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Jaiswal R, Santosh V, Braud B, Washington A, Escalante CR. Cryo-EM Structure of AAV2 Rep68 bound to integration site AAVS1: Insights into the mechanism of DNA melting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587759. [PMID: 38617369 PMCID: PMC11014581 DOI: 10.1101/2024.04.02.587759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The Rep68 protein from Adeno-Associated Virus (AAV) is a multifunctional SF3 helicase that performs most of the DNA transactions required for the viral life cycle. During AAV DNA replication, Rep68 assembles at the origin and catalyzes the DNA melting and nicking reactions during the hairpin rolling replication process to complete the second-strand synthesis of the AAV genome. Here, we report the Cryo-EM structures of Rep68 bound to double-stranded DNA (dsDNA) containing the sequence of the AAVS1 integration site in different nucleotide-bound states. In the apo state, Rep68 forms a heptameric complex around DNA, with three Origin Binding Domains (OBDs) bound to the Rep Binding Site (RBS) sequence and three other OBDs forming transient dimers with them. The AAA+ domains form an open ring with no interactions between subunits and with DNA. We hypothesize the heptameric quaternary structure is necessary to load onto dsDNA. In the ATPγS-bound state, a subset of three subunits binds the nucleotide, undergoing a large conformational change, inducing the formation of intersubunit interactions interaction and interaction with three consecutive DNA phosphate groups. Moreover, the induced conformational change positions three phenylalanine residues to come in close contact with the DNA backbone, producing a distortion in the DNA. We propose that the phenylalanine residues can potentially act as a hydrophobic wedge in the DNA melting process.
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Affiliation(s)
- R. Jaiswal
- Department of Physiology and Biophysics, Virginia Commonwealth University, School of Medicine, Richmond VA, 23298
- Current address: Department of Biochemistry and Molecular Biology, University of Arkansas for the Medical Sciences, Little Rock AR 72205
| | - V. Santosh
- Department of Physiology and Biophysics, Virginia Commonwealth University, School of Medicine, Richmond VA, 23298
- Current address: US Army DEVCOM Chemical Biological Center, Gunpowder MD
| | - B. Braud
- Department of Physiology and Biophysics, Virginia Commonwealth University, School of Medicine, Richmond VA, 23298
| | - A. Washington
- Department of Physiology and Biophysics, Virginia Commonwealth University, School of Medicine, Richmond VA, 23298
- Current address: Mayo Clinic Graduate School of Biomedical Research, Department of Biochemistry and Molecular Biology, Rochester, MN 55905
| | - Carlos R. Escalante
- Department of Physiology and Biophysics, Virginia Commonwealth University, School of Medicine, Richmond VA, 23298
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Zheludev IN, Edgar RC, Lopez-Galiano MJ, de la Peña M, Babaian A, Bhatt AS, Fire AZ. Viroid-like colonists of human microbiomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576352. [PMID: 38293115 PMCID: PMC10827157 DOI: 10.1101/2024.01.20.576352] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Here, we describe the "Obelisks," a previously unrecognised class of viroid-like elements that we first identified in human gut metatranscriptomic data. "Obelisks" share several properties: (i) apparently circular RNA ~1kb genome assemblies, (ii) predicted rod-like secondary structures encompassing the entire genome, and (iii) open reading frames coding for a novel protein superfamily, which we call the "Oblins". We find that Obelisks form their own distinct phylogenetic group with no detectable sequence or structural similarity to known biological agents. Further, Obelisks are prevalent in tested human microbiome metatranscriptomes with representatives detected in ~7% of analysed stool metatranscriptomes (29/440) and in ~50% of analysed oral metatranscriptomes (17/32). Obelisk compositions appear to differ between the anatomic sites and are capable of persisting in individuals, with continued presence over >300 days observed in one case. Large scale searches identified 29,959 Obelisks (clustered at 90% nucleotide identity), with examples from all seven continents and in diverse ecological niches. From this search, a subset of Obelisks are identified to code for Obelisk-specific variants of the hammerhead type-III self-cleaving ribozyme. Lastly, we identified one case of a bacterial species (Streptococcus sanguinis) in which a subset of defined laboratory strains harboured a specific Obelisk RNA population. As such, Obelisks comprise a class of diverse RNAs that have colonised, and gone unnoticed in, human, and global microbiomes.
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Affiliation(s)
- Ivan N Zheludev
- Stanford University, Department of Biochemistry, Stanford, CA, USA
| | | | - Maria Jose Lopez-Galiano
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-CSIC, Valencia, Spain
| | - Marcos de la Peña
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-CSIC, Valencia, Spain
| | - Artem Babaian
- University of Toronto, Department of Molecular Genetics, Ontario, Canada
- University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Ontario, Canada
| | - Ami S Bhatt
- Stanford University, Department of Genetics, Stanford, CA, USA
- Stanford University, Department of Medicine, Division of Hematology, Stanford, CA, USA
| | - Andrew Z Fire
- Stanford University, Department of Genetics, Stanford, CA, USA
- Stanford University, Department of Pathology, Stanford, CA, USA
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Vargas-Bermudez DS, Mogollon JD, Franco-Rodriguez C, Jaime J. The Novel Porcine Parvoviruses: Current State of Knowledge and Their Possible Implications in Clinical Syndromes in Pigs. Viruses 2023; 15:2398. [PMID: 38140639 PMCID: PMC10747800 DOI: 10.3390/v15122398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/04/2023] [Accepted: 11/06/2023] [Indexed: 12/24/2023] Open
Abstract
Parvoviruses (PVs) affect various animal species causing different diseases. To date, eight different porcine parvoviruses (PPV1 through PPV8) are recognized in the swine population, all of which are distributed among subfamilies and genera of the Parvoviridae family. PPV1 is the oldest and is recognized as the primary agent of SMEDI, while the rest of the PPVs (PPV2 through PPV8) are called novel PPVs (nPPVs). The pathogenesis of nPPVs is still undefined, and whether these viruses are putative disease agents is unknown. Structurally, the PPVs are very similar; the differences occur mainly at the level of their genomes (ssDNA), where there is variation in the number and location of the coding genes. Additionally, it is considered that the genome of PVs has mutation rates similar to those of ssRNA viruses, that is, in the order of 10-5-10-4 nucleotide/substitution/year. These mutations manifest mainly in the VP protein, constituting the viral capsid, affecting virulence, tropism, and viral antigenicity. For nPPVs, mutation rates have already been established that are similar to those already described; however, within this group of viruses, the highest mutation rate has been reported for PPV7. In addition to the mutations, recombinations are also reported, mainly in PPV2, PPV3, and PPV7; these have been found between strains of domestic pigs and wild boars and in a more significant proportion in VP sequences. Regarding affinity for cell types, nPPVs have been detected with variable prevalence in different types of organs and tissues; this has led to the suggestion that they have a broad tropism, although proportionally more have been found in lung and lymphoid tissue such as spleen, tonsils, and lymph nodes. Regarding their epidemiology, nPPVs are present on all continents (except PPV8, only in Asia), and within pig farms, the highest prevalences detecting viral genomes have been seen in the fattener and finishing groups. The relationship between nPPVs and clinical manifestations has been complicated to establish. However, there is already some evidence that establishes associations. One of them is PPV2 with porcine respiratory disease complex (PRDC), where causality tests (PCR, ISH, and histopathology) lead to proposing the PPV2 virus as a possible agent involved in this syndrome. With the other nPPVs, there is still no clear association with any pathology. These have been detected in different systems (respiratory, reproductive, gastrointestinal, urinary, and nervous), and there is still insufficient evidence to classify them as disease-causing agents. In this regard, nPPVs (except PPV8) have been found to cause porcine reproductive failure (PRF), with the most prevalent being PPV4, PPV6, and PPV7. In the case of PRDC, nPPVs have also been detected, with PPV2 having the highest viral loads in the lungs of affected pigs. Regarding coinfections, nPPVs have been detected in concurrence in healthy and sick pigs, with primary PRDC and PRF viruses such as PCV2, PCV3, and PRRSV. The effect of these coinfections is not apparent; it is unknown whether they favor the replication of the primary agents, the severity of the clinical manifestations, or have no effect. The most significant limitation in the study of nPPVs is that their isolation has been impossible; therefore, there are no studies on their pathogenesis both in vitro and in vivo. For all of the above, it is necessary to propose basic and applied research on nPPVs to establish if they are putative disease agents, establish their effect on coinfections, and measure their impact on swine production.
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Affiliation(s)
| | | | | | - Jairo Jaime
- Universidad Nacional de Colombia, Sede Bogotá, Facultad de Medicina Veterinaria y de Zootecnia, Departamento de Salud Animal, Centro de Investigación en Infectología e Inmunología Veterinaria (CI3V), Carrera 30 No. 45-03, Bogotá 111321, CP, Colombia; (D.S.V.-B.); (J.D.M.); (C.F.-R.)
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Bunke LE, Larsen CIS, Pita-Aquino JN, Jones IK, Majumder K. The DNA Damage Sensor MRE11 Regulates Efficient Replication of the Autonomous Parvovirus Minute Virus of Mice. J Virol 2023; 97:e0046123. [PMID: 37098896 PMCID: PMC10231137 DOI: 10.1128/jvi.00461-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 04/07/2023] [Indexed: 04/27/2023] Open
Abstract
Parvoviruses are single-stranded DNA viruses that utilize host proteins to vigorously replicate in the nuclei of host cells, leading to cell cycle arrest. The autonomous parvovirus, minute virus of mice (MVM), forms viral replication centers in the nucleus which are adjacent to cellular DNA damage response (DDR) sites, many of which are fragile genomic regions prone to undergoing DDR during the S phase. Since the cellular DDR machinery has evolved to transcriptionally suppress the host epigenome to maintain genomic fidelity, the successful expression and replication of MVM genomes at these cellular sites suggest that MVM interacts with DDR machinery distinctly. Here, we show that efficient replication of MVM requires binding of the host DNA repair protein MRE11 in a manner that is independent of the MRE11-RAD50-NBS1 (MRN) complex. MRE11 binds to the replicating MVM genome at the P4 promoter, remaining distinct from RAD50 and NBS1, which associate with cellular DNA break sites to generate DDR signals in the host genome. Ectopic expression of wild-type MRE11 in CRISPR knockout cells rescues virus replication, revealing a dependence on MRE11 for efficient MVM replication. Our findings suggest a new model utilized by autonomous parvoviruses to usurp local DDR proteins that are crucial for viral pathogenesis and distinct from those of dependoparvoviruses, like adeno-associated virus (AAV), which require a coinfected helper virus to inactivate the local host DDR. IMPORTANCE The cellular DNA damage response (DDR) machinery protects the host genome from the deleterious consequences of DNA breaks and recognizes invading viral pathogens. DNA viruses that replicate in the nucleus have evolved distinct strategies to evade or usurp these DDR proteins. We have discovered that the autonomous parvovirus, MVM, which is used to target cancer cells as an oncolytic agent, depends on the initial DDR sensor protein MRE11 to express and replicate efficiently in host cells. Our studies reveal that the host DDR interacts with replicating MVM molecules in ways that are distinct from viral genomes being recognized as simple broken DNA molecules. These findings suggest that autonomous parvoviruses have evolved distinct mechanisms to usurp DDR proteins, which can be used to design potent DDR-dependent oncolytic agents.
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Affiliation(s)
| | - Clairine I. S. Larsen
- Institute for Molecular Virology, Madison, Wisconsin, USA
- Cell and Molecular Biology Graduate Program, Madison, Wisconsin, USA
| | - Jessica N. Pita-Aquino
- Institute for Molecular Virology, Madison, Wisconsin, USA
- Cell and Molecular Biology Graduate Program, Madison, Wisconsin, USA
| | | | - Kinjal Majumder
- Institute for Molecular Virology, Madison, Wisconsin, USA
- McArdle Laboratory for Cancer Research, Madison, Wisconsin, USA
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- University of Wisconsin Carbone Cancer Center, Madison, Wisconsin, USA
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5
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Larsen CIS, Majumder K. The Autonomous Parvovirus Minute Virus of Mice Localizes to Cellular Sites of DNA Damage Using ATR Signaling. Viruses 2023; 15:1243. [PMID: 37376543 DOI: 10.3390/v15061243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Minute Virus of Mice (MVM) is an autonomous parvovirus of the Parvoviridae family that replicates in mouse cells and transformed human cells. MVM genomes localize to cellular sites of DNA damage with the help of their essential non-structural phosphoprotein NS1 to establish viral replication centers. MVM replication induces a cellular DNA damage response that is mediated by signaling through the ATM kinase pathway, while inhibiting induction of the ATR kinase signaling pathway. However, the cellular signals regulating virus localization to cellular DNA damage response sites has remained unknown. Using chemical inhibitors to DNA damage response proteins, we have discovered that NS1 localization to cellular DDR sites is independent of ATM or DNA-PK signaling but is dependent on ATR signaling. Pulsing cells with an ATR inhibitor after S-phase entry leads to attenuated MVM replication. These observations suggest that the initial localization of MVM to cellular DDR sites depends on ATR signaling before it is inactivated by vigorous virus replication.
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Affiliation(s)
- Clairine I S Larsen
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI 53706, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Kinjal Majumder
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI 53706, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
- University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
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6
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Sanchez JL, Ghadirian N, Horton NC. High-Resolution Structure of the Nuclease Domain of the Human Parvovirus B19 Main Replication Protein NS1. J Virol 2022; 96:e0216421. [PMID: 35435730 PMCID: PMC9093113 DOI: 10.1128/jvi.02164-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/15/2022] [Indexed: 12/11/2022] Open
Abstract
Two new structures of the N-terminal domain of the main replication protein, NS1, of human parvovirus B19 (B19V) are presented here. This domain (NS1-nuc) plays an important role in the "rolling hairpin" replication of the single-stranded B19V DNA genome, recognizing origin of replication sequences in double-stranded DNA, and cleaving (i.e., nicking) single-stranded DNA at a nearby site known as the terminal resolution site (trs). The three-dimensional structure of NS1-nuc is well conserved between the two forms, as well as with a previously solved structure of a sequence variant of the same domain; however, it is shown here at a significantly higher resolution (2.4 Å). Using structures of NS1-nuc homologues bound to single- and double-stranded DNA, models for DNA recognition and nicking by B19V NS1-nuc are presented that predict residues important for DNA cleavage and for sequence-specific recognition at the viral origin of replication. IMPORTANCE The high-resolution structure of the DNA binding and cleavage domain of the main replicative protein, NS1, from the human-pathogenic virus human parvovirus B19 is presented here. Included also are predictions of how the protein recognizes important sequences in the viral DNA which are required for viral replication. These predictions can be used to further investigate the function of this protein, as well as to predict the effects on viral viability due to mutations in the viral protein and viral DNA sequences. Finally, the high-resolution structure facilitates structure-guided drug design efforts to develop antiviral compounds against this important human pathogen.
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Affiliation(s)
- Jonathan L. Sanchez
- BMCB Graduate Program, University of Arizona, Tucson, Arizona, USA
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Niloofar Ghadirian
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Nancy C. Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
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Liblekas L, Piirsoo A, Laanemets A, Tombak EM, Laaneväli A, Ustav E, Ustav M, Piirsoo M. Analysis of the Replication Mechanisms of the Human Papillomavirus Genomes. Front Microbiol 2021; 12:738125. [PMID: 34733254 PMCID: PMC8558456 DOI: 10.3389/fmicb.2021.738125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/22/2021] [Indexed: 11/27/2022] Open
Abstract
The life-cycle of human papillomaviruses (HPVs) includes three distinct phases of the viral genome replication. First, the viral genome is amplified in the infected cells, and this amplification is often accompanied by the oligomerization of the viral genomes. Second stage includes the replication of viral genomes in concert with the host cell genome. The viral genome is further amplified during the third stage of the viral-life cycle, which takes place only in the differentiated keratinocytes. We have previously shown that the HPV18 genomes utilize at least two distinct replication mechanisms during the initial amplification. One of these mechanisms is a well-described bidirectional replication via theta type of replication intermediates. The nature of another replication mechanism utilized by HPV18 involves most likely recombination-dependent replication. In this paper, we show that the usage of different replication mechanisms is a property shared also by other HPV types, namely HPV11 and HPV5. We further show that the emergence of the recombination dependent replication coincides with the oligomerization of the viral genomes and is dependent on the replicative DNA polymerases. We also show that the oligomeric genomes of HPV18 replicate almost exclusively using recombination dependent mechanism, whereas monomeric HPV31 genomes replicate bi-directionally during the maintenance phase of the viral life-cycle.
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Affiliation(s)
- Lisett Liblekas
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Alla Piirsoo
- Institute of Technology, University of Tartu, Tartu, Estonia
| | | | | | | | - Ene Ustav
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Mart Ustav
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Marko Piirsoo
- Institute of Technology, University of Tartu, Tartu, Estonia
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Markarian NM, Abrahamyan L. AMDV Vaccine: Challenges and Perspectives. Viruses 2021; 13:v13091833. [PMID: 34578415 PMCID: PMC8472842 DOI: 10.3390/v13091833] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/09/2021] [Accepted: 09/09/2021] [Indexed: 12/13/2022] Open
Abstract
Aleutian mink disease virus (AMDV) is known to cause the most significant disease in the mink industry. It is globally widespread and manifested as a deadly plasmacytosis and hyperglobulinemia. So far, measures to control the viral spread have been limited to manual serological testing for AMDV-positive mink. Further, due to the persistent nature of this virus, attempts to eradicate Aleutian disease (AD) have largely failed. Therefore, effective strategies to control the viral spread are of crucial importance for wildlife protection. One potentially key tool in the fight against this disease is by the immunization of mink against AMDV. Throughout many years, several researchers have tried to develop AMDV vaccines and demonstrated varying degrees of protection in mink by those vaccines. Despite these attempts, there are currently no vaccines available against AMDV, allowing the continuation of the spread of Aleutian disease. Herein, we summarize previous AMDV immunization attempts in mink as well as other preventative measures with the purpose to shed light on future studies designing such a potentially crucial preventative tool against Aleutian disease.
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Affiliation(s)
- Nathan M. Markarian
- Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada;
| | - Levon Abrahamyan
- Swine and Poultry Infectious Diseases Research Center (CRIPA), Research Group on Infectious Diseases of Production Animals (GREMIP), Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC J2S 2M2, Canada
- Correspondence:
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Hairpin transfer-independent Parvovirus DNA Replication Produces Infectious Virus. J Virol 2021; 95:e0110821. [PMID: 34346761 DOI: 10.1128/jvi.01108-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Parvoviruses package a linear single-stranded DNA genome with hairpin structures at both ends. It has been thought that terminal hairpin sequences are indispensable for viral DNA replication. Here, we provide evidence that the hairpin-deleted duplex genomes of human bocavirus 1 (HBoV1) replicate in human embryonic kidney (HEK) 293 cells. We propose an alternative model for HBoV1 DNA replication in which the leading strand can initiate strand-displacement without "hairpin-transfer." The transfection of the HBoV1 duplex genomes that retain a minimal replication origin at the right-end (OriR), but with extensive deletions in the right-end hairpin (REH), generated viruses in HEK293 cells at a level 10-20 times lower than the wild-type (WT) duplex genome. Importantly, these viruses that have a genome with various deletions after the OriR, but not the one retaining only the OriR, replicated in polarized human airway epithelia. We discovered that the 18-nt sequence (nt 5,403-5,420) beyond the OriR was sufficient to confer virus replication in polarized human airway epithelia, although its progeny virus production was ∼5 times lower than that of the WT virus. Thus, our study demonstrates that hairpin transfer-independent productive parvovirus DNA replication can occur. Importance Hairpin transfer-independent parvovirus replication was modeled with human bocavirus 1 (HBoV1) duplex genomes whose 5' hairpin structure was ablated by various deletions. In HEK293 cells, these duplex viral genomes with ablated 5'/hairpin sequence replicated efficiently and generated viruses that productively infected polarized human airway epithelium. Thus, for the first time, we reveal a previously unknown phenomenon that the productive parvovirus DNA replication does not depend on the hairpin sequence at REH to initiate "rolling hairpin" DNA replication. Notably, the intermediates of viral DNA replication, as revealed two-dimensional electrophoresis, from transfections of hairpin sequence-deleted duplex genome and full-length genome in HEK293 cells, as well as from virus infection of polarized human airway epithelia are similar. Thus, the establishment of the hairpin transfer-independent parvoviral DNA replication deepens our understanding in viral DNA replication and may have implications in development of parvovirus-based viral vectors with alternative properties.
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Mattola S, Hakanen S, Salminen S, Aho V, Mäntylä E, Ihalainen TO, Kann M, Vihinen-Ranta M. Concepts to Reveal Parvovirus-Nucleus Interactions. Viruses 2021; 13:1306. [PMID: 34372512 PMCID: PMC8310053 DOI: 10.3390/v13071306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/24/2021] [Accepted: 07/02/2021] [Indexed: 01/23/2023] Open
Abstract
Parvoviruses are small single-stranded (ss) DNA viruses, which replicate in the nucleoplasm and affect both the structure and function of the nucleus. The nuclear stage of the parvovirus life cycle starts at the nuclear entry of incoming capsids and culminates in the successful passage of progeny capsids out of the nucleus. In this review, we will present past, current, and future microscopy and biochemical techniques and demonstrate their potential in revealing the dynamics and molecular interactions in the intranuclear processes of parvovirus infection. In particular, a number of advanced techniques will be presented for the detection of infection-induced changes, such as DNA modification and damage, as well as protein-chromatin interactions.
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Affiliation(s)
- Salla Mattola
- Department of Biological and Environmental Science, University of Jyvaskyla, 40500 Jyvaskyla, Finland; (S.M.); (S.H.); (S.S.); (V.A.)
| | - Satu Hakanen
- Department of Biological and Environmental Science, University of Jyvaskyla, 40500 Jyvaskyla, Finland; (S.M.); (S.H.); (S.S.); (V.A.)
| | - Sami Salminen
- Department of Biological and Environmental Science, University of Jyvaskyla, 40500 Jyvaskyla, Finland; (S.M.); (S.H.); (S.S.); (V.A.)
| | - Vesa Aho
- Department of Biological and Environmental Science, University of Jyvaskyla, 40500 Jyvaskyla, Finland; (S.M.); (S.H.); (S.S.); (V.A.)
| | - Elina Mäntylä
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (E.M.); (T.O.I.)
| | - Teemu O. Ihalainen
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (E.M.); (T.O.I.)
| | - Michael Kann
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 41390 Gothenburg, Sweden;
- Department of Clinical Microbiology, Sahlgrenska University Hospital, 41345 Gothenburg, Sweden
| | - Maija Vihinen-Ranta
- Department of Biological and Environmental Science, University of Jyvaskyla, 40500 Jyvaskyla, Finland; (S.M.); (S.H.); (S.S.); (V.A.)
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11
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Meier AF, Tobler K, Leisi R, Lkharrazi A, Ros C, Fraefel C. Herpes simplex virus co-infection facilitates rolling circle replication of the adeno-associated virus genome. PLoS Pathog 2021; 17:e1009638. [PMID: 34061891 PMCID: PMC8195378 DOI: 10.1371/journal.ppat.1009638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/11/2021] [Accepted: 05/13/2021] [Indexed: 12/12/2022] Open
Abstract
Adeno-associated virus (AAV) genome replication only occurs in the presence of a co-infecting helper virus such as adenovirus type 5 (AdV5) or herpes simplex virus type 1 (HSV-1). AdV5-supported replication of the AAV genome has been described to occur in a strand-displacement rolling hairpin replication (RHR) mechanism initiated at the AAV 3' inverted terminal repeat (ITR) end. It has been assumed that the same mechanism applies to HSV-1-supported AAV genome replication. Using Southern analysis and nanopore sequencing as a novel, high-throughput approach to study viral genome replication we demonstrate the formation of double-stranded head-to-tail concatemers of AAV genomes in the presence of HSV-1, thus providing evidence for an unequivocal rolling circle replication (RCR) mechanism. This stands in contrast to the textbook model of AAV genome replication when HSV-1 is the helper virus.
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Affiliation(s)
| | - Kurt Tobler
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Remo Leisi
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Anouk Lkharrazi
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Carlos Ros
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Cornel Fraefel
- Institute of Virology, University of Zurich, Zurich, Switzerland
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Song J, Kim HY, Kim S, Jung Y, Park HG. Self-priming phosphorothioated hairpin-mediated isothermal amplification. Biosens Bioelectron 2021; 178:113051. [PMID: 33548651 DOI: 10.1016/j.bios.2021.113051] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 01/21/2021] [Accepted: 01/27/2021] [Indexed: 01/06/2023]
Abstract
We herein describe a novel technology, termed self-priming phosphorothioated hairpin-mediated isothermal amplification (SP-HAMP), enabling target nucleic acid detection. Isothermal amplification strategies are a simple process that efficiently raises the amount of nucleic acid at a constant temperature, but still has lots of problems such as the requirement of multiple exogenous primers and enzymes, which trigger non-specific background signal and increase the complexity of procedures. The key component for overcoming the above-mentioned limitations is the designed hairpin probe (HP) consisting of self-priming region along the 3' stem and the 3' overhang and phosphorothioate modifications at the 5' overhang and the specific loop part. The HP was designed to open through binding to target nucleic acid. Upon opening of HP, its self-priming (SP) region is rearranged to form a smaller hairpin whose 3' end could serve as a primer. The following extension produces the extended HP and displaces the bound target nucleic acid, which is then recycled to open another HP. Due to the reduced stability caused by the specific two phosphorothioate (PS) modifications, the 3' end of EP1 is readily rearranged to form the foldback hairpin structure, which would promote the foldback extension to produce once more extended HP. Since the two PS modifications are always located at the same positions along the 5' stem within the further extended HPs, the foldback reaction followed by the extension would be continuously repeated, consequently producing a large number of the long hairpin concatamers. Based on this unique design principle, we successfully detected even a single copy of target DNA with outstanding discrimination capability under an isothermal condition by employing only a single HP without the requirement for the complicated multiple primers. In conclusion, the sophisticated design principle employed in this work would provide great insight for the development of self-operative isothermal amplifying system enabling short target nucleic acid detection such as microRNAs or any target which is less than 200 mer.
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Affiliation(s)
- Jayeon Song
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyo Yong Kim
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Soohyun Kim
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yujin Jung
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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13
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Majumder K, Boftsi M, Whittle FB, Wang J, Fuller MS, Joshi T, Pintel DJ. The NS1 protein of the parvovirus MVM Aids in the localization of the viral genome to cellular sites of DNA damage. PLoS Pathog 2020; 16:e1009002. [PMID: 33064772 PMCID: PMC7592911 DOI: 10.1371/journal.ppat.1009002] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/28/2020] [Accepted: 09/24/2020] [Indexed: 12/14/2022] Open
Abstract
The autonomous parvovirus Minute Virus of Mice (MVM) localizes to cellular DNA damage sites to establish and sustain viral replication centers, which can be visualized by focal deposition of the essential MVM non-structural phosphoprotein NS1. How such foci are established remains unknown. Here, we show that NS1 localized to cellular sites of DNA damage independently of its ability to covalently bind the 5’ end of the viral genome, or its consensus DNA binding sequence. Many of these sites were identical to those occupied by virus during infection. However, localization of the MVM genome to DNA damage sites occurred only when wild-type NS1, but not its DNA-binding mutant was expressed. Additionally, wild-type NS1, but not its DNA binding mutant, could localize a heterologous DNA molecule containing the NS1 binding sequence to DNA damage sites. These findings suggest that NS1 may function as a bridging molecule, helping the MVM genome localize to cellular DNA damage sites to facilitate ongoing virus replication. Parvoviruses are among the simplest of viruses, depending almost exclusively on host cell factors to successfully replicate. We have previously shown that the parvovirus Minute Virus of Mice (MVM) establishes replication centers at sites that are associated with cellular regions of DNA damage. These sites are primed to contain factors necessary to efficiently initiate vigorous virus lytic infection. The process by which viral proteins and viral DNA specifically localize to these sites has previously remained unknown. In this study we show that the essential viral protein NS1 possesses the intrinsic ability to localize to cellular sites of DNA damage. Additionally, wild-type NS1, but not its DNA binding mutant, could localize to sites of DNA damage both the MVM genome, or a heterologous DNA molecule engineered to contain NS1 binding sites. This work provides the first evidence that NS1 may function as a bridging molecule to localize the MVM genome to cellular sites of DNA damage to facilitate ongoing replication.
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Affiliation(s)
- Kinjal Majumder
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States of America
- * E-mail: (KM); (DJP)
| | - Maria Boftsi
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States of America
- Pathobiology Area Graduate Program, University of Missouri, Columbia, Missouri, United States of America
| | - Fawn B. Whittle
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States of America
| | - Juexin Wang
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States of America
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, United States of America
| | - Matthew S. Fuller
- Ultragenyx Gene Therapy, Cambridge, Massachusetts, United States of America
| | - Trupti Joshi
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States of America
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, United States of America
- Department of Health Management and Informatics, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- MU Institute of Data Science and Informatics, University of Missouri, Columbia, Missouri, United States of America
| | - David J. Pintel
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States of America
- * E-mail: (KM); (DJP)
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14
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Koonin EV, Dolja VV, Krupovic M, Varsani A, Wolf YI, Yutin N, Zerbini FM, Kuhn JH. Global Organization and Proposed Megataxonomy of the Virus World. Microbiol Mol Biol Rev 2020; 84:e00061-19. [PMID: 32132243 PMCID: PMC7062200 DOI: 10.1128/mmbr.00061-19] [Citation(s) in RCA: 295] [Impact Index Per Article: 73.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Viruses and mobile genetic elements are molecular parasites or symbionts that coevolve with nearly all forms of cellular life. The route of virus replication and protein expression is determined by the viral genome type. Comparison of these routes led to the classification of viruses into seven "Baltimore classes" (BCs) that define the major features of virus reproduction. However, recent phylogenomic studies identified multiple evolutionary connections among viruses within each of the BCs as well as between different classes. Due to the modular organization of virus genomes, these relationships defy simple representation as lines of descent but rather form complex networks. Phylogenetic analyses of virus hallmark genes combined with analyses of gene-sharing networks show that replication modules of five BCs (three classes of RNA viruses and two classes of reverse-transcribing viruses) evolved from a common ancestor that encoded an RNA-directed RNA polymerase or a reverse transcriptase. Bona fide viruses evolved from this ancestor on multiple, independent occasions via the recruitment of distinct cellular proteins as capsid subunits and other structural components of virions. The single-stranded DNA (ssDNA) viruses are a polyphyletic class, with different groups evolving by recombination between rolling-circle-replicating plasmids, which contributed the replication protein, and positive-sense RNA viruses, which contributed the capsid protein. The double-stranded DNA (dsDNA) viruses are distributed among several large monophyletic groups and arose via the combination of distinct structural modules with equally diverse replication modules. Phylogenomic analyses reveal the finer structure of evolutionary connections among RNA viruses and reverse-transcribing viruses, ssDNA viruses, and large subsets of dsDNA viruses. Taken together, these analyses allow us to outline the global organization of the virus world. Here, we describe the key aspects of this organization and propose a comprehensive hierarchical taxonomy of viruses.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Mart Krupovic
- Institut Pasteur, Archaeal Virology Unit, Department of Microbiology, Paris, France
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - F Murilo Zerbini
- Departamento de Fitopatologia/Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
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15
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Abstract
Parvoviruses are structurally simple viruses with linear single-stranded DNA genomes and nonenveloped icosahedral capsids. They infect a wide range of animals from insects to humans. Parvovirus B19 is a long-known human pathogen, whereas adeno-associated viruses are nonpathogenic. Since 2005, many parvoviruses have been discovered in human-derived samples: bocaviruses 1-4, parvovirus 4, bufavirus, tusavirus, and cutavirus. Some human parvoviruses have already been shown to cause disease during acute infection, some are associated with chronic diseases, and others still remain to be proven clinically relevant-or harmless commensals, a distinction not as apparent as it might seem. One initially human-labeled parvovirus might not even be a human virus, whereas another was originally overlooked due to inadequate diagnostics. The intention of this review is to follow the rocky road of emerging human parvoviruses from discovery of a DNA sequence to current and future clinical status, highlighting the perils along the way.
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16
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Abstract
Single-stranded (ss)DNA viruses are extremely widespread, infect diverse hosts from all three domains of life and include important pathogens. Most ssDNA viruses possess small genomes that replicate by the rolling-circle-like mechanism initiated by a distinct virus-encoded endonuclease. High throughput genome sequencing and improved bioinformatics tools have yielded vast information on presence of ssDNA viruses in diverse habitats. The simple genome of ssDNA viruses have high propensity to undergo mutation and recombination often emerging as threat to human civilization. Interestingly their genome is found embedded in fossils dating back to million years. The unusual evolutionary history of ssDNA viruses reveal evidences of horizontal gene transfer, sometimes between different species and genera.
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17
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Matz B, Kupfer B, Kallies R, Külshammer M, Flötenmeyer M, Kreil TR, Eis-Hübinger AM. Secondary structure of DNA released from purified capsids of human parvovirus B19 under moderate denaturing conditions. J Gen Virol 2019; 100:812-827. [PMID: 30924765 DOI: 10.1099/jgv.0.001253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Parvovirus B19 (B19V) possesses a linear single-stranded DNA genome of either positive or negative polarity. Due to intramolecular sequence homologies, either strand may theoretically be folded in several alternative ways. Viral DNA, when extracted from virions by several procedures, presents as linear single-stranded and/or linear double-stranded molecules, except when one particular commercial kit is used. This protocol yields DNA with an aberrant electrophoretic mobility in addition to linear double-stranded molecules, but never any single-stranded molecules. This peculiar kind of DNA was found in all plasma or serum samples tested and so we decided to analyse its secondary structure. In line with our results for one- and two-dimensional electrophoresis, mobility shift assays, DNA preparation by an in-house extraction method with moderate denaturing conditions, density gradient ultracentrifugation, DNA digestion experiments and competition hybridization assays, we conclude that (i) the unique internal portions of this distinctive single-stranded molecules are folded into tight tangles and (ii) the two terminal redundant regions are associated with each other, yielding non-covalently closed pseudo-circular molecules stabilized by a short (18 nucleotides) intramolecular stem, whereas the extreme 3'- and 5'-ends are folded back on themselves, forming a structure resembling a twin hairpin. The question arises as to whether this fairly unstable structure represents the encapsidated genome structure. The answer to this question remains quite relevant in terms of comprehending the initiation and end of B19V genome replication.
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Affiliation(s)
- Bertfried Matz
- 1Institute of Virology, University of Bonn Medical Centre, Germany
| | - Bernd Kupfer
- 1Institute of Virology, University of Bonn Medical Centre, Germany
| | - René Kallies
- 1Institute of Virology, University of Bonn Medical Centre, Germany.,2Helmholtz Centre for Environmental Research, Leipzig, Germany
| | | | - Matthias Flötenmeyer
- 3Max-Planck-Institute for Developmental Biology, Tübingen, Germany.,4Centre for Microscopy and Microanalysis, University of Queensland, St Lucia/Brisbane, Australia
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18
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Grecco S, Iraola G, Decaro N, Alfieri A, Alfieri A, Gallo Calderón M, da Silva AP, Name D, Aldaz J, Calleros L, Marandino A, Tomás G, Maya L, Francia L, Panzera Y, Pérez R. Inter- and intracontinental migrations and local differentiation have shaped the contemporary epidemiological landscape of canine parvovirus in South America. Virus Evol 2018; 4:vey011. [PMID: 29657837 PMCID: PMC5892152 DOI: 10.1093/ve/vey011] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Canine parvovirus (CPV) is a fast-evolving single-stranded DNA virus that causes one of the most significant infectious diseases of dogs. Although the virus dispersed over long distances in the past, current populations are considered to be spatially confined and with only a few instances of migration between specific localities. It is unclear whether these dynamics occur in South America where global studies have not been performed. The aim of this study is to analyze the patterns of genetic variability in South American CPV populations and explore their evolutionary relationships with global strains. Genomic sequences of sixty-three strains from South America and Europe were generated and analyzed using a phylodynamic approach. All the obtained strains belong to the CPV-2a lineage and associate with global strains in four monophyletic groups or clades. European and South American strains from all the countries here analyzed are representative of a widely distributed clade (Eur-I) that emerged in Southern Europe during 1990–98 to later spread to South America in the early 2000s. The emergence and spread of the Eur-I clade were correlated with a significant rise in the CPV effective population size in Europe and South America. The Asia-I clade includes strains from Asia and Uruguay. This clade originated in Asia during the late 1980s and evolved locally before spreading to South America during 2009–10. The third clade (Eur-II) comprises strains from Italy, Brazil, and Ecuador. This clade appears in South America as a consequence of an early introduction from Italy to Ecuador in the middle 1980s and has experienced extensive local genetic differentiation. Some strains from Argentina, Uruguay, and Brazil constitute an exclusive South American clade (SA-I) that emerged in Argentina in the 1990s. These results indicate that the current epidemiological scenario is a consequence of inter- and intracontinental migrations of strains with different geographic and temporal origins that set the conditions for competition and local differentiation of CPV populations. The coexistence and interaction of highly divergent strains are the main responsible for the drastic epidemiological changes observed in South America in the last two decades. This highlights the threat of invasion from external sources and the importance of whole-genome resolution to robustly infer the origin and spread of new CPV variants. From a taxonomic standpoint, the findings herein show that the classification system that uses a single amino acid to identify variants (2a, 2b, and 2c) within the CPV-2a lineage does not reflect phylogenetic relationships and is not suitable to analyze CPV evolution. In this regard, the identification of clades or sublineages within circulating CPV strains is the first step towards a genetic and evolutionary classification of the virus.
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Affiliation(s)
- Sofía Grecco
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Gregorio Iraola
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.,Unidad de Bioinformática, Institut Pasteur Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
| | - Nicola Decaro
- Department of Veterinary Medicine, University of Bari, Strada Provinciale per Casamassima Km 3, 70010 Valenzano, Bari, Italy
| | - Alice Alfieri
- Laboratory of Animal Virology, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, PO Box 6001, Rodovia Celso Garcia Cid, PR 445 Km 380, Londrina, Paraná 86051-990, Brazil
| | - Amauri Alfieri
- Laboratory of Animal Virology, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, PO Box 6001, Rodovia Celso Garcia Cid, PR 445 Km 380, Londrina, Paraná 86051-990, Brazil
| | - Marina Gallo Calderón
- Instituto de Ciencia y Tecnología Dr. Cesar Milstein, CONICET, Saladillo 2468, C1440FFX Ciudad Autónoma de Buenos Aires, Argentina
| | - Ana Paula da Silva
- Laboratory of Animal Virology, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, PO Box 6001, Rodovia Celso Garcia Cid, PR 445 Km 380, Londrina, Paraná 86051-990, Brazil
| | - Daniela Name
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.,Laboratory of Animal Virology, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, PO Box 6001, Rodovia Celso Garcia Cid, PR 445 Km 380, Londrina, Paraná 86051-990, Brazil
| | - Jaime Aldaz
- Escuela de Medicina Veterinaria y Zootecnia, Facultad de Ciencias Agropecuarias, Universidad Estatal de Bolívar, Av. Ernesto Che Guevara s/n. Guaranda, Ecuador
| | - Lucía Calleros
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Ana Marandino
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Gonzalo Tomás
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Leticia Maya
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Lourdes Francia
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Yanina Panzera
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Ruben Pérez
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
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19
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Tang YW, Stratton CW. The Role of the Human Bocavirus (HBoV) in Respiratory Infections. ADVANCED TECHNIQUES IN DIAGNOSTIC MICROBIOLOGY 2018. [PMCID: PMC7120174 DOI: 10.1007/978-3-319-95111-9_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The human bocavirus is one of the most common respiratory viruses and occurs in all age groups. Because Koch’s postulates have been fulfilled unintendedly, it is currently accepted that the virus is a real pathogen associated with upper and lower respiratory tract infections causing clinical symptoms ranging from a mild common cold to life-threatening respiratory diseases. In order to exclude a viremia, serological analysis should be included during laboratory diagnostics, as acute and chronic infections cannot be differentiated by detection of viral nucleic acids in respiratory specimen alone due to prolonged viral shedding. Besides its ability to persist, the virus appears to trigger chronic lung disease and increases clinical symptoms by causing fibrotic lung diseases. Due to the lack of an animal model, clinical trials remain the major method for studying the long-term effects of HBoV infections.
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Affiliation(s)
- Yi-Wei Tang
- Departments of Laboratory Medicine and Internal Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Charles W. Stratton
- Department of Pathology, Microbiology and Immunology and Medicine, Vanderbilt University Medical Center, Nashville, TN USA
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20
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Wawrzyniak P, Płucienniczak G, Bartosik D. The Different Faces of Rolling-Circle Replication and Its Multifunctional Initiator Proteins. Front Microbiol 2017; 8:2353. [PMID: 29250047 PMCID: PMC5714925 DOI: 10.3389/fmicb.2017.02353] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/15/2017] [Indexed: 11/13/2022] Open
Abstract
Horizontal gene transfer (HGT) contributes greatly to the plasticity and evolution of prokaryotic and eukaryotic genomes. The main carriers of foreign DNA in HGT are mobile genetic elements (MGEs) that have extremely diverse genetic structures and properties. Various strategies are used for the maintenance and spread of MGEs, including (i) vegetative replication, (ii) transposition (and other types of recombination), and (iii) conjugal transfer. In many MGEs, all of these processes are dependent on rolling-circle replication (RCR). RCR is one of the most well characterized models of DNA replication. Although many studies have focused on describing its mechanism, the role of replication initiator proteins has only recently been subject to in-depth analysis, which indicates their involvement in multiple biological process associated with RCR. In this review, we present a general overview of RCR and its impact in HGT. We focus on the molecular characteristics of RCR initiator proteins belonging to the HUH and Rep_trans protein families. Despite analogous mechanisms of action these are distinct groups of proteins with different catalytic domain structures. This is the first review describing the multifunctional character of various types of RCR initiator proteins, including the latest discoveries in the field. Recent reports provide evidence that (i) proteins initiating vegetative replication (Rep) or mobilization for conjugal transfer (Mob) may also have integrase (Int) activity, (ii) some Mob proteins are capable of initiating vegetative replication (Rep activity), and (iii) some Rep proteins can act like Mob proteins to mobilize plasmid DNA for conjugal transfer. These findings have significant consequences for our understanding of the role of RCR, not only in DNA metabolism but also in the biology of many MGEs.
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Affiliation(s)
- Paweł Wawrzyniak
- Department of Bioengineering, Institute of Biotechnology and Antibiotics, Warsaw, Poland.,Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Grażyna Płucienniczak
- Department of Bioengineering, Institute of Biotechnology and Antibiotics, Warsaw, Poland
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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21
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Identification of Vaccinia Virus Replisome and Transcriptome Proteins by Isolation of Proteins on Nascent DNA Coupled with Mass Spectrometry. J Virol 2017; 91:JVI.01015-17. [PMID: 28747503 DOI: 10.1128/jvi.01015-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 07/19/2017] [Indexed: 12/22/2022] Open
Abstract
Poxviruses replicate within the cytoplasm and encode proteins for DNA and mRNA synthesis. To investigate poxvirus replication and transcription from a new perspective, we incorporated 5-ethynyl-2'-deoxyuridine (EdU) into nascent DNA in cells infected with vaccinia virus (VACV). The EdU-labeled DNA was conjugated to fluor- or biotin-azide and visualized by confocal, superresolution, and transmission electron microscopy. Nuclear labeling decreased dramatically after infection, accompanied by intense labeling of cytoplasmic foci. The nascent DNA colocalized with the VACV single-stranded DNA binding protein I3 in multiple puncta throughout the interior of factories, which were surrounded by endoplasmic reticulum. Complexes containing EdU-biotin-labeled DNA cross-linked to proteins were captured on streptavidin beads. After elution and proteolysis, the peptides were analyzed by mass spectrometry to identify proteins associated with nascent DNA. The known viral replication proteins, a telomere binding protein, and a protein kinase were associated with nascent DNA, as were the DNA-dependent RNA polymerase and intermediate- and late-stage transcription initiation and elongation factors, plus the capping and methylating enzymes. These results suggested that the replicating pool of DNA is transcribed and that few if any additional viral proteins directly engaged in replication and transcription remain to be discovered. Among the host proteins identified by mass spectrometry, topoisomerases IIα and IIβ and PCNA were noteworthy. The association of the topoisomerases with nascent DNA was dependent on expression of the viral DNA ligase, in accord with previous proteomic studies. Further investigations are needed to determine possible roles for PCNA and other host proteins detected.IMPORTANCE Poxviruses, unlike many well-characterized animal DNA viruses, replicate entirely within the cytoplasm of animal cells, raising questions regarding the relative roles of viral and host proteins. We adapted newly developed procedures for click chemistry and iPOND (Isolation of proteins on nascent DNA) to investigate vaccinia virus (VACV), the prototype poxvirus. Nuclear DNA synthesis ceased almost immediately following VACV infection, followed swiftly by the synthesis of viral DNA within discrete cytoplasmic foci. All viral proteins known from genetic and proteomic studies to be required for poxvirus DNA replication were identified in the complexes containing nascent DNA. The additional detection of the viral DNA-dependent RNA polymerase and intermediate and late transcription factors provided evidence for a temporal coupling of replication and transcription. Further studies are needed to assess the potential roles of host proteins, including topoisomerases IIα and IIβ and PCNA, which were found associated with nascent DNA.
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22
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Lau SKP, Ahmed SS, Yeung HC, Li KSM, Fan RYY, Cheng TYC, Cai JP, Wang M, Zheng BJ, Wong SSY, Woo PCY, Yuen KY. Identification and interspecies transmission of a novel bocaparvovirus among different bat species in China. J Gen Virol 2016; 97:3345-3358. [PMID: 27902362 DOI: 10.1099/jgv.0.000645] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We report the discovery of a novel bocaparvovirus, bat bocaparvovirus (BtBoV), in one spleen, four respiratory and 61 alimentary samples from bats of six different species belonging to three families, Hipposideridae, Rhinolophidae and Vespertilionidae. BtBoV showed a higher detection rate in alimentary samples of Rhinolophus sinicus (5.7 %) than those of other bat species (0.43-1.59 %), supporting R. sinicus as the primary reservoir and virus spillover to accidental bat species. BtBoV peaked during the lactating season of R. sinicus, and it was more frequently detected among female than male adult bats (P<0.05), and among lactating than non-lactating female bats (P<0.0001). Positive BtBoV detection was associated with lower body weight in lactating bats (P<0.05). Ten nearly complete BtBoV genomes from three bat species revealed a unique large ORF1 spanning NS1 and NP1 in eight genomes and conserved splicing signals leading to multiple proteins, as well as a unique substitution in the conserved replication initiator motif within NS1. BtBoV was phylogenetically distantly related to known bocaparvoviruses with ≤57.3 % genome identities, supporting BtBoV as a novel species. Ms-BtBoV from Miniopterus schreibersii and Hp-BtBoV from Hipposideros pomona demonstrated 97.2-99.9 % genome identities with Rs-BtBoVs from R. sinicus, supporting infection of different bat species by a single BtBoV species. Rs-BtBoV_str15 represents the first bat parvovirus genome with non-coding regions sequenced, which suggested the presence of head-to-tail genomic concatamers or episomal forms of the genome. This study represents the first to describe interspecies transmission in BoVs. The high detection rates in lactating female and juvenile bats suggest possible vertical transmission of BtBoV.
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Affiliation(s)
- Susanna K P Lau
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, PR China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Syed Shakeel Ahmed
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Hazel C Yeung
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Kenneth S M Li
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Rachel Y Y Fan
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Toni Y C Cheng
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Jian-Piao Cai
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Ming Wang
- Guangzhou Center for Disease Control and Prevention, Guangzhou, PR China
| | - Bo-Jian Zheng
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, PR China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, PR China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR China.,Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Samson S Y Wong
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, PR China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, PR China
| | - Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, PR China.,Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, PR China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR China
| | - Kwok-Yung Yuen
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, PR China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, PR China
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23
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Zhao H, Cheng Y, Wang J, Lin P, Yi L, Sun Y, Ren J, Tong M, Cao Z, Li J, Deng J, Cheng S. Profiling of Host Cell Response to Successive Canine Parvovirus Infection Based on Kinetic Proteomic Change Identification. Sci Rep 2016; 6:29560. [PMID: 27406444 PMCID: PMC4942776 DOI: 10.1038/srep29560] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/20/2016] [Indexed: 01/15/2023] Open
Abstract
Canine parvovirus (CPV) reproduces by co-opting the resources of host cells, inevitably causing cytotoxic effects to the host cells. Feline kidney F81 cells are sensitive to CPV infection and show disparate growing statuses at different time points post-infection. This study analysed the response of F81 cells to CPV infection at successive infection time points by iTRAQ-based quantitative proteomics. Differentially expressed proteins (DEPs) during 60 h of infection and at selected time points post-infection were identified by an analysis of variance test and a two-tailed unpaired t test, respectively. DEPs with similar quantitative changes were clustered by hierarchical clustering and analysed by gene ontology enrichment, revealing that 12 h and 60 h post-infection were the optimal times to analyse the autonomous parvovirus replication and apoptosis processes, respectively. Using the MetacoreTM database, 29 DEPs were enriched in a network involved in p53 regulation. Besides, a significantly enriched pathway suggests that the CPV-induced cytopathic effect was probably due to the deficiency of functional CFTR caused by CPV infection. This study uncovered the systemic changes in key cellular factors involved in CPV infection and help to understand the molecular mechanisms of the anti-cancer activity of CPV and the cytopathic effects induced by CPV infection.
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Affiliation(s)
- Hang Zhao
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Yuening Cheng
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Jianke Wang
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Peng Lin
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Li Yi
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Yaru Sun
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Jingqiang Ren
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Mingwei Tong
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Zhigang Cao
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Jiawei Li
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Jinliang Deng
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Shipeng Cheng
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
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24
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Schildgen O, Schildgen V. Respiratory infections of the human bocavirus. THE MICROBIOLOGY OF RESPIRATORY SYSTEM INFECTIONS 2016. [PMCID: PMC7149820 DOI: 10.1016/b978-0-12-804543-5.00005-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The human bocavirus is one of the most common respiratory viruses and occurs in all age groups. It is associated with upper and lower respiratory tract infections, and causes clinical symptoms from the mild common cold to life threatening respiratory diseases. Besides its ability to persist the virus appears to trigger chronic lung disease and increase the clinical symptoms, while being a putative trigger for fibrotic lung diseases. Laboratory diagnostics should include serological diagnostics in order to rule out a viremia because due to prolonged viral shedding acute and chronic infections cannot be differentiated on the detection of viral nucleic acids in respiratory specimen alone. Although Koch’s postulates cannot be formally fulfilled due to the lack of an animal model and the chance for clinical trials with volunteers are limited due to the long term effects of HBoV infections, there is no doubt that the virus is a serious pathogen and requires attention. The aim of the chapter is to present an overview of our current knowledge on respiratory infections with the human bocavirus, and to provide basic and essential information on clinical features, molecular diagnostics, and epidemiologic challenges arising with this pathogen.
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25
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First complete genome of an Ambidensovirus; Cherax quadricarinatus densovirus, from freshwater crayfish Cherax quadricarinatus. Mar Genomics 2015; 24 Pt 3:305-12. [DOI: 10.1016/j.margen.2015.07.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 07/29/2015] [Accepted: 07/29/2015] [Indexed: 11/18/2022]
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26
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Lentz TB, Samulski RJ. Insight into the mechanism of inhibition of adeno-associated virus by the Mre11/Rad50/Nbs1 complex. J Virol 2015; 89:181-94. [PMID: 25320294 PMCID: PMC4301101 DOI: 10.1128/jvi.01990-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 10/03/2014] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Adeno-associated virus (AAV) is a dependent virus of the family Parvoviridae. The gene expression and replication of AAV and derived recombinant AAV (rAAV) vectors are severely limited (>10-fold) by the cellular DNA damage-sensing complex made up of Mre11, Rad50, and Nbs1 (MRN). The AAV genome does not encode the means to circumvent this block to productive infection but relies on coinfecting helper virus to do so. Using adenovirus helper proteins E1B55k and E4orf6, which enhance the transduction of AAV via degradation of MRN, we investigated the mechanism through which this DNA damage complex inhibits gene expression from rAAV. We tested the substrate specificity of inhibition and the contribution of different functions of the MRN complex. Our results demonstrate that both single- and double-stranded rAAV vectors are inhibited by MRN, which is in contrast to the predominant model that inhibition is the result of a block to second-strand synthesis. Exploring the contribution of known functions of MRN, we found that inhibition of rAAV does not require downstream DNA damage response factors, including signaling kinases ATM and ATR. The nuclease domain of Mre11 appears to play only a minor role in inhibition, while the DNA binding domain makes a greater contribution. Additionally, mutation of the inverted terminal repeat of the rAAV genome, which has been proposed to be the signal for interaction with MRN, is tolerated by the mechanism of inhibition. These results articulate a model of inhibition of gene expression in which physical interaction is more important than enzymatic activity and several key downstream damage repair factors are dispensable. IMPORTANCE Many viruses modulate the host DNA damage response (DDR) in order to create a cellular environment permissive for infection. The MRN complex is a primary sensor of damage in the cell but also responds to invading viral genomes, often posing a block to infection. AAV is greatly inhibited by MRN and dependent on coinfecting helper virus, such as adenovirus, to remove this factor. Currently, the mechanism through which MRN inhibits AAV and other viruses is poorly understood. Our results reform the predominant model that inhibition of rAAV by MRN is due to limiting second-strand DNA synthesis. Instead, a novel mechanism of inhibition of gene expression independent of a block in rAAV DNA synthesis or downstream damage factors is indicated. These findings have clear implications for understanding this restriction to transduction of AAV and rAAV vectors, which have high therapeutic relevance and likely translate to other viruses that must navigate the DDR.
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Affiliation(s)
- Thomas B Lentz
- Gene Therapy Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - R Jude Samulski
- Gene Therapy Center, University of North Carolina, Chapel Hill, North Carolina, USA Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, USA
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27
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Porcine bocavirus: achievements in the past five years. Viruses 2014; 6:4946-60. [PMID: 25514206 PMCID: PMC4276938 DOI: 10.3390/v6124946] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 12/01/2014] [Accepted: 12/02/2014] [Indexed: 01/05/2023] Open
Abstract
Porcine bocavirus is a recently discovered virus that infects pigs and is classified within the Bocavirus genus (family Parvoviridae, subfamily Parvovirinae). The viral genome constitutes linear single-stranded DNA and has three open reading frames that encode four proteins: NS1, NP1, VP1, and VP2. There have been more than seven genotypes discovered to date. These genotypes have been classified into three groups based on VP1 sequence. Porcine bocavirus is much more prevalent in piglets that are co-infected with other pathogens than in healthy piglets. The virus can be detected using PCR, loop-mediated isothermal amplification, cell cultures, indirect immunofluorescence, and other molecular virology techniques. Porcine bocavirus has been detected in various samples, including stool, serum, lymph nodes, and tonsils. Because this virus was discovered only five years ago, there are still many unanswered questions that require further research. This review summarizes the current state of knowledge and primary research achievements regarding porcine bocavirus.
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28
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Pérez R, Calleros L, Marandino A, Sarute N, Iraola G, Grecco S, Blanc H, Vignuzzi M, Isakov O, Shomron N, Carrau L, Hernández M, Francia L, Sosa K, Tomás G, Panzera Y. Phylogenetic and genome-wide deep-sequencing analyses of canine parvovirus reveal co-infection with field variants and emergence of a recent recombinant strain. PLoS One 2014; 9:e111779. [PMID: 25365348 PMCID: PMC4218814 DOI: 10.1371/journal.pone.0111779] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 09/30/2014] [Indexed: 11/28/2022] Open
Abstract
Canine parvovirus (CPV), a fast-evolving single-stranded DNA virus, comprises three antigenic variants (2a, 2b, and 2c) with different frequencies and genetic variability among countries. The contribution of co-infection and recombination to the genetic variability of CPV is far from being fully elucidated. Here we took advantage of a natural CPV population, recently formed by the convergence of divergent CPV-2c and CPV-2a strains, to study co-infection and recombination. Complete sequences of the viral coding region of CPV-2a and CPV-2c strains from 40 samples were generated and analyzed using phylogenetic tools. Two samples showed co-infection and were further analyzed by deep sequencing. The sequence profile of one of the samples revealed the presence of CPV-2c and CPV-2a strains that differed at 29 nucleotides. The other sample included a minor CPV-2a strain (13.3% of the viral population) and a major recombinant strain (86.7%). The recombinant strain arose from inter-genotypic recombination between CPV-2c and CPV-2a strains within the VP1/VP2 gene boundary. Our findings highlight the importance of deep-sequencing analysis to provide a better understanding of CPV molecular diversity.
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Affiliation(s)
- Ruben Pérez
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- * E-mail:
| | - Lucía Calleros
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ana Marandino
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Nicolás Sarute
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Gregorio Iraola
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Sofia Grecco
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Hervé Blanc
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique, Paris, France
| | - Marco Vignuzzi
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique, Paris, France
| | - Ofer Isakov
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lucía Carrau
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Martín Hernández
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Lourdes Francia
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Katia Sosa
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Gonzalo Tomás
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Yanina Panzera
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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29
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Infectious hypodermal and hematopoietic necrosis virus from Brazil: Sequencing, comparative analysis and PCR detection. Virus Res 2014; 189:136-46. [DOI: 10.1016/j.virusres.2014.05.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 05/07/2014] [Accepted: 05/11/2014] [Indexed: 12/11/2022]
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30
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Abstract
Parvoviruses are small, rugged, nonenveloped protein particles containing a linear, nonpermuted, single-stranded DNA genome of ∼5 kb. Their limited coding potential requires optimal adaptation to the environment of particular host cells, where entry is mediated by a variable program of capsid dynamics, ultimately leading to genome ejection from intact particles within the host nucleus. Genomes are amplified by a continuous unidirectional strand-displacement mechanism, a linear adaptation of rolling circle replication that relies on the repeated folding and unfolding of small hairpin telomeres to reorient the advancing fork. Progeny genomes are propelled by the viral helicase into the preformed capsid via a pore at one of its icosahedral fivefold axes. Here we explore how the fine-tuning of this unique replication system and the mechanics that regulate opening and closing of the capsid fivefold portals have evolved in different viral lineages to create a remarkably complex spectrum of phenotypes.
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Affiliation(s)
| | - Peter Tattersall
- Departments of 1Laboratory Medicine and.,Genetics, Yale University Medical School, New Haven, Connecticut 06510;
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31
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Fernandes S, Boisvert M, Szelei J, Tijssen P. Differential replication of two porcine parvovirus strains in bovine cell lines ensues from initial DNA processing and NS1 expression. J Gen Virol 2014; 95:910-921. [DOI: 10.1099/vir.0.059741-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Porcine parvovirus (PPV) is a small DNA virus with restricted coding capacity. The 5 kb genome expresses three major non-structural proteins (NS1, NS2 and SAT), and two structural proteins (VP1 and VP2). These few viral proteins are pleiotropic and interact with cellular components throughout viral replication. In this regard, very few cell lines have been shown to replicate the virus efficiently. Cell lines were established from a primary culture of bovine cells that allowed allotropic variants of PPV to be distinguished. Three cell lines were differentially sensitive to infection by two prototype PPV strains, NADL-2 and Kresse. In the first cell line (D10), infection was restricted early in the infectious cycle and was not productive. Infection of the second cell line (G11) was 1000 times less efficient with the NADL-2 strain compared with porcine cells, while production of infectious virus of the Kresse strain was barely detectable. Restriction points in these cells were the initial generation of DNA replication intermediates and NS1 production. Infection with chimeras between NADL-2 and Kresse showed that residues outside the previously described allotropic determinant were also partially responsible for the restriction to Kresse replication in G11 cells. F4 cells were permissive to both strains, although genome replication and infectious virus production were lower than in the porcine cells used for comparison. These results highlight the dependent nature of parvovirus tropism on host factors and suggest that cells from a non-host origin can fully support a productive infection by both strains.
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Affiliation(s)
- Sandra Fernandes
- INRS-Institut Armand-Frappier, Université du Québec, 531 boulevard des Prairies, Laval, Québec, Canada H7V 1B7
| | - Maude Boisvert
- INRS-Institut Armand-Frappier, Université du Québec, 531 boulevard des Prairies, Laval, Québec, Canada H7V 1B7
| | - Jozsef Szelei
- INRS-Institut Armand-Frappier, Université du Québec, 531 boulevard des Prairies, Laval, Québec, Canada H7V 1B7
| | - Peter Tijssen
- INRS-Institut Armand-Frappier, Université du Québec, 531 boulevard des Prairies, Laval, Québec, Canada H7V 1B7
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32
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Abstract
HUH endonucleases are numerous and widespread in all three domains of life. The major function of these enzymes is processing a range of mobile genetic elements by catalysing cleavage and rejoining of single-stranded DNA using an active-site Tyr residue to make a transient 5'-phosphotyrosine bond with the DNA substrate. These enzymes have a key role in rolling-circle replication of plasmids and bacteriophages, in plasmid transfer, in the replication of several eukaryotic viruses and in various types of transposition. They have also been appropriated for cellular processes such as intron homing and the processing of bacterial repeated extragenic palindromes. Here, we provide an overview of these fascinating enzymes and their functions, using well-characterized examples of Rep proteins, relaxases and transposases, and we explore the molecular mechanisms used in their diverse activities.
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33
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Xiao CT, Giménez-Lirola LG, Jiang YH, Halbur PG, Opriessnig T. Characterization of a novel porcine parvovirus tentatively designated PPV5. PLoS One 2013; 8:e65312. [PMID: 23762339 PMCID: PMC3676418 DOI: 10.1371/journal.pone.0065312] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 04/25/2013] [Indexed: 12/28/2022] Open
Abstract
A new porcine parvovirus (PPV), provisionally designated as PPV5, was identified in U.S. pigs. Cloning and sequencing from a circular or head-to-tail concatemeric array revealed that the PPV5 possesses the typical genomic organization of parvoviruses with two major predicted open reading frames (ORF1 and ORF2), and is most closely related to PPV4 with overall genomic identities of 64.1–67.3%. The amino acid identities between PPV5 and PPV4 were 84.6%–85.1% for ORF1 and 54.0%–54.3% for ORF2. Unlike PPV4, but similar to bovine parvovirus 2 (BPV2), PPV5 lacks the additional ORF3 and has a much longer ORF2. Moreover, the amino acid sequences of ORF1 and ORF2 of BPV2 showed higher homologies to PPV5 than to PPV4. The conserved motifs of the Ca2+ binding loop (YXGXG) and the catalytic center (HDXXY) of phospholipase A2 (PLA2) were identified in VP1 (ORF2) of PPV5, as well as in BPV2, but were not present in PPV4. Phylogenetic analyses revealed that PPV5, PPV4 and BPV2 form a separate clade different from the genera Parvovirus and Bocavirus. Further epidemiologic investigations of PPV4 and PPV5 in U.S. pigs of different ages indicated a slightly higher prevalence for PPV5 (6.6%; 32/483) compared to PPV4 (4.1%; 20/483), with detection of concurrent PPV4 and PPV5 in 15.6% (7/45) of lungs of infected pigs. Evidence for potential vertical transmission or association with reproductive failure was minimal for both PPV4 and PPV5. The high similarity to PPV4 and the lack of ORF3 may suggest PPV5 is an intermediate of PPV4 during the evolution of parvoviruses in pigs.
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Affiliation(s)
- Chao-Ting Xiao
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Luis G. Giménez-Lirola
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Yong-Hou Jiang
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Patrick G. Halbur
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Tanja Opriessnig
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
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34
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Abstract
Parvoviruses are a group of small DNA viruses with ssDNA genomes flanked by two inverted terminal structures. Due to a limited genetic resource they require host cellular factors and sometimes a helper virus for efficient viral replication. Recent studies have shown that parvoviruses interact with the DNA damage machinery, which has a significant impact on the life cycle of the virus as well as the fate of infected cells. In addition, due to special DNA structures of the viral genomes, parvoviruses are useful tools for the study of the molecular mechanisms underlying viral infection-induced DNA damage response (DDR). This review aims to summarize recent advances in parvovirus-induced DDR, with a focus on the diverse DDR pathways triggered by different parvoviruses and the consequences of DDR on the viral life cycle as well as the fate of infected cells.
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Affiliation(s)
- Yong Luo
- Department of Microbiology, Molecular Genetics & Immunology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Jianming Qiu
- Department of Microbiology, Molecular Genetics & Immunology, University of Kansas Medical Center, Kansas City, KS, USA
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35
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Lentz TB, Gray SJ, Samulski RJ. Viral vectors for gene delivery to the central nervous system. Neurobiol Dis 2012; 48:179-88. [PMID: 22001604 PMCID: PMC3293995 DOI: 10.1016/j.nbd.2011.09.014] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 08/17/2011] [Accepted: 09/29/2011] [Indexed: 12/19/2022] Open
Abstract
The potential benefits of gene therapy for neurological diseases such as Parkinson's, Amyotrophic Lateral Sclerosis (ALS), Epilepsy, and Alzheimer's are enormous. Even a delay in the onset of severe symptoms would be invaluable to patients suffering from these and other diseases. Significant effort has been placed in developing vectors capable of delivering therapeutic genes to the CNS in order to treat neurological disorders. At the forefront of potential vectors, viral systems have evolved to efficiently deliver their genetic material to a cell. The biology of different viruses offers unique solutions to the challenges of gene therapy, such as cell targeting, transgene expression and vector production. It is important to consider the natural biology of a vector when deciding whether it will be the most effective for a specific therapeutic function. In this review, we outline desired features of the ideal vector for gene delivery to the CNS and discuss how well available viral vectors compare to this model. Adeno-associated virus, retrovirus, adenovirus and herpesvirus vectors are covered. Focus is placed on features of the natural biology that have made these viruses effective tools for gene delivery with emphasis on their application in the CNS. Our goal is to provide insight into features of the optimal vector and which viral vectors can provide these features.
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Affiliation(s)
- Thomas B. Lentz
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Steven J. Gray
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - R. Jude Samulski
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Schildgen O, Qiu J, Söderlund-Venermo M. Genomic features of the human bocaviruses. Future Virol 2012; 7:31-39. [PMID: 22389649 DOI: 10.2217/fvl.11.136] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The human bocavirus (HBoV) was initially discovered in 2005 as the second pathogenic member of the parvovirus family, next to the human parvovirus B19. HBoV has since been shown to be extremely common worldwide and to cause a systemic infection in small children often resulting in respiratory disease. Three more, presumably enteric, human bocaviruses (HBoV2-4) have been identified in stool samples. Parvoviruses are assumed to replicate via their genomic terminal hairpin-like structures in a so-called 'rolling-hairpin model'. These terminal sequences have recently been partially identified in head-to-tail HBoV-PCR amplicons from clinical samples, and are most likely hybrid relics of HBoV's predecessors, namely bovine parvovirus 1 on the left-hand side and minute virus of canines on the right, shown for the first time in this article. Thereby, the replication model postulated for HBoV remains questionable as the occurrence of head-to-tail sequences is not a typical feature of the rolling-hairpin replication model. However, such episomes can also be persistent storage forms of the genome.
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Affiliation(s)
- Oliver Schildgen
- Institut für Pathologie, Kliniken der Stadt Köln gGmbH, Klinikum der Privaten Universität Witten/Herdecke, Cologne, Germany
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Janus LM, Bleich A. Coping with parvovirus infections in mice: health surveillance and control. Lab Anim 2012; 46:14-23. [DOI: 10.1258/la.2011.011025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Parvoviruses of mice, minute virus of mice (MVM) and mouse parvovirus (MPV), are challenging pathogens to eradicate from laboratory animal facilities. Due to the impediment on rodent-based research, recent studies have focused on the assessment of re-derivation techniques and parvoviral potential to induce persistent infections. Summarizing recent data, this review gives an overview on studies associated with parvoviral impact on research, diagnostic methods, parvoviral persistence and re-derivation techniques, demonstrating the complex nature of parvovirus infection in mice and unfolding the challenge of controlling parvovirus infections in laboratory animal facilities.
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Affiliation(s)
- Lydia M Janus
- Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Andre Bleich
- Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
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Kivovich V, Gilbert L, Vuento M, Naides SJ. The putative metal coordination motif in the endonuclease domain of human Parvovirus B19 NS1 is critical for NS1 induced S phase arrest and DNA damage. Int J Biol Sci 2011; 8:79-92. [PMID: 22211107 PMCID: PMC3248650 DOI: 10.7150/ijbs.8.79] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 11/02/2011] [Indexed: 12/14/2022] Open
Abstract
The non-structural proteins (NS) of the parvovirus family are highly conserved multi-functional molecules that have been extensively characterized and shown to be integral to viral replication. Along with NTP-dependent helicase activity, these proteins carry within their sequences domains that allow them to bind DNA and act as nucleases in order to resolve the concatameric intermediates developed during viral replication. The parvovirus B19 NS1 protein contains sequence domains highly similar to those previously implicated in the above-described functions of NS proteins from adeno-associated virus (AAV), minute virus of mice (MVM) and other non-human parvoviruses. Previous studies have shown that transient transfection of B19 NS1 into human liver carcinoma (HepG2) cells initiates the intrinsic apoptotic cascade, ultimately resulting in cell death. In an effort to elucidate the mechanism of mammalian cell demise in the presence of B19 NS1, we undertook a mutagenesis analysis of the protein's endonuclease domain. Our studies have shown that, unlike wild-type NS1, which induces an accumulation of DNA damage, S phase arrest and apoptosis in HepG2 cells, disruptions in the metal coordination motif of the B19 NS1 protein reduce its ability to induce DNA damage and to trigger S phase arrest and subsequent apoptosis. These studies support our hypothesis that, in the absence of replicating B19 genomes, NS1-induced host cell DNA damage is responsible for apoptotic cell death observed in parvoviral infection of non-permissive mammalian cells.
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Affiliation(s)
- Violetta Kivovich
- Pennsylvania State College of Medicine/ Milton S. Hershey Medical Center, Hershey, PA, USA
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Martin DP, Biagini P, Lefeuvre P, Golden M, Roumagnac P, Varsani A. Recombination in eukaryotic single stranded DNA viruses. Viruses 2011; 3:1699-738. [PMID: 21994803 PMCID: PMC3187698 DOI: 10.3390/v3091699] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 08/18/2011] [Accepted: 09/05/2011] [Indexed: 12/23/2022] Open
Abstract
Although single stranded (ss) DNA viruses that infect humans and their domesticated animals do not generally cause major diseases, the arthropod borne ssDNA viruses of plants do, and as a result seriously constrain food production in most temperate regions of the world. Besides the well known plant and animal-infecting ssDNA viruses, it has recently become apparent through metagenomic surveys of ssDNA molecules that there also exist large numbers of other diverse ssDNA viruses within almost all terrestrial and aquatic environments. The host ranges of these viruses probably span the tree of life and they are likely to be important components of global ecosystems. Various lines of evidence suggest that a pivotal evolutionary process during the generation of this global ssDNA virus diversity has probably been genetic recombination. High rates of homologous recombination, non-homologous recombination and genome component reassortment are known to occur within and between various different ssDNA virus species and we look here at the various roles that these different types of recombination may play, both in the day-to-day biology, and in the longer term evolution, of these viruses. We specifically focus on the ecological, biochemical and selective factors underlying patterns of genetic exchange detectable amongst the ssDNA viruses and discuss how these should all be considered when assessing the adaptive value of recombination during ssDNA virus evolution.
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Affiliation(s)
- Darren P. Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa; E-Mail:
| | - Philippe Biagini
- UMR CNRS 6578 Anthropologie Bioculturelle, Equipe “Emergence et co-évolution virale”, Etablissement Français du Sang Alpes-Méditerranée, Université de la Méditerranée, 27 Bd. Jean Moulin, 13005 Marseille, France; E-Mail:
| | - Pierre Lefeuvre
- CIRAD, UMR 53 PVBMT CIRAD-Université de la Réunion, Pôle de Protection des Plantes, Ligne Paradis, 97410, Saint Pierre, La Réunion, France; E-Mail:
| | - Michael Golden
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa; E-Mail:
| | - Philippe Roumagnac
- CIRAD, UMR BGPI, TA A-54/K, Campus International de Montferrier-Baillarguet, 34398 Montpellier, France; E-Mail:
| | - Arvind Varsani
- Electron Microscope Unit, University of Cape Town, Rondebosch, Cape Town 7701, South Africa; E-Mail:
- Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
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Streiter M, Malecki M, Prokop A, Schildgen V, Lüsebrink J, Guggemos A, Wisskirchen M, Weiss M, Cremer R, Brockmann M, Schildgen O. Does human bocavirus infection depend on helper viruses? A challenging case report. Virol J 2011; 8:417. [PMID: 21871135 PMCID: PMC3179752 DOI: 10.1186/1743-422x-8-417] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 08/29/2011] [Indexed: 12/21/2022] Open
Abstract
A case of severe diarrhoea associated with synergistic human bocavirus type 1 (HBoV) and human herpes virus type 6 (HHV6) is reported. The case supports the hypotheses that HBoV infection under clinical conditions may depend on helper viruses, or that HBoV replicates by a mechanism that is atypical for parvoviruses, or that HBoV infection can be specifically treated with cidofovir.
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Affiliation(s)
- Monika Streiter
- Klinik für Kinder- und Jugendmedizin, Kinderkrankenhaus, Kliniken der Stadt Köln gGmbH, Amsterdamer Str. 59, Cologne 50735, Germany
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41
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Lüsebrink J, Schildgen V, Tillmann RL, Wittleben F, Böhmer A, Müller A, Schildgen O. Detection of head-to-tail DNA sequences of human bocavirus in clinical samples. PLoS One 2011; 6:e19457. [PMID: 21573237 PMCID: PMC3087758 DOI: 10.1371/journal.pone.0019457] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 03/30/2011] [Indexed: 12/30/2022] Open
Abstract
Parvoviruses are single stranded DNA viruses that replicate in a so called “rolling-hairpin” mechanism, a variant of the rolling circle replication known for bacteriophages like ϕX174. The replication intermediates of parvoviruses thus are concatemers of head-to-head or tail-to-tail structure. Surprisingly, in case of the novel human bocavirus, neither head-to-head nor tail-to-tail DNA sequences were detected in clinical isolates; in contrast head-to-tail DNA sequences were identified by PCR and sequencing. Thereby, the head-to-tail sequences were linked by a novel sequence of 54 bp of which 20 bp also occur as conserved structures of the palindromic ends of parvovirus MVC which in turn is a close relative to human bocavirus.
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Affiliation(s)
- Jessica Lüsebrink
- Institut für Pathologie, Kliniken der Stadt Köln gGmbH, Klinikum der Privaten Universität Witten-Herdecke, Köln (Cologne), Germany
| | - Verena Schildgen
- Institut für Pathologie, Kliniken der Stadt Köln gGmbH, Klinikum der Privaten Universität Witten-Herdecke, Köln (Cologne), Germany
| | - Ramona Liza Tillmann
- Institut für Pathologie, Kliniken der Stadt Köln gGmbH, Klinikum der Privaten Universität Witten-Herdecke, Köln (Cologne), Germany
| | - Felix Wittleben
- Institut für Pathologie, Kliniken der Stadt Köln gGmbH, Klinikum der Privaten Universität Witten-Herdecke, Köln (Cologne), Germany
| | - Anne Böhmer
- Institut für Pathologie, Kliniken der Stadt Köln gGmbH, Klinikum der Privaten Universität Witten-Herdecke, Köln (Cologne), Germany
| | - Andreas Müller
- Department of Paediatrics, University Hospital Bonn, Bonn, Germany
| | - Oliver Schildgen
- Institut für Pathologie, Kliniken der Stadt Köln gGmbH, Klinikum der Privaten Universität Witten-Herdecke, Köln (Cologne), Germany
- * E-mail:
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Abstract
Since recombinant adeno-associated virus (rAAV) was first described as a potential mammalian cell transducing system, frequent reports purportedly solving the problems of scalable production have appeared. Yet few of these processes have enabled the development of robust and economical rAAV production. Two production platforms have emerged that have gained broad support for producing both research and clinical grade vectors. These processes differ fundamentally in several aspects. One approach is based on adherent mammalian cells and uses optimized chemical transient transfection for introducing the essential genetic components into the cells. The other approach utilizes suspension cultures of invertebrate cells. Baculovirus expression vectors are used for introducing the AAV genes into the cells. In addition, the baculovirus provides the helper functions necessary for efficient AAV DNA replication. The use of suspension cell culture provides an intrinsically more scalable platform system than using adherent cells. The upstream processes for suspension cultures are amenable for automation and are easily monitored and regulated to maintain optimum conditions that produce consistent yields of rAAV. Issues relating to developing new and improving existing rAAV production methods are discussed.
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Affiliation(s)
- Robert M Kotin
- Laboratory of Molecular Virology and Gene Therapy, Center for Developmental Biology and Genetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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43
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Glauser DL, Fraefel C. Interactions between AAV-2 and HSV-1: implications for hybrid vector design. Future Virol 2011. [DOI: 10.2217/fvl.11.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herpes simplex virus type 1 (HSV-1)-based amplicon vectors have a transgene capacity of up to 150 kbp and can efficiently transduce many different cell types in culture and in vivo without causing cytopathic effects. However, these vectors do not support long-term transgene expression. Adeno-associated virus type 2 (AAV-2) has the capacity to integrate its genome into a specific site on human chromosome 19, but AAV-2-derived gene therapy vectors have a transgene capacity of only 4.5 kb. To combine the large transgene capacity of HSV-1 with the potential for site-specific genomic integration and long-term transgene expression of AAV-2, HSV/AAV hybrid vectors have been developed. This review describes the design, applications and limitations of these hybrid vectors. However, as HSV-1 is a full helper virus for AAV-2 replication, the main focus is the analysis of the molecular mechanisms of interaction between the two viruses. The knowledge of these interactions will have direct implications on the design of novel HSV/AAV hybrid vectors.
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Affiliation(s)
- Daniel L Glauser
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Cornel Fraefel
- Institute of Virology, University of Zurich, Winterthurerstr. 266a, 8057 Zurich, Switzerland
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44
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Krimer DB, Hof JV. Extrachromosomal DNA of pea (Pisum sativum) root-tip cells replicates by strand displacement. Proc Natl Acad Sci U S A 2010; 80:1933-7. [PMID: 16593302 PMCID: PMC393725 DOI: 10.1073/pnas.80.7.1933] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In cultured pea roots there is extrachromosomal DNA associated with cells that differentiate from the G(2) phase of the cell cycle that is absent from those that differentiate from the G(1) phase. We examined this extrachromosomal DNA by electron microscopy and found that it consisted of three types: (i) double-stranded linear molecules with single-stranded branches (74%), (ii) double-stranded molecules without branches (26%), and (iii) free single-stranded molecules. The double-stranded molecules with or without branches were similar in length, having a modal length of 10-15 mum. The free single-stranded molecules were shorter and had a mean length of 3.8 mum. The length of the branches attached to the duplex molecules was only slightly less than that of the free form. The duplex molecules with branches were interpreted as configurations reflecting an ongoing strand-displacement process that results in free single-stranded molecules. Finally, measurements on duplex molecules with multiple branches suggested that the extrachromosomal DNA may exist in the form of tandemly repeated sequences.
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Affiliation(s)
- D B Krimer
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973
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45
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Lefeuvre P, Lett JM, Varsani A, Martin DP. Widely conserved recombination patterns among single-stranded DNA viruses. J Virol 2009; 83:2697-707. [PMID: 19116260 PMCID: PMC2648288 DOI: 10.1128/jvi.02152-08] [Citation(s) in RCA: 181] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Accepted: 12/23/2008] [Indexed: 01/19/2023] Open
Abstract
The combinatorial nature of genetic recombination can potentially provide organisms with immediate access to many more positions in sequence space than can be reached by mutation alone. Recombination features particularly prominently in the evolution of a diverse range of viruses. Despite rapid progress having been made in the characterization of discrete recombination events for many species, little is currently known about either gross patterns of recombination across related virus families or the underlying processes that determine genome-wide recombination breakpoint distributions observable in nature. It has been hypothesized that the networks of coevolved molecular interactions that define the epistatic architectures of virus genomes might be damaged by recombination and therefore that selection strongly influences observable recombination patterns. For recombinants to thrive in nature, it is probably important that the portions of their genomes that they have inherited from different parents work well together. Here we describe a comparative analysis of recombination breakpoint distributions within the genomes of diverse single-stranded DNA (ssDNA) virus families. We show that whereas nonrandom breakpoint distributions in ssDNA virus genomes are partially attributable to mechanistic aspects of the recombination process, there is also a significant tendency for recombination breakpoints to fall either outside or on the peripheries of genes. In particular, we found significantly fewer recombination breakpoints within structural protein genes than within other gene types. Collectively, these results imply that natural selection acting against viruses expressing recombinant proteins is a major determinant of nonrandom recombination breakpoint distributions observable in most ssDNA virus families.
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Affiliation(s)
- P Lefeuvre
- CIRAD, UMR 53 PVBMT CIRAD-Université de la Réunion, Pôle de Protection des Plantes, Ligne Paradis, 97410 Saint Pierre, La Réunion, France
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Negrete A, Kotin RM. Strategies for manufacturing recombinant adeno-associated virus vectors for gene therapy applications exploiting baculovirus technology. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2008; 7:303-11. [PMID: 18632744 DOI: 10.1093/bfgp/eln034] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The development of recombinant adeno-associated virus (rAAV) gene therapy applications is hampered by the inability to produce rAAV in sufficient quantities to support pre-clinical and clinical trials. Contrasting with adherent cell cultures, suspension cultures provide a straightforward means for expansion, however, transiently expressing the necessary, but cytotoxic virus proteins remains the challenge for rAAV production. Both the expansion and expression issues are resolved by using the baculovirus expression vector (bev) and insect cell culture system. This review addresses strategies for the production of rAAV exploiting baculovirus technology at different scales using different configurations of bioreactors as well as processing and product characterization issues. The yields obtained with these optimized processes exceed approximately 1 x 10(14) vector particles per liter of cell culture suitable for pre-clinical and clinical trials and possible commercialization.
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47
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Balaz M, Li BC, Jockusch S, Ellestad GA, Berova N. Tetraarylporphyrin as a selective molecular cap for non-Watson-Crick guanine-adenine base-pair sequences. Angew Chem Int Ed Engl 2007; 45:3530-3. [PMID: 16625664 DOI: 10.1002/anie.200504431] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Milan Balaz
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA.
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48
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Odom GL, Gregorevic P, Chamberlain JS. Viral-mediated gene therapy for the muscular dystrophies: successes, limitations and recent advances. BIOCHIMICA ET BIOPHYSICA ACTA 2007; 1772:243-62. [PMID: 17064882 PMCID: PMC1894910 DOI: 10.1016/j.bbadis.2006.09.007] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Revised: 09/16/2006] [Accepted: 09/20/2006] [Indexed: 02/07/2023]
Abstract
Much progress has been made over the past decade elucidating the molecular basis for a variety of muscular dystrophies (MDs). Accordingly, there are examples of mouse models of MD whose disease progression has been halted in large part with the use of viral vector technology. Even so, we must acknowledge significant limitations of present vector systems that must be overcome prior to successful treatment of humans with such approaches. This review will present a variety of viral-mediated therapeutic strategies aimed at counteracting the muscle-wasting symptoms associated with muscular dystrophy. We include viral vector systems used for muscle gene transfer, with a particular emphasis on adeno-associated virus. Findings of several encouraging studies focusing on repair of the mutant dystrophin gene are also included. Lastly, we present a discussion of muscle compensatory therapeutics being considered that include pathways involved in the up-regulation of utrophin, promotion of cellular adhesion, enhancement of muscle mass, and antagonism of the inflammatory response. Considering the complexity of the muscular dystrophies, it appears likely that a multilayered approach tailored to a patient sub-group may be warranted in order to effectively contest the progression of this devastating disease.
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Affiliation(s)
- Guy L. Odom
- Department of Neurology Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Washington School of Medicine, 1959 NE Pacific Street, Seattle, WA, 98195-7720, USA
| | - Paul Gregorevic
- Department of Neurology Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Washington School of Medicine, 1959 NE Pacific Street, Seattle, WA, 98195-7720, USA
| | - Jeffrey S. Chamberlain
- Department of Neurology Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Washington School of Medicine, 1959 NE Pacific Street, Seattle, WA, 98195-7720, USA
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49
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Pegoraro G, Marcello A, Myers MP, Giacca M. Regulation of adeno-associated virus DNA replication by the cellular TAF-I/set complex. J Virol 2006; 80:6855-64. [PMID: 16809291 PMCID: PMC1489034 DOI: 10.1128/jvi.00383-06] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The Rep proteins of the adeno-associated virus (AAV) are required for viral replication in the presence of adenovirus helper functions and as yet poorly characterized cellular factors. In an attempt to identify such factors, we purified Flag-Rep68-interacting proteins from human cell lysates. Several polypeptides were identified by mass spectrometry, among which was ANP32B, a member of the acidic nuclear protein 32 family which takes part in the formation of the template-activating factor I/Set oncoprotein (TAF-I/Set) complex. The N terminus of Rep was found to specifically bind the acidic domain of ANP32B; through this interaction, Rep was also able to recruit other members of the TAF-I/Set complex, including the ANP32A protein and the histone chaperone TAF-I/Set. Further experiments revealed that silencing of ANP32A and ANP32B inhibited AAV replication, while overexpression of all of the components of the TAF-I/Set complex increased de novo AAV DNA synthesis in permissive cells. Besides being the first indication that the TAF-I/Set complex participates in wild-type AAV replication, these findings have important implications for the generation of recombinant AAV vectors since overexpression of the TAF-I/Set components was found to markedly increase viral vector production.
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Affiliation(s)
- Gianluca Pegoraro
- Molecular Medicine Laboratory, International Center for Genetic Engineering and Biotechnology, Triste, Italy
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50
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Balaz M, Li BC, Jockusch S, Ellestad GA, Berova N. Tetraarylporphyrin as a Selective Molecular Cap for Non-Watson–Crick Guanine–Adenine Base-Pair Sequences. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200504431] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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