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Pakorn Aiewsakun - One of the best experts on this subject based on the ideXlab platform.
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Evaluation of the genomic diversity of Viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towards a unified taxonomy.
Journal of General Virology, 2018Co-Authors: Pakorn Aiewsakun, Andrew M Kropinski, Evelien M. Adriaenssens, Rob Lavigne, Peter SimmondsAbstract:Genome Relationship Applied to Virus Taxonomy (GRAViTy) is a genetics-based tool that computes sequence relatedness between Viruses. Composite generalized Jaccard (CGJ) distances combine measures of homology between encoded viral genes and similarities in genome organizational features (gene orders and orientations). This scoring framework effectively recapitulates the current, largely morphology and phenotypic-based, family-level classification of Eukaryotic Viruses. Eukaryotic Virus families typically formed monophyletic groups with consistent CGJ distance cut-off dividing between and within family divergence ranges. In the current study, a parallel analysis of prokaryotic Virus families revealed quite different sequence relationships, particularly those of tailed phage families (Siphoviridae, Myoviridae and Podoviridae), where members of the same family were generally far more divergent and often not detectably homologous to each other. Analysis of the 20 currently classified prokaryotic Virus families indeed split them into 70 separate clusters of tailed phages genetically equivalent to family-level assignments of Eukaryotic Viruses. It further divided several bacterial (Sphaerolipoviridae, Tectiviridae) and archaeal (Lipothrixviridae) families. We also found that the subfamily-level groupings of tailed phages were generally more consistent with the family assignments of Eukaryotic Viruses, and this supports ongoing reclassifications, including Spounavirinae and Vi1Virus taxa as new Virus families. The current study applied a common benchmark with which to compare taxonomies of Eukaryotic and prokaryotic Viruses. The findings support the planned shift away from traditional morphology-based classifications of prokaryotic Viruses towards a genome-based taxonomy. They demonstrate the feasibility of a unified taxonomy of Viruses into which the vast body of metagenomic viral sequences may be consistently assigned.
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Virus classification where do you draw the line
Archives of Virology, 2018Co-Authors: Peter Simmonds, Pakorn AiewsakunAbstract:High-throughput sequencing (HTS) and its use in recovering and assembling novel Virus sequences from environmental, human clinical, veterinary and plant samples has unearthed a vast new catalogue of Viruses. Their classification, known by their sequences alone, sets a major challenge to traditional Virus taxonomy, especially at the family and species levels, which have been historically based largely on descriptive taxon definitions. These typically entail some knowledge of their phenotypic properties, including replication strategies, virion structure and clinical and epidemiological features, such as host range, geographical distribution and disease outcomes. Little to no information on these attributes is available, however, for Viruses identified in metagenomic datasets. If such Viruses are to be included in Virus taxonomy, their assignments will have to be guided largely or entirely by metrics of genetic relatedness. The immediate problem here is that the International Committee on Taxonomy of Viruses (ICTV), an organisation that authorises the taxonomic classification of Viruses, provides little or no guidance on how similar or how divergent Viruses must be in order to be considered members of new species or new families. We have recently developed a method for scoring genomic (dis)similarity between Viruses (Genome Relationships Applied to Virus Taxonomy - GRAViTy) among the Eukaryotic and prokaryotic Viruses currently classified by the ICTV. At the family and genus levels, we found large-scale consistency between genetic relationships and their taxonomic assignments for Eukaryotic Viruses of all genome configurations and genome sizes. Family assignments of prokaryotic Viruses have, however, been made at a quite different genetic level, and groupings currently classified as sub-families are a much better match to the Eukaryotic Virus family level. These findings support the ongoing reorganisation of bacteriophage taxonomy by the ICTV Phage Study Group. A rapid and objective means to explore metagenomic viral diversity and make evidence-based assignments for such Viruses at each taxonomic layer is essential. Analysis of sequences by GRAViTy provides evidence that family (and genus) assignments of currently classified Viruses are largely underpinned by genomic relatedness, and these features could serve as a guide towards an evidence-based classification of metagenomic Viruses in the future.
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the genomic underpinnings of Eukaryotic Virus taxonomy creating a sequence based framework for family level Virus classification
Microbiome, 2018Co-Authors: Pakorn Aiewsakun, Peter SimmondsAbstract:The International Committee on Taxonomy of Viruses (ICTV) classifies Viruses into families, genera and species and provides a regulated system for their nomenclature that is universally used in Virus descriptions. Virus taxonomic assignments have traditionally been based upon Virus phenotypic properties such as host range, virion morphology and replication mechanisms, particularly at family level. However, gene sequence comparisons provide a clearer guide to their evolutionary relationships and provide the only information that may guide the incorporation of Viruses detected in environmental (metagenomic) studies that lack any phenotypic data. The current study sought to determine whether the existing Virus taxonomy could be reproduced by examination of genetic relationships through the extraction of protein-coding gene signatures and genome organisational features. We found large-scale consistency between genetic relationships and taxonomic assignments for Viruses of all genome configurations and genome sizes. The analysis pipeline that we have called ‘Genome Relationships Applied to Virus Taxonomy’ (GRAViTy) was highly effective at reproducing the current assignments of Viruses at family level as well as inter-family groupings into orders. Its ability to correctly differentiate assigned Viruses from unassigned Viruses, and classify them into the correct taxonomic group, was evaluated by threefold cross-validation technique. This predicted family membership of Eukaryotic Viruses with close to 100% accuracy and specificity potentially enabling the algorithm to predict assignments for the vast corpus of metagenomic sequences consistently with ICTV taxonomy rules. In an evaluation run of GRAViTy, over one half (460/921) of (near)-complete genome sequences from several large published metagenomic Eukaryotic Virus datasets were assigned to 127 novel family-level groupings. If corroborated by other analysis methods, these would potentially more than double the number of Eukaryotic Virus families in the ICTV taxonomy. A rapid and objective means to explore metagenomic viral diversity and make informed recommendations for their assignments at each taxonomic layer is essential. GRAViTy provides one means to make rule-based assignments at family and order levels in a manner that preserves the integrity and underlying organisational principles of the current ICTV taxonomy framework. Such methods are increasingly required as the vast virosphere is explored.
Stewart Shuman - One of the best experts on this subject based on the ideXlab platform.
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characterization of mimiVirus nad dependent dna ligase
Virology, 2006Co-Authors: Delphine Benarroch, Stewart ShumanAbstract:Abstract MimiVirus, a parasite of Acanthamoeba polyphaga , is the largest DNA Virus known; it encodes a cornucopia of proteins with imputed functions in DNA replication, modification, and repair. Here we produced, purified, and characterized mimiVirus DNA ligase (MimiLIG), an NAD + -dependent nick joining enzyme homologous to bacterial LigA and entomopoxVirus DNA ligase. MimiLIG is a 636-aa polypeptide composed of an N-terminal NAD + specificity module (domain Ia), linked to nucleotidyltransferase, OB-fold, helix–hairpin–helix, and BRCT domains, but it lacks the tetracysteine Zn-binding module found in all bacterial LigA enzymes. MimiLIG requires conserved domain Ia residues Tyr36, Asp46, Tyr49, and Asp50 for its initial reaction with NAD + to form the ligase–AMP intermediate, but not for the third step of phosphodiester formation at a preadenylylated nick. MimiLIG differs from bacterial LigA enzymes in that its activity is strongly dependent on the C-terminal BRCT domain, deletion of which reduced its specific activity in nick joining by 75-fold without affecting the ligase adenylylation step. The ΔBRCT mutant of MimiLIG was impaired in sealing at a preadenylylated nick. We propose that eukaryal DNA Viruses acquired the NAD + -dependent ligases by horizontal transfer from a bacterium and that MimiLIG predates entomopoxVirus ligase, which lacks both the tetracysteine and BRCT domains. We speculate that the dissemination of NAD + -dependent ligase from bacterium to Eukaryotic Virus might have occurred within an amoebal host.
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NAD+-dependent DNA Ligase Encoded by a Eukaryotic Virus
Journal of Biological Chemistry, 2001Co-Authors: Verl Sriskanda, Richard W. Moyer, Stewart ShumanAbstract:Abstract We report the production, purification, and characterization of an NAD+-dependent DNA ligase encoded by the Amsacta moorei entomopoxVirus (AmEPV), the first example of an NAD+ ligase from a source other than eubacteria. AmEPV ligase lacks the zinc-binding tetracysteine domain and the BRCT domain that are present in all eubacterial NAD+ ligases. Nonetheless, the monomeric 532-amino acid AmEPV ligase catalyzed strand joining on a singly nicked DNA in the presence of a divalent cation and NAD+. Neither ATP, dATP, nor any other nucleoside triphosphate could substitute for NAD+. Structure probing by limited proteolysis showed that AmEPV ligase is punctuated by a surface-accessible loop between the nucleotidyltransferase domain, which is common to all ligases, and the N-terminal domain Ia, which is unique to the NAD+ ligases. Deletion of domain Ia of AmEPV ligase abolished the sealing of 3′-OH/5′-PO4 nicks and the reaction with NAD+ to form ligase-adenylate, but had no effect on phosphodiester formation at a pre-adenylated nick. Alanine substitutions at residues within domain Ia either reduced (Tyr39, Tyr40, Asp48, and Asp52) or abolished (Tyr51) sealing of a 5′-PO4 nick and adenylyl transfer from NAD+without affecting ligation of DNA-adenylate. We conclude that: (i) NAD+-dependent ligases exist in the Eukaryotic domain of the phylogenetic tree; and (ii) ligase structural domain Ia is a determinant of cofactor specificity and is likely to interact directly with the nicotinamide mononucleotide moiety of NAD+.
Peter Simmonds - One of the best experts on this subject based on the ideXlab platform.
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Evaluation of the genomic diversity of Viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towards a unified taxonomy.
Journal of General Virology, 2018Co-Authors: Pakorn Aiewsakun, Andrew M Kropinski, Evelien M. Adriaenssens, Rob Lavigne, Peter SimmondsAbstract:Genome Relationship Applied to Virus Taxonomy (GRAViTy) is a genetics-based tool that computes sequence relatedness between Viruses. Composite generalized Jaccard (CGJ) distances combine measures of homology between encoded viral genes and similarities in genome organizational features (gene orders and orientations). This scoring framework effectively recapitulates the current, largely morphology and phenotypic-based, family-level classification of Eukaryotic Viruses. Eukaryotic Virus families typically formed monophyletic groups with consistent CGJ distance cut-off dividing between and within family divergence ranges. In the current study, a parallel analysis of prokaryotic Virus families revealed quite different sequence relationships, particularly those of tailed phage families (Siphoviridae, Myoviridae and Podoviridae), where members of the same family were generally far more divergent and often not detectably homologous to each other. Analysis of the 20 currently classified prokaryotic Virus families indeed split them into 70 separate clusters of tailed phages genetically equivalent to family-level assignments of Eukaryotic Viruses. It further divided several bacterial (Sphaerolipoviridae, Tectiviridae) and archaeal (Lipothrixviridae) families. We also found that the subfamily-level groupings of tailed phages were generally more consistent with the family assignments of Eukaryotic Viruses, and this supports ongoing reclassifications, including Spounavirinae and Vi1Virus taxa as new Virus families. The current study applied a common benchmark with which to compare taxonomies of Eukaryotic and prokaryotic Viruses. The findings support the planned shift away from traditional morphology-based classifications of prokaryotic Viruses towards a genome-based taxonomy. They demonstrate the feasibility of a unified taxonomy of Viruses into which the vast body of metagenomic viral sequences may be consistently assigned.
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Virus classification where do you draw the line
Archives of Virology, 2018Co-Authors: Peter Simmonds, Pakorn AiewsakunAbstract:High-throughput sequencing (HTS) and its use in recovering and assembling novel Virus sequences from environmental, human clinical, veterinary and plant samples has unearthed a vast new catalogue of Viruses. Their classification, known by their sequences alone, sets a major challenge to traditional Virus taxonomy, especially at the family and species levels, which have been historically based largely on descriptive taxon definitions. These typically entail some knowledge of their phenotypic properties, including replication strategies, virion structure and clinical and epidemiological features, such as host range, geographical distribution and disease outcomes. Little to no information on these attributes is available, however, for Viruses identified in metagenomic datasets. If such Viruses are to be included in Virus taxonomy, their assignments will have to be guided largely or entirely by metrics of genetic relatedness. The immediate problem here is that the International Committee on Taxonomy of Viruses (ICTV), an organisation that authorises the taxonomic classification of Viruses, provides little or no guidance on how similar or how divergent Viruses must be in order to be considered members of new species or new families. We have recently developed a method for scoring genomic (dis)similarity between Viruses (Genome Relationships Applied to Virus Taxonomy - GRAViTy) among the Eukaryotic and prokaryotic Viruses currently classified by the ICTV. At the family and genus levels, we found large-scale consistency between genetic relationships and their taxonomic assignments for Eukaryotic Viruses of all genome configurations and genome sizes. Family assignments of prokaryotic Viruses have, however, been made at a quite different genetic level, and groupings currently classified as sub-families are a much better match to the Eukaryotic Virus family level. These findings support the ongoing reorganisation of bacteriophage taxonomy by the ICTV Phage Study Group. A rapid and objective means to explore metagenomic viral diversity and make evidence-based assignments for such Viruses at each taxonomic layer is essential. Analysis of sequences by GRAViTy provides evidence that family (and genus) assignments of currently classified Viruses are largely underpinned by genomic relatedness, and these features could serve as a guide towards an evidence-based classification of metagenomic Viruses in the future.
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the genomic underpinnings of Eukaryotic Virus taxonomy creating a sequence based framework for family level Virus classification
Microbiome, 2018Co-Authors: Pakorn Aiewsakun, Peter SimmondsAbstract:The International Committee on Taxonomy of Viruses (ICTV) classifies Viruses into families, genera and species and provides a regulated system for their nomenclature that is universally used in Virus descriptions. Virus taxonomic assignments have traditionally been based upon Virus phenotypic properties such as host range, virion morphology and replication mechanisms, particularly at family level. However, gene sequence comparisons provide a clearer guide to their evolutionary relationships and provide the only information that may guide the incorporation of Viruses detected in environmental (metagenomic) studies that lack any phenotypic data. The current study sought to determine whether the existing Virus taxonomy could be reproduced by examination of genetic relationships through the extraction of protein-coding gene signatures and genome organisational features. We found large-scale consistency between genetic relationships and taxonomic assignments for Viruses of all genome configurations and genome sizes. The analysis pipeline that we have called ‘Genome Relationships Applied to Virus Taxonomy’ (GRAViTy) was highly effective at reproducing the current assignments of Viruses at family level as well as inter-family groupings into orders. Its ability to correctly differentiate assigned Viruses from unassigned Viruses, and classify them into the correct taxonomic group, was evaluated by threefold cross-validation technique. This predicted family membership of Eukaryotic Viruses with close to 100% accuracy and specificity potentially enabling the algorithm to predict assignments for the vast corpus of metagenomic sequences consistently with ICTV taxonomy rules. In an evaluation run of GRAViTy, over one half (460/921) of (near)-complete genome sequences from several large published metagenomic Eukaryotic Virus datasets were assigned to 127 novel family-level groupings. If corroborated by other analysis methods, these would potentially more than double the number of Eukaryotic Virus families in the ICTV taxonomy. A rapid and objective means to explore metagenomic viral diversity and make informed recommendations for their assignments at each taxonomic layer is essential. GRAViTy provides one means to make rule-based assignments at family and order levels in a manner that preserves the integrity and underlying organisational principles of the current ICTV taxonomy framework. Such methods are increasingly required as the vast virosphere is explored.
Carlos R. Escalante - One of the best experts on this subject based on the ideXlab platform.
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structural insights into the assembly of the adeno associated Virus type 2 rep68 protein on the integration site aavs1
Journal of Biological Chemistry, 2015Co-Authors: Faik N Musayev, Francisco Zarateperez, Clayton Bishop, John W Burgner, Carlos R. EscalanteAbstract:Adeno-associated Virus (AAV) is the only Eukaryotic Virus with the property of establishing latency by integrating site-specifically into the human genome. The integration site known as AAVS1 is located in chromosome 19 and contains multiple GCTC repeats that are recognized by the AAV non-structural Rep proteins. These proteins are multifunctional, with an N-terminal origin-binding domain (OBD) and a helicase domain joined together by a short linker. As a first step to understand the process of site-specific integration, we proceeded to characterize the recognition and assembly of Rep68 onto the AAVS1 site. We first determined the x-ray structure of AAV-2 Rep68 OBD in complex with the AAVS1 DNA site. Specificity is achieved through the interaction of a glycine-rich loop that binds the major groove and an α-helix that interacts with a downstream minor groove on the same face of the DNA. Although the structure shows a complex with three OBD molecules bound to the AAVS1 site, we show by using analytical centrifugation and electron microscopy that the full-length Rep68 forms a heptameric complex. Moreover, we determined that a minimum of two direct repeats is required to form a stable complex and to melt DNA. Finally, we show that although the individual domains bind DNA poorly, complex assembly requires oligomerization and cooperation between its OBD, helicase, and the linker domains.
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protein on the integration site aavs1
2015Co-Authors: Faik N Musayev, Francisco Zarateperez, Clayton Bishop, John W Burgner, Carlos R. EscalanteAbstract:ABSTRACT Adeno-Associated Virus (AAV) is the only Eukaryotic Virus with the property of establishing latency by integrating site-specifically into the human genome. The integration site known as AAVS1 is located in chromosome 19 and contains multiple GCTC repeats that are recognized by the AAV non-structural Rep proteins. These proteins are multifunctional, with an N-terminal origin-binding domain (OBD) and a helicase domain joined together by a short linker. As a first step to understand the process of site-specific integration, we set up to characterize the recognition and assembly of Rep68 onto the AAVS1 site. We first determined the X-ray structure of AAV-2 Rep68 OBD in complex with the AAVS1 DNA site. Specificity is achieved through the interaction of a glycine-rich loop that binds the major groove and an α-helix that interacts with a downstream minor groove on the same face of the DNA. Although the structure shows a complex with three OBD molecules bound to the AAVS1 site, we show using analytical centrifugation and electron microscopy that the full length Rep68 forms a heptameric complex. Moreover, we determine The latest version is at http://www.jbc.org/cgi/doi/10.1074/jbc.M115.669960 JBC Papers in Press. Published on September 14, 2015 as Manuscript M115.669960
Bing Liu - One of the best experts on this subject based on the ideXlab platform.
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a bacteriophage dna mimic protein employs a non specific strategy to inhibit the bacterial rna polymerase
Frontiers in Microbiology, 2021Co-Authors: Zhihao Wang, Hongliang Wang, Yawen Wang, Nancy Mulvenna, Maximo Sanzhernandez, Peipei Zhang, Steve Matthews, Sivaramesh Wigneshweraraj, Bing LiuAbstract:DNA mimicry by proteins is a strategy that employed by some proteins to occupy the binding sites of the DNA-binding proteins and deny further access to these sites by DNA. Such proteins have been found in bacteriophage, Eukaryotic Virus, prokaryotic, and Eukaryotic cells to imitate non-coding functions of DNA. Here, we report another phage protein Gp44 from bacteriophage SPO1 of Bacillus subtilis, employing mimicry as part of unusual strategy to inhibit host RNA polymerase. Consisting of three simple domains, Gp44 contains a DNA binding motif, a flexible DNA mimic domain and a random-coiled domain. Gp44 is able to anchor to host genome and interact bacterial RNA polymerase via the β and β' subunit, resulting in bacterial growth inhibition. Our findings represent a non-specific strategy that SPO1 phage uses to target different bacterial transcription machinery regardless of the structural variations of RNA polymerases. This feature may have potential applications like generation of genetic engineered phages with Gp44 gene incorporated used in phage therapy to target a range of bacterial hosts.