Browse
Submit Data
Databases
API
Help

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Details of ssDNA annealing revealed by an HSV-1 ICP8-ssDNA binary complex.

ABSTRACT: Infected cell protein 8 (ICP8) from herpes simplex virus 1 was first identified as a single-strand (ss) DNA-binding protein. It is essential for, and abundant during, viral replication. Studies in vitro have shown that ICP8 stimulates model replication reactions, catalyzes annealing of complementary ssDNAs and, in combination with UL12 exonuclease, will catalyze ssDNA annealing homologous recombination. DNA annealing and strand transfer occurs within large oligomeric filaments of ssDNA-bound ICP8. We present the first 3D reconstruction of a novel ICP8-ssDNA complex, which seems to be the basic unit of the DNA annealing machine. The reconstructed volume consists of two nonameric rings containing ssDNA stacked on top of each other, corresponding to a molecular weight of 2.3 MDa. Fitting of the ICP8 crystal structure suggests a mechanism for the annealing reaction catalyzed by ICP8, which is most likely a general mechanism for protein-driven DNA annealing.

SUBMITTER: Tolun G

PROVIDER: S-EPMC3675482 | biostudies-literature | 2013 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Details of ssDNA annealing revealed by an HSV-1 ICP8-ssDNA binary complex.

Tolun Gökhan G Makhov Alexander M AM Ludtke Steven J SJ Griffith Jack D JD

Nucleic acids research 20130419 11

Infected cell protein 8 (ICP8) from herpes simplex virus 1 was first identified as a single-strand (ss) DNA-binding protein. It is essential for, and abundant during, viral replication. Studies in vitro have shown that ICP8 stimulates model replication reactions, catalyzes annealing of complementary ssDNAs and, in combination with UL12 exonuclease, will catalyze ssDNA annealing homologous recombination. DNA annealing and strand transfer occurs within large oligomeric filaments of ssDNA-bound ICP ...[more]

PMID: 23605044

Similar Datasets

ICP8-vhs- HSV-2 Vaccine Expressing B7 Costimulation Molecules Optimizes Safety and Efficacy against HSV-2 Infection in Mice.

Project description:Herpes simplex virus 2 (HSV-2) causes most sexually transmitted genital ulcerative disease. No effective prophylactic vaccine is currently available. Replication-defective (ICP8-) HSV stimulates immune responses in animals without producing progeny virus, making it potentially useful as a safe form of a live vaccine against HSV. We previously demonstrated that mice generate a stronger response to ICP8- virus encoding B7-2 costimulation molecules than to the parental replication-defective virus. We have also demonstrated enhanced immunogenicity of an ICP8-, virion host shutoff (vhs)- virus which can no longer destabilize viral and host mRNAs. Here, we constructed a triple mutant, ICP8-vhs-B7-2+ strain, and compared it to both double mutant viruses. Immunization of mice with a single dose of ICP8-B7-2+ or ICP8-vhs-B7-2+ virus decreased challenge virus replication in the vaginal mucosa, genital disease, and mortality more effectively than immunization with the ICP8-vhs- virus. Immunization with ICP8-B7-2+ or ICP8-vhs-B7-2+ virus also effectively suppressed subsequent HSV-2 infection of the nervous system compared to immunization with the ICP8-vhs- virus. ICP8-B7-2+ and ICP8-vhs-B7-2+ strains induced more IFN gamma-producing CD8 T cells and memory CD8 T cells than did ICP8-vhs- virus, potentially explaining the enhanced protective effects. Thus, B7 costimulation molecules expressed from a replication-defective vaccine can enhance vaccine efficacy, even in an immunocompetent host.

| S-EPMC10384616 | biostudies-literature

Identification of a divalent metal cation binding site in herpes simplex virus 1 (HSV-1) ICP8 required for HSV replication.

Project description:Herpes simplex virus 1 (HSV-1) ICP8 is a single-stranded DNA-binding protein that is necessary for viral DNA replication and exhibits recombinase activity in vitro. Alignment of the HSV-1 ICP8 amino acid sequence with ICP8 homologs from other herpesviruses revealed conserved aspartic acid (D) and glutamic acid (E) residues. Amino acid residue D1087 was conserved in every ICP8 homolog analyzed, indicating that it is likely critical for ICP8 function. We took a genetic approach to investigate the functions of the conserved ICP8 D and E residues in HSV-1 replication. The E1086A D1087A mutant form of ICP8 failed to support the replication of an ICP8 mutant virus in a complementation assay. E1086A D1087A mutant ICP8 bound DNA, albeit with reduced affinity, demonstrating that the protein is not globally misfolded. This mutant form of ICP8 was also recognized by a conformation-specific antibody, further indicating that its overall structure was intact. A recombinant virus expressing E1086A D1087A mutant ICP8 was defective in viral replication, viral DNA synthesis, and late gene expression in Vero cells. A class of enzymes called DDE recombinases utilize conserved D and E residues to coordinate divalent metal cations in their active sites. We investigated whether the conserved D and E residues in ICP8 were also required for binding metal cations and found that the E1086A D1087A mutant form of ICP8 exhibited altered divalent metal binding in an in vitro iron-induced cleavage assay. These results identify a novel divalent metal cation-binding site in ICP8 that is required for ICP8 functions during viral replication.

| S-EPMC3393532 | biostudies-literature

Herpes simplex virus 1 ICP8 mutant lacking annealing activity is deficient for viral DNA replication.

Project description:Most DNA viruses that use recombination-dependent mechanisms to replicate their DNA encode a single-strand annealing protein (SSAP). The herpes simplex virus (HSV) single-strand DNA binding protein (SSB), ICP8, is the central player in all stages of DNA replication. ICP8 is a classical replicative SSB and interacts physically and/or functionally with the other viral replication proteins. Additionally, ICP8 can promote efficient annealing of complementary ssDNA and is thus considered to be a member of the SSAP family. The role of annealing during HSV infection has been difficult to assess in part, because it has not been possible to distinguish between the role of ICP8 as an SSAP from its role as a replicative SSB during viral replication. In this paper, we have characterized an ICP8 mutant, Q706A/F707A (QF), that lacks annealing activity but retains many other functions characteristic of replicative SSBs. Like WT ICP8, the QF mutant protein forms filaments in vitro, binds ssDNA cooperatively, and stimulates the activities of other replication proteins including the viral polymerase, helicase-primase complex, and the origin binding protein. Interestingly, the QF mutant does not complement an ICP8-null virus for viral growth, replication compartment formation, or DNA replication. Thus, we have been able to separate the activities of ICP8 as a replicative SSB from its annealing activity. Taken together, our data indicate that the annealing activity of ICP8 is essential for viral DNA replication in the context of infection and support the notion that HSV-1 uses recombination-dependent mechanisms during DNA replication.

| S-EPMC6338833 | biostudies-literature

ssDNA-dependent colocalization of adeno-associated virus Rep and herpes simplex virus ICP8 in nuclear replication domains.

Project description:The subnuclear distribution of replication complex proteins is being recognized as an important factor for the control of DNA replication. Herpes simplex virus (HSV) single-strand (ss)DNA-binding protein, ICP8 (infected cell protein 8) accumulates in nuclear replication domains. ICP8 also serves as helper function for the replication of adeno-associated virus (AAV). Using quantitative 3D colocalization analysis we show that upon coinfection of AAV and HSV the AAV replication protein Rep and ICP8 co-reside in HSV replication domains. In contrast, Rep expressed by a recombinant HSV, in the absence of AAV DNA, displayed a nuclear distribution pattern distinct from that of ICP8. Colocal ization of Rep and ICP8 was restored by the reintroduction of single-stranded AAV vector genomes. In vitro, ICP8 displayed direct binding to Rep78. Single-stranded recombinant AAV DNA strongly stimulated this interaction, whereas double-stranded DNA was ineffective. Our findings suggest that ICP8 by its strong ssDNA-binding activity exploits the unique single-strandedness of the AAV genome to form a tripartite complex with Rep78 and AAV ssDNA. This novel mechanism for recruiting components of a functional replication complex directs AAV to subnuclear HSV replication compartments where the HSV replication complex can replicate the AAV genome.

| S-EPMC275469 | biostudies-literature

Hybrid Binary Dragonfly Algorithm with Simulated Annealing for Feature Selection.

Project description:There are various fields are affected by the growth of data dimensionality. The major problems which are resulted from high dimensionality of data including high memory requirements, high computational cost, and low machine learning classifier performance. Therefore, proper selection of relevant features from the set of available features and the removal of irrelevant features will solve these problems. Therefore, to solve the feature selection problem, an improved version of Dragonfly Algorithm (DA) is proposed by combining it with Simulated Annealing (SA), where the improved algorithm named BDA-SA. To solve the local optima problem of DA and enhance its ability in selecting the best subset of features for classification problems, Simulated Annealing (SA) was applied to the best solution found by Binary Dragonfly algorithm in attempt to improve its accuracy. A set of frequently used data sets from UCI repository was utilized to evaluate the performance of the proposed FS approach. Results show that the proposed hybrid approach, named BDA-SA, has superior performance when compared to wrapper-based FS methods including a feature selection method based on the basic version of Binary Dragonfly Algorithm.Supplementary informationThe online version contains supplementary material available at 10.1007/s42979-021-00687-5.

| S-EPMC8147911 | biostudies-literature

Rad52-mediated DNA annealing after Rad51-mediated DNA strand exchange promotes second ssDNA capture.

Project description:Rad51, Rad52, and RPA play central roles in homologous DNA recombination. Rad51 mediates DNA strand exchange, a key reaction in DNA recombination. Rad52 has two distinct activities: to recruit Rad51 onto single-strand (ss)DNA that is complexed with the ssDNA-binding protein, RPA, and to anneal complementary ssDNA complexed with RPA. Here, we report that Rad52 promotes annealing of the ssDNA strand that is displaced by DNA strand exchange by Rad51 and RPA, to a second ssDNA strand. An RPA that is recombination-deficient (RPA(rfa1-t11)) failed to support annealing, explaining its in vivo phenotype. Escherichia coli RecO and SSB proteins, which are functional homologues of Rad52 and RPA, also facilitated the same reaction, demonstrating its conserved nature. We also demonstrate that the two activities of Rad52, recruiting Rad51 and annealing DNA, are coordinated in DNA strand exchange and second ssDNA capture.

| S-EPMC1679760 | biostudies-literature

Protective Effect of Polyoxometalates in {Mo132}/Maghemite Binary Superlattices Under Annealing.

Project description:The binary assembly DDA-{Mo132}/OA-?-Fe2O3 (DDA = didodecyldimethylammonium, {Mo132} = [Mo132O372(CH3COO)30(H2O)72]42-, OA = oleic acid) constitutes one of the two examples in the literature of binary superlattices made of a mixing of nanocrystals and oxo-clusters. In a precedent work, we reported in details the preparation of such magnetic binary systems and studied the effect of the nature of the polyoxometalates (POMs) on the magnetic properties. In the present paper, we study the stability of this model binary assembly under heating at various temperatures. Indeed, especially if magnetic and/or transport properties are targeted, an annealing can be essential to change the phase of the nanocrystals in a more magnetic one and/or to desorb the organic capping of the nano-objects that can constitute an obstacle to the electronic communication between the nano-objects. We gave evidence that the maghemite organization in the binary assembly is maintained until 370°C under vacuum thanks to the presence of the POMs. This latter evolve in the phase MoO3, but still permits to avoid the aggregation of the nanocrystals as well as preserve their periodical arrangement. On the contrary, an assembly made of pure ?-Fe2O3 nanocrystals displays a clear aggregation of the nano-objects from 370°C, as attested by transmission and scanning electronic microscopies and confirmed by magnetic measurements. The stability of the magnetic nanocrystals in such POMs/nanocrystals assemblies opens the way to (i) the elaboration of new binary assemblies from POMs and numerous kinds of nanocrystals with a good control on the magnetic properties and to (ii) the investigation of new physical properties as exchange coupling, or magneto-transport in such systems.

| S-EPMC6895896 | biostudies-literature

Structural details of a Class B GPCR-arrestin complex revealed by genetically encoded crosslinkers in living cells.

Project description:Understanding the molecular basis of arrestin-mediated regulation of GPCRs is critical for deciphering signaling mechanisms and designing functional selectivity. However, structural studies of GPCR-arrestin complexes are hampered by their highly dynamic nature. Here, we dissect the interaction of arrestin-2 (arr2) with the secretin-like parathyroid hormone 1 receptor PTH1R using genetically encoded crosslinking amino acids in live cells. We identify 136 intermolecular proximity points that guide the construction of energy-optimized molecular models for the PTH1R-arr2 complex. Our data reveal flexible receptor elements missing in existing structures, including intracellular loop 3 and the proximal C-tail, and suggest a functional role of a hitherto overlooked positively charged region at the arrestin N-edge. Unbiased MD simulations highlight the stability and dynamic nature of the complex. Our integrative approach yields structural insights into protein-protein complexes in a biologically relevant live-cell environment and provides information inaccessible to classical structural methods, while also revealing the dynamics of the system.

| S-EPMC9977954 | biostudies-literature

Upper atmospheric gravity wave details revealed in nightglow satellite imagery.

Project description:Gravity waves (disturbances to the density structure of the atmosphere whose restoring forces are gravity and buoyancy) comprise the principal form of energy exchange between the lower and upper atmosphere. Wave breaking drives the mean upper atmospheric circulation, determining boundary conditions to stratospheric processes, which in turn influence tropospheric weather and climate patterns on various spatial and temporal scales. Despite their recognized importance, very little is known about upper-level gravity wave characteristics. The knowledge gap is mainly due to lack of global, high-resolution observations from currently available satellite observing systems. Consequently, representations of wave-related processes in global models are crude, highly parameterized, and poorly constrained, limiting the description of various processes influenced by them. Here we highlight, through a series of examples, the unanticipated ability of the Day/Night Band (DNB) on the NOAA/NASA Suomi National Polar-orbiting Partnership environmental satellite to resolve gravity structures near the mesopause via nightglow emissions at unprecedented subkilometric detail. On moonless nights, the Day/Night Band observations provide all-weather viewing of waves as they modulate the nightglow layer located near the mesopause (∼ 90 km above mean sea level). These waves are launched by a variety of physical mechanisms, ranging from orography to convection, intensifying fronts, and even seismic and volcanic events. Cross-referencing the Day/Night Band imagery with conventional thermal infrared imagery also available helps to discern nightglow structures and in some cases to attribute their sources. The capability stands to advance our basic understanding of a critical yet poorly constrained driver of the atmospheric circulation.

| S-EPMC4679010 | biostudies-other

Human Rad52 binds and wraps single-stranded DNA and mediates annealing via two hRad52-ssDNA complexes.

Project description:Rad52 promotes the annealing of complementary strands of DNA bound by replication protein A (RPA) during discrete repair pathways. Here, we used a fluorescence resonance energy transfer (FRET) between two fluorescent dyes incorporated into DNA substrates to probe the mechanism by which human Rad52 (hRad52) interacts with and mediates annealing of ssDNA-hRPA complexes. Human Rad52 bound ssDNA or ssDNA-hRPA complex in two, concentration-dependent modes. At low hRad52 concentrations, ssDNA was wrapped around the circumference of the protein ring, while at higher protein concentrations, ssDNA was stretched between multiple hRad52 rings. Annealing by hRad52 occurred most efficiently when each complementary DNA strand or each ssDNA-hRPA complex was bound by hRad52 in a wrapped configuration, suggesting homology search and annealing occur via two hRad52-ssDNA complexes. In contrast to the wild type protein, hRad52(RQK/AAA) and hRad52(1-212) mutants with impaired ability to bind hRPA protein competed with hRPA for binding to ssDNA and failed to counteract hRPA-mediated duplex destabilization highlighting the importance of hRad52-hRPA interactions in promoting efficient DNA annealing.

| S-EPMC2875008 | biostudies-other

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data