly detailed map of HCMV genomic diversity in human hosts to date and informs our understanding of the distribution of HCMV genomic diversity within human hosts.human cytomegalovirus | HCMV | congenital CMV | virology | evolution

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Section: Discussionmentioning

confidence: 99%

Limits and patterns of cytomegalovirus genomic diversity in humans

Renzette

Pokalyuk

Gibson

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

113

129

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“…This type of processivity factor would be quite distinct from the toroidal sliding clamps associated with prokaryotic (Escherichia coli ␤ complex (40,41)) and eukaryotic (e.g. mammalian proliferating cell nuclear antigen (42,43)) replication machinery and much more like the herpes simplex virus (HSV UL42 monomer (44)) and cytomegalovirus (UL44 dimer (45)) processivity factors.…”

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confidence: 99%

Evaluation of the Role of the Vaccinia Virus Uracil DNA Glycosylase and A20 Proteins as Intrinsic Components of the DNA Polymerase Holoenzyme

Boyle

Stanitsa

Greseth

et al. 2011

Journal of Biological Chemistry

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The vaccinia virus DNA polymerase is inherently distributive but acquires processivity by associating with a heterodimeric processivity factor comprised of the viral A20 and D4 proteins. D4 is also an enzymatically active uracil DNA glycosylase (UDG). The presence of an active repair protein as an essential component of the polymerase holoenzyme is a unique feature of the replication machinery. We have shown previously that the A20-UDG complex has a stoichiometry of ϳ1:1, and our data suggest that A20 serves as a bridge between polymerase and UDG. Here we show that conserved hydrophobic residues in the N terminus of A20 are important for its binding to UDG. Our data argue against the assembly of D4 into higher order multimers, suggesting that the processivity factor does not form a toroidal ring around the DNA. Instead, we hypothesize that the intrinsic, processive DNA scanning activity of UDG tethers the holoenzyme to the DNA template. The inclusion of UDG as an essential holoenzyme component suggests that replication and base excision repair may be coupled. Here we show that the DNA polymerase can utilize dUTP as a substrate in vitro. Moreover, uracil moieties incorporated into the nascent strand during holoenzyme-mediated DNA synthesis can be excised by the viral UDG present within this holoenzyme, leaving abasic sites. Finally, we show that the polymerase stalls upon encountering an abasic site in the template strand, indicating that, like many replicative polymerases, the poxviral holoenzyme cannot perform translesion synthesis across an abasic site.The faithful and efficient duplication of genomic DNA is one of the most conserved processes across all forms of life. Although this is a necessary and highly regulated process, it seems that each model organism has evolved unique modifications during this process. Members of the poxvirus family, of which variola virus is the most notable member and vaccinia virus is the experimental prototype, are no exception. Poxviruses are unique in that they complete the replication and maturation of their ϳ200-kb double-stranded DNA genome in the cytoplasm of the infected host cell. This autonomy dictates that poxviruses encode many of the proteins necessary for nucleotide precursor synthesis and metabolism as well as the core set of enzymes and DNA binding proteins that act directly at the replication fork (1, 2). Indeed, genetic, genomic, and biochemical analysis has revealed that eight proteins are responsible for vaccinia virus DNA synthesis and maturation. This repertoire includes the catalytic DNA polymerase (E9 (3-11)), a stoichiometric component of the heterodimeric processivity factor (A20 (12-15)), a second component of the processivity factor (D4) that also possesses uracil DNA glycosylase (UDG) 2 activity (16 -18), a putative superfamily III helicase with known NTPase and DNA primase activity (D5 (19 -23)), a serine/threonine protein kinase (B1 (24 -26)), an abundant phosphoprotein with essential roles in viral replication, transcription, and morphogenesis (H5 ...

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“…How these and other proteins are organized within HCMV replication compartments is unclear but may involve UL44. UL44, a homodimer, is a structural homologue of the cellular proliferating cell nuclear antigen (PCNA), which exists as a trimer (Appleton et al, 2004(Appleton et al, , 2006Loregian et al, 2004a, b There are few reports of cellular proteins localizing to HCMV replication compartments, although it is known that both p53 and replication protein A are recruited to the interior of replication compartments (Fortunato & Spector, 1998). Their roles within replication compartments are unknown but may involve modulation of cellular responses to infection and promoting efficient viral DNA synthesis.…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…The binding of proteins to UL44 is increasingly well characterized. Studies investigating the binding of UL54 to UL44 have revealed that, like PCNA, UL44 is able to bind proteins within 'hydrophobic pockets'; crevices located in the N termini of UL44 containing several hydrophobic amino acids into which proteins binding UL44 insert their binding domains (Appleton et al, 2004(Appleton et al, , 2006Loregian et al, 2004a, b). Unexpectedly, UL44 can also associates with proteins outside the hydrophobic pockets, as it has been demonstrated that the association of UL84 with UL44 is not dependent upon binding in the hydrophobic pocket (Strang et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

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Viral and cellular subnuclear structures in human cytomegalovirus-infected cells

Strang

2015

Journal of General Virology

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In human cytomegalovirus (HCMV)-infected cells, a dramatic remodelling of the nuclear architecture is linked to the creation, utilization and manipulation of subnuclear structures. This review outlines the involvement of several viral and cellular subnuclear structures in areas of HCMV replication and virus-host interaction that include viral transcription, viral DNA synthesis and the production of DNA-filled viral capsids. The structures discussed include those that promote or impede HCMV replication (such as viral replication compartments and promyelocytic leukaemia nuclear bodies, respectively) and those whose role in the infected cell is unclear (for example, nucleoli and nuclear speckles). Viral and cellular proteins associated with subnuclear structures are also discussed. The data reviewed here highlight advances in our understanding of HCMV biology and emphasize the complexity of HCMV replication and virus-host interactions in the nucleus. IntroductionThe betaherpesvirus human cytomegalovirus (HCMV) is a widespread opportunistic pathogen that severely affects immunocompromised and immunodeficient populations (Mocarski et al., 2007). Like all herpesviruses, HCMV undergoes either productive or latent infection. During productive infection, infectious virus is produced, while in latent infection the virus becomes largely transcriptionally quiescent (Mocarski et al., 2007). Like other herpesviruses, many events that are critical for productive HCMV replication take place within the nucleus. These include essential steps in viral replication, such as: the transcriptional cascade of immediate-early (IE), early and late viral RNA transcripts, synthesis of viral DNA and the production of DNA-containing capsids (Mocarski et al., 2007). Compared with the prototype human herpesvirus, the alphaherpesvirus herpes simplex virus (HSV), certain features of productive HCMV infection are not well characterized. However, it is clear that several subnuclear structures are involved in HCMV genome replication and virus-host interactions. Uncovering the roles of these structures has led to significant advances in our understanding of HCMV biology. This review summarizes the involvement of several viral and cellular subnuclear structures in productive HCMV infection. The participation of each structure in HCMV replication and virus-host interactions is described from entry of the viral genome into the nucleus to the egress of viral capsids through the nuclear membrane. The data discussed highlight recent advances in our understanding of subnuclear structure function, introduce viral and cellular factors associated with subnuclear structures and indicate what questions have yet to be answered.Entry of the HCMV genome into the nucleus: the nuclear pore complex, nuclear speckles, promyelocytic leukaemia protein nuclear bodies and pp150 bodies HCMV genome entry into the nucleus is poorly defined but may be similar to movement of the HSV DNA genome through the nuclear pore complex (NPC) (Kobiler et al., 2012) (Fig. 1a). HCMV capsid ...

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The Cytomegalovirus DNA Polymerase Subunit UL44 Forms a C Clamp-Shaped Dimer

Cited by 97 publications

References 47 publications

Limits and patterns of cytomegalovirus genomic diversity in humans

Limits and patterns of cytomegalovirus genomic diversity in humans

Evaluation of the Role of the Vaccinia Virus Uracil DNA Glycosylase and A20 Proteins as Intrinsic Components of the DNA Polymerase Holoenzyme

Viral and cellular subnuclear structures in human cytomegalovirus-infected cells

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