The Experts below are selected from a list of 81 Experts worldwide ranked by ideXlab platform
Gloria Arriagada - One of the best experts on this subject based on the ideXlab platform.
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Molecular Properties and Evolutionary Origins of a Parvovirus-Derived Myosin Fusion Gene in Guinea Pigs.
Journal of virology, 2019Co-Authors: Ignacio Valencia-herrera, Robert J. Gifford, Fernando Faunes, Eduardo Cena-ahumada, Rodrigo Ibarra-karmy, Gloria ArriagadaAbstract:Sequences derived from parvoviruses (family Parvoviridae) are relatively common in animal genomes, but the functional significance of these endogenous parvoviral element (EPV) sequences remains unclear. In this study, we used a combination of in silico and molecular biological approaches to investigate a fusion gene carried by guinea pigs (genus Cavia) that is partially derived from an EPV. This gene, named enRep-M9l, encodes a predicted polypeptide gene product comprising a partial myosin9-like (M9l) gene fused to a 3' truncated, EPV-encoded replicase. We examined the genomic and phylogenetic characteristics of the EPV locus (enRep) that encodes the viral portions of enRep-M9l, revealing that it derives from an ancient Dependoparvovirus (genus Dependoparvovirus) that was incorporated into the guinea pig germ line between approximately 22 and 35 million years ago (MYA). Despite these ancient origins, the regions of the enRep locus that are expressed in the enRep-M9l gene are conserved across multiple species in the family Caviidae (guinea pigs and cavies), consistent with a potential function at the amino acid level. Using molecular biological approaches, we further demonstrated that (i) enRep-M9l mRNA is broadly transcribed in guinea pig cells, (ii) the cloned enRep-M9l transcript can express a protein of the expected size in guinea pig cells in vitro, and (iii) the expressed protein localizes to the cytosol. Our findings demonstrate that, consistent with a functional role, the enRep-M9l fusion gene is evolutionarily conserved, broadly transcribed, and capable of expressing protein.IMPORTANCE DNA from viruses has been "horizontally transferred" to mammalian genomes during evolution, but the impact of this process on mammalian biology remains poorly understood. The findings of our study indicate that a novel gene has evolved in guinea pigs through fusion of host and virus genes.
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Molecular properties and evolutionary origins of a parvovirus-derived myosin fusion gene in guinea pigs
2019Co-Authors: Ignacio Valencia-herrera, Robert J. Gifford, Fernando Faunes, Eduardo Cena-ahumada, Rodrigo Ibarra-karmy, Gloria ArriagadaAbstract:Abstract Sequences derived from parvoviruses (family Parvoviridae) are relatively common in animal genomes, but the functional significance of these endogenous parvoviral element (EPV) sequences remains unclear. In this study we use a combination of in silico and molecular biological approaches to investigate a fusion gene encoded by guinea pigs (genus Cavia) that is partially derived from an EPV. This gene, named enRep-Myo9, encodes a predicted polypeptide gene product comprising a partial myosin9 (Myo9)-like gene fused to a 3’ truncated, EPV- encoded replicase. We first examined the genomic and phylogenetic characteristics of the EPV locus that encodes the viral portions of enRep-Myo9. We show that this locus, named enRep, is specific to guinea pigs and derives from an ancient representative of the parvoviral genus Dependoparvovirus that integrated into the guinea pig germline 22-35 million years ago. Despite these ancient origins, however, the regions of enRep that are incorporated into the coding sequence of the enRep-Myo9 gene are conserved across multiple species in the family Caviidae (guinea pigs and cavies) consistent with purifying selection. Using molecular biological approaches, we further demonstrate that: (i) enRep-Myo9 mRNA is broadly transcribed in guinea pig cells; (ii) the cloned enRep-Myo9 transcript can express a protein of the expected size in guinea pig cells in vitro, and; (iii) the expressed protein localizes to the cytosol. Our findings demonstrate that, consistent with a functional role, the enRep-Myo9 fusion gene is evolutionarily conserved, broadly transcribed, and capable of expressing protein. Importance DNA from viruses has been ‘horizontally transferred’ to mammalian genomes during evolution, but the impact of this process on mammalian biology remains poorly understood. The findings of our study indicate that in guinea pigs a novel gene has evolved through fusion of host and virus genes.
Ignacio Valencia-herrera - One of the best experts on this subject based on the ideXlab platform.
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Molecular Properties and Evolutionary Origins of a Parvovirus-Derived Myosin Fusion Gene in Guinea Pigs.
Journal of virology, 2019Co-Authors: Ignacio Valencia-herrera, Robert J. Gifford, Fernando Faunes, Eduardo Cena-ahumada, Rodrigo Ibarra-karmy, Gloria ArriagadaAbstract:Sequences derived from parvoviruses (family Parvoviridae) are relatively common in animal genomes, but the functional significance of these endogenous parvoviral element (EPV) sequences remains unclear. In this study, we used a combination of in silico and molecular biological approaches to investigate a fusion gene carried by guinea pigs (genus Cavia) that is partially derived from an EPV. This gene, named enRep-M9l, encodes a predicted polypeptide gene product comprising a partial myosin9-like (M9l) gene fused to a 3' truncated, EPV-encoded replicase. We examined the genomic and phylogenetic characteristics of the EPV locus (enRep) that encodes the viral portions of enRep-M9l, revealing that it derives from an ancient Dependoparvovirus (genus Dependoparvovirus) that was incorporated into the guinea pig germ line between approximately 22 and 35 million years ago (MYA). Despite these ancient origins, the regions of the enRep locus that are expressed in the enRep-M9l gene are conserved across multiple species in the family Caviidae (guinea pigs and cavies), consistent with a potential function at the amino acid level. Using molecular biological approaches, we further demonstrated that (i) enRep-M9l mRNA is broadly transcribed in guinea pig cells, (ii) the cloned enRep-M9l transcript can express a protein of the expected size in guinea pig cells in vitro, and (iii) the expressed protein localizes to the cytosol. Our findings demonstrate that, consistent with a functional role, the enRep-M9l fusion gene is evolutionarily conserved, broadly transcribed, and capable of expressing protein.IMPORTANCE DNA from viruses has been "horizontally transferred" to mammalian genomes during evolution, but the impact of this process on mammalian biology remains poorly understood. The findings of our study indicate that a novel gene has evolved in guinea pigs through fusion of host and virus genes.
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Molecular properties and evolutionary origins of a parvovirus-derived myosin fusion gene in guinea pigs
2019Co-Authors: Ignacio Valencia-herrera, Robert J. Gifford, Fernando Faunes, Eduardo Cena-ahumada, Rodrigo Ibarra-karmy, Gloria ArriagadaAbstract:Abstract Sequences derived from parvoviruses (family Parvoviridae) are relatively common in animal genomes, but the functional significance of these endogenous parvoviral element (EPV) sequences remains unclear. In this study we use a combination of in silico and molecular biological approaches to investigate a fusion gene encoded by guinea pigs (genus Cavia) that is partially derived from an EPV. This gene, named enRep-Myo9, encodes a predicted polypeptide gene product comprising a partial myosin9 (Myo9)-like gene fused to a 3’ truncated, EPV- encoded replicase. We first examined the genomic and phylogenetic characteristics of the EPV locus that encodes the viral portions of enRep-Myo9. We show that this locus, named enRep, is specific to guinea pigs and derives from an ancient representative of the parvoviral genus Dependoparvovirus that integrated into the guinea pig germline 22-35 million years ago. Despite these ancient origins, however, the regions of enRep that are incorporated into the coding sequence of the enRep-Myo9 gene are conserved across multiple species in the family Caviidae (guinea pigs and cavies) consistent with purifying selection. Using molecular biological approaches, we further demonstrate that: (i) enRep-Myo9 mRNA is broadly transcribed in guinea pig cells; (ii) the cloned enRep-Myo9 transcript can express a protein of the expected size in guinea pig cells in vitro, and; (iii) the expressed protein localizes to the cytosol. Our findings demonstrate that, consistent with a functional role, the enRep-Myo9 fusion gene is evolutionarily conserved, broadly transcribed, and capable of expressing protein. Importance DNA from viruses has been ‘horizontally transferred’ to mammalian genomes during evolution, but the impact of this process on mammalian biology remains poorly understood. The findings of our study indicate that in guinea pigs a novel gene has evolved through fusion of host and virus genes.
John F. Engelhardt - One of the best experts on this subject based on the ideXlab platform.
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human bocavirus 1 is a novel helper for adeno associated virus replication
Journal of Virology, 2017Co-Authors: Zekun Wang, Xuefeng Deng, John F. Engelhardt, Wei Zou, Ziying Yan, Jianming QiuAbstract:Human bocavirus 1 (HBoV1) is an autonomous parvovirus that infects well-differentiated primary human airway epithelia (HAE) in vitro In human embryonic kidney HEK293 cells, the transfection of a duplex HBoV1 genome initiates viral DNA replication and produces progeny virions that are infectious in HAE. HBoV1 takes advantage of signaling pathways in the DNA damage response for efficient genome amplification in both well-differentiated (nondividing) HAE and dividing HEK293 cells. On the other hand, adeno-associated virus 2 (AAV2) is a helper-dependent Dependoparvovirus, and productive AAV2 replication requires coinfection with a helper virus (e.g., adenovirus or herpesvirus) or treatment with genotoxic agents. Here, we report that HBoV1 is a novel helper virus for AAV2 replication. Coinfection by HBoV1 and AAV2 rescued AAV2 replication in HAE cells. The helper function of HBoV1 for AAV2 is not limited to HAE cells but also includes HEK293 and HeLa cells. Importantly, the helper function of HBoV1 for AAV2 relies on neither HBoV1 replication nor the DNA damage response. Following transfection of HEK293 cells, the minimal requirements for the replication of the AAV2 duplex DNA genome and the production of progeny virions included the HBoV1 NP1 and NS4 proteins and a newly identified viral long noncoding RNA (BocaSR). However, following infection of HEK293 and HeLa cells with AAV2 virions, HBoV1 NS2 (but not NS4), NP1, and BocaSR were required for AAV2 DNA replication and progeny virion formation. These new methods for packaging the AAV2 genome may be useful for generating recombinant AAV-packaging cell lines and the directed evolution of AAV capsids.IMPORTANCE We first report that an autonomous parvovirus, HBoV1, helps the replication of a Dependoparvovirus, AAV2, in differentiated human airway epithelia. We identified the minimal sets of HBoV1 genes required to facilitate the replication of the AAV2 duplex genome and for AAV2 infection. Notably, together with the expression of the NP1 and BocaSR genes, HBoV1 NS2 is required for the productive infection of HEK293 and HeLa cells by AAV2, whereas NS4 is sufficient for viral DNA replication of an AAV2 duplex genome. The identification of HBoV1 as a helper virus for AAV2 replication has implications for the improvement of recombinant AAV production in HEK293 cells and cell types that do not express the adenovirus E1 gene as well as for the rescue of wild-type AAV genomes from tissues during directed evolution in the absence of wild-type adenovirus. A further understanding of the mechanism underlying HBoV1 helper-dependent AAV2 replication may also provide insights into its functions in HBoV1 replication.
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analysis of cis and trans requirements for dna replication at the right end hairpin of the human bocavirus 1 genome
Journal of Virology, 2016Co-Authors: Weiran Shen, Xuefeng Deng, John F. EngelhardtAbstract:UNLABELLED: Parvoviruses are single-stranded DNA viruses that use the palindromic structures at the ends of the viral genome for their replication. The mechanism of parvovirus replication has been studied mostly in the Dependoparvovirus adeno-associated virus 2 (AAV2) and the protoparvovirus minute virus of mice (MVM). Here, we used human bocavirus 1 (HBoV1) to understand the replication mechanism of bocaparvovirus. HBoV1 is pathogenic to humans, causing acute respiratory tract infections, especially in young children under 2 years old. By using the duplex replicative form of the HBoV1 genome in human embryonic kidney 293 (HEK293) cells, we identified the HBoV1 minimal replication origin at the right-end hairpin (OriR). Mutagenesis analyses confirmed the putative NS1 binding and nicking sites within the OriR. Of note, unlike the large nonstructural protein (Rep78/68 or NS1) of other parvoviruses, HBoV1 NS1 did not specifically bind OriR in vitro, indicating that other viral and cellular components or the oligomerization of NS1 is required for NS1 binding to the OriR. In vivo studies demonstrated that residues responsible for NS1 binding and nicking are within the origin-binding domain. Further analysis identified that the small nonstructural protein NP1 is required for HBoV1 DNA replication at OriR. NP1 and other viral nonstructural proteins (NS1 to NS4) colocalized within the viral DNA replication centers in both OriR-transfected cells and virus-infected cells, highlighting a direct involvement of NP1 in viral DNA replication at OriR. Overall, our study revealed the characteristics of HBoV1 DNA replication at OriR, suggesting novel characteristics of autonomous parvovirus DNA replication. IMPORTANCE: Human bocavirus 1 (HBoV1) causes acute respiratory tract infections in young children. The duplex HBoV1 genome replicates in HEK293 cells and produces progeny virions that are infectious in well-differentiated airway epithelial cells. A recombinant AAV2 vector pseudotyped with an HBoV1 capsid has been developed to efficiently deliver the cystic fibrosis transmembrane conductance regulator gene to human airway epithelia. Here, we identified both cis-acting elements and trans-acting proteins that are required for HBoV1 DNA replication at the right-end hairpin in HEK293 cells. We localized the minimal replication origin, which contains both NS1 nicking and binding sites, to a 46-nucleotide sequence in the right-end hairpin. The identification of these essential elements of HBoV1 DNA replication acting both in cis and in trans will provide guidance to develop antiviral strategies targeting viral DNA replication at the right-end hairpin and to design next-generation recombinant HBoV1 vectors, a promising tool for gene therapy of lung diseases.
Liang Tang - One of the best experts on this subject based on the ideXlab platform.
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structures of minute virus of mice replication initiator protein n terminal domain insights into dna nicking and origin binding
Virology, 2015Co-Authors: Sunil Kumar Tewary, Susan F Cotmore, Peter Tattersall, Lingfei Liang, Anna Y Lynn, Haiyan Zhao, Liang TangAbstract:Members of the Parvoviridae family all encode a non-structural protein 1 (NS1) that directs replication of single-stranded viral DNA, packages viral DNA into capsid, and serves as a potent transcriptional activator. Here we report the X-ray structure of the minute virus of mice (MVM) NS1 N-terminal domain at 1.45 A resolution, showing that sites for dsDNA binding, ssDNA binding and cleavage, nuclear localization, and other functions are integrated on a canonical fold of the histidine-hydrophobic-histidine superfamily of nucleases, including elements specific for this Protoparvovirus but distinct from its Bocaparvovirus or Dependoparvovirus orthologs. High resolution structural analysis reveals a nickase active site with an architecture that allows highly versatile metal ligand binding. The structures support a unified mechanism of replication origin recognition for homotelomeric and heterotelomeric parvoviruses, mediated by a basic-residue-rich hairpin and an adjacent helix in the initiator proteins and by tandem tetranucleotide motifs in the replication origins.
Robert J. Gifford - One of the best experts on this subject based on the ideXlab platform.
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Evolution of Dependoparvoviruses across geological timescales-implications for design of AAV-based gene therapy vectors.
Virus evolution, 2020Co-Authors: Evin Hildebrandt, Judit J. Pénzes, Robert J. Gifford, Mavis Agbandje-mckenna, Robert M. KotinAbstract:Endogenous viral elements (EVEs) are genetic remnants of viruses that have integrated into host genomes millions of years ago and retained as heritable elements passed on to offspring until present-day. As a result, EVEs provide an opportunity to analyse the genomes of extinct viruses utilizing these genomic viral fossils to study evolution of viruses over large timescales. Analysis of sequences from near full-length EVEs of dependoparvoviral origin identified within three mammalian taxa, Whippomorpha (whales and hippos), Vespertilionidae (smooth-nosed bats), and Lagomorpha (rabbits, hares, and pikas), indicates that distinct ancestral Dependoparvovirus species integrated into these host genomes approximately 77 to 23 million years ago. These ancestral viruses are unique relative to modern adeno-associated viruses (AAVs), and distinct from extant species of genus Dependoparvovirus. These EVE sequences show characteristics previously unseen in modern, mammalian AAVs, but instead appear more similar to the more primitive, autonomously replicating and pathogenic waterfowl Dependoparvoviruses. Phylogeny reconstruction suggests that the whippomorph EVE orthologue derives from exogenous ancestors of autonomous and highly pathogenic Dependoparvovirus lineages, believed to have uniquely co-evolved with waterfowl birds to present date. In contrast, ancestors of the two other mammalian orthologues (Lagomorpha and Vespertilionidae) likely shared the same lineage as all other known mammalian exogenous AAVs. Comparative in silico analysis of the EVE genomes revealed remarkable overall conservation of AAV rep and cap genes, despite millions of years of integration within the host germline. Modelling these proteins identified unexpected variety, even between orthologues, in previously defined capsid viral protein (VP) variable regions, especially in those related to the three- and fivefold symmetry axes of the capsid. Moreover, the normally well-conserved phospholipase A2 domain of the predicted minor VP1 also exhibited a high degree of sequence variance. These findings may indicate unique biological properties for these virus 'fossils' relative to extant Dependoparvoviruses and suggest key regions to explore within capsid sequences that may confer novel properties for engineered gene therapy vectors based on paleovirology data.
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Molecular Properties and Evolutionary Origins of a Parvovirus-Derived Myosin Fusion Gene in Guinea Pigs.
Journal of virology, 2019Co-Authors: Ignacio Valencia-herrera, Robert J. Gifford, Fernando Faunes, Eduardo Cena-ahumada, Rodrigo Ibarra-karmy, Gloria ArriagadaAbstract:Sequences derived from parvoviruses (family Parvoviridae) are relatively common in animal genomes, but the functional significance of these endogenous parvoviral element (EPV) sequences remains unclear. In this study, we used a combination of in silico and molecular biological approaches to investigate a fusion gene carried by guinea pigs (genus Cavia) that is partially derived from an EPV. This gene, named enRep-M9l, encodes a predicted polypeptide gene product comprising a partial myosin9-like (M9l) gene fused to a 3' truncated, EPV-encoded replicase. We examined the genomic and phylogenetic characteristics of the EPV locus (enRep) that encodes the viral portions of enRep-M9l, revealing that it derives from an ancient Dependoparvovirus (genus Dependoparvovirus) that was incorporated into the guinea pig germ line between approximately 22 and 35 million years ago (MYA). Despite these ancient origins, the regions of the enRep locus that are expressed in the enRep-M9l gene are conserved across multiple species in the family Caviidae (guinea pigs and cavies), consistent with a potential function at the amino acid level. Using molecular biological approaches, we further demonstrated that (i) enRep-M9l mRNA is broadly transcribed in guinea pig cells, (ii) the cloned enRep-M9l transcript can express a protein of the expected size in guinea pig cells in vitro, and (iii) the expressed protein localizes to the cytosol. Our findings demonstrate that, consistent with a functional role, the enRep-M9l fusion gene is evolutionarily conserved, broadly transcribed, and capable of expressing protein.IMPORTANCE DNA from viruses has been "horizontally transferred" to mammalian genomes during evolution, but the impact of this process on mammalian biology remains poorly understood. The findings of our study indicate that a novel gene has evolved in guinea pigs through fusion of host and virus genes.
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Molecular properties and evolutionary origins of a parvovirus-derived myosin fusion gene in guinea pigs
2019Co-Authors: Ignacio Valencia-herrera, Robert J. Gifford, Fernando Faunes, Eduardo Cena-ahumada, Rodrigo Ibarra-karmy, Gloria ArriagadaAbstract:Abstract Sequences derived from parvoviruses (family Parvoviridae) are relatively common in animal genomes, but the functional significance of these endogenous parvoviral element (EPV) sequences remains unclear. In this study we use a combination of in silico and molecular biological approaches to investigate a fusion gene encoded by guinea pigs (genus Cavia) that is partially derived from an EPV. This gene, named enRep-Myo9, encodes a predicted polypeptide gene product comprising a partial myosin9 (Myo9)-like gene fused to a 3’ truncated, EPV- encoded replicase. We first examined the genomic and phylogenetic characteristics of the EPV locus that encodes the viral portions of enRep-Myo9. We show that this locus, named enRep, is specific to guinea pigs and derives from an ancient representative of the parvoviral genus Dependoparvovirus that integrated into the guinea pig germline 22-35 million years ago. Despite these ancient origins, however, the regions of enRep that are incorporated into the coding sequence of the enRep-Myo9 gene are conserved across multiple species in the family Caviidae (guinea pigs and cavies) consistent with purifying selection. Using molecular biological approaches, we further demonstrate that: (i) enRep-Myo9 mRNA is broadly transcribed in guinea pig cells; (ii) the cloned enRep-Myo9 transcript can express a protein of the expected size in guinea pig cells in vitro, and; (iii) the expressed protein localizes to the cytosol. Our findings demonstrate that, consistent with a functional role, the enRep-Myo9 fusion gene is evolutionarily conserved, broadly transcribed, and capable of expressing protein. Importance DNA from viruses has been ‘horizontally transferred’ to mammalian genomes during evolution, but the impact of this process on mammalian biology remains poorly understood. The findings of our study indicate that in guinea pigs a novel gene has evolved through fusion of host and virus genes.
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endogenous parvoviral elements in the pit viper protobothrops mucrosuamatus and in three members of three mammalian orders implications for ecology and evolution of genera amdoparvovirus and protoparvovirus
bioRxiv, 2018Co-Authors: Judit J. Pénzes, Soledad Marsilemedun, Mavis Agbandjemckenna, Robert J. GiffordAbstract:Amdoparvoviruses (family Parvoviridae: genus Amdoparvovirus) infect carnivores, and are a major cause of morbidity and mortality in farmed mink. Relatively little is known about amdoparvovirus evolution, partly because so few endogenous parvoviral elements (PVe) derived from amdoparvovirus-like viruses have been identified. In this study, we systematically screened animal genomes to identify PVe disclosing a high degree of similarity to amdoparvoviruses, and investigated their genomic, phylogenetic and protein structural features. We report the first full-length, amdoparvovirus-derived PVe in the genome of the Transcaucasian mole vole (Ellobius lutescens). Furthermore, we identify four further PVe in mammal and reptile genomes that are intermediate between amdoparvoviruses and protoparvoviruses (genus Protoparvovirus) in terms of their phylogenetic placement and genomic features. In particular, we identified a genome-length PVe in the genome of a pit viper (Protobothrops mucrosquamatus) that is protoparvovirus-like in terms of its phylogenetic placement and the structural features of its capsid protein (as revealed by homology modeling), but exhibits characteristically amdoparvovirus-like features including (i) a putative middle ORF gene, and (ii) the lack of the phospholipase A2 (PLA2) domain as well as (iii) the putative transcription of VP1. These findings indicate that either: (i) amdoparvoviruses evolved from protoparvoviruses via a series of transitional forms, or; (ii) there are as yet uncharacterised parvovirus lineages that possess a mixture of proto- and amdoparvovirus-like characteristics. Our investigation also provides evidence that amdoparvovirus host range has extended to rodents in the past, and that reptilian parvoviruses exist outside of genus Dependoparvovirus. Finally, we show that PVe in the mole vole and pit viper encode intact, expressible replicase genes, adding to a growing body of evidence that these genes have repeatedly been co-opted or exapted in vertebrate genomes.