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The Ancient Evolutionary History of Polyomaviruses.

Buck CB, Van Doorslaer K, Peretti A, Geoghegan EM, Tisza MJ, An P, Katz JP, Pipas JM, McBride AA, Camus AC, McDermott AJ, Dill JA, Delwart E, Ng TF, Farkas K, Austin C, Kraberger S, Davison W, Pastrana DV, Varsani A - PLoS Pathog. (2016)

Bottom Line: To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods.Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages.The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae.

View Article: PubMed Central - PubMed

Affiliation: Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America.

ABSTRACT
Polyomaviruses are a family of DNA tumor viruses that are known to infect mammals and birds. To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. Analyses drawing upon the divergent new sequences indicate that polyomaviruses have been gradually co-evolving with their animal hosts for at least half a billion years. Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages. The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae.

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Structural modeling of LT proteins.The solved OBD-Zn-ATPase SV40 LT structure (PDB identifier 4GDF) was used as template for all OBD and Zn-ATPase domain models. The model of the guitarfish polyomavirus J domain was generated using the solved structure of the SV40 LT DNAJ domain (PDB identifier 1GH6) as template. For the DNAJ domain of scorpion polyomavirus LT, the best modeling template match is a Thermus thermophilus DNAJ protein (PDB identifier 4J7Z). The solved structure of the bacterial DNAJ is highlighted in magenta in the pairwise superimposition (top left). The LT proteins of the indicated polyomavirus species are shown in black. The known structures of SV40 LT domains are superimposed in gold. The conserved HPD motif of the DNAJ domain is positioned on the top and highlighted in cyan. The N-terminal domain of the notothen polyomavirus has no discernible structural similarity to known DNAJ structures.
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ppat.1005574.g002: Structural modeling of LT proteins.The solved OBD-Zn-ATPase SV40 LT structure (PDB identifier 4GDF) was used as template for all OBD and Zn-ATPase domain models. The model of the guitarfish polyomavirus J domain was generated using the solved structure of the SV40 LT DNAJ domain (PDB identifier 1GH6) as template. For the DNAJ domain of scorpion polyomavirus LT, the best modeling template match is a Thermus thermophilus DNAJ protein (PDB identifier 4J7Z). The solved structure of the bacterial DNAJ is highlighted in magenta in the pairwise superimposition (top left). The LT proteins of the indicated polyomavirus species are shown in black. The known structures of SV40 LT domains are superimposed in gold. The conserved HPD motif of the DNAJ domain is positioned on the top and highlighted in cyan. The N-terminal domain of the notothen polyomavirus has no discernible structural similarity to known DNAJ structures.

Mentions: Computer-based modeling was used to investigate the possible structural conservation of the apparent LTs of the new fish and arthropod polyomaviruses. SV40 LT is divided into discrete structural domains that are thought to exist in a “beads on a string” configuration (reviewed in [20]). The structures of individual LT domains have been solved [21, 22]. The modeled structures of the scorpion and fish LT origin binding domain (OBD), zinc finger domain, and ATPase domain each show a good fit with the known SV40 structures (Fig 2). A conservation map for the DNAJ and Zn-ATPase domains is shown in S2 Fig. These results confirm that the fish- and scorpion-derived sequences represent bona fide polyomavirus LT proteins.


The Ancient Evolutionary History of Polyomaviruses.

Buck CB, Van Doorslaer K, Peretti A, Geoghegan EM, Tisza MJ, An P, Katz JP, Pipas JM, McBride AA, Camus AC, McDermott AJ, Dill JA, Delwart E, Ng TF, Farkas K, Austin C, Kraberger S, Davison W, Pastrana DV, Varsani A - PLoS Pathog. (2016)

Structural modeling of LT proteins.The solved OBD-Zn-ATPase SV40 LT structure (PDB identifier 4GDF) was used as template for all OBD and Zn-ATPase domain models. The model of the guitarfish polyomavirus J domain was generated using the solved structure of the SV40 LT DNAJ domain (PDB identifier 1GH6) as template. For the DNAJ domain of scorpion polyomavirus LT, the best modeling template match is a Thermus thermophilus DNAJ protein (PDB identifier 4J7Z). The solved structure of the bacterial DNAJ is highlighted in magenta in the pairwise superimposition (top left). The LT proteins of the indicated polyomavirus species are shown in black. The known structures of SV40 LT domains are superimposed in gold. The conserved HPD motif of the DNAJ domain is positioned on the top and highlighted in cyan. The N-terminal domain of the notothen polyomavirus has no discernible structural similarity to known DNAJ structures.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4836724&req=5

ppat.1005574.g002: Structural modeling of LT proteins.The solved OBD-Zn-ATPase SV40 LT structure (PDB identifier 4GDF) was used as template for all OBD and Zn-ATPase domain models. The model of the guitarfish polyomavirus J domain was generated using the solved structure of the SV40 LT DNAJ domain (PDB identifier 1GH6) as template. For the DNAJ domain of scorpion polyomavirus LT, the best modeling template match is a Thermus thermophilus DNAJ protein (PDB identifier 4J7Z). The solved structure of the bacterial DNAJ is highlighted in magenta in the pairwise superimposition (top left). The LT proteins of the indicated polyomavirus species are shown in black. The known structures of SV40 LT domains are superimposed in gold. The conserved HPD motif of the DNAJ domain is positioned on the top and highlighted in cyan. The N-terminal domain of the notothen polyomavirus has no discernible structural similarity to known DNAJ structures.
Mentions: Computer-based modeling was used to investigate the possible structural conservation of the apparent LTs of the new fish and arthropod polyomaviruses. SV40 LT is divided into discrete structural domains that are thought to exist in a “beads on a string” configuration (reviewed in [20]). The structures of individual LT domains have been solved [21, 22]. The modeled structures of the scorpion and fish LT origin binding domain (OBD), zinc finger domain, and ATPase domain each show a good fit with the known SV40 structures (Fig 2). A conservation map for the DNAJ and Zn-ATPase domains is shown in S2 Fig. These results confirm that the fish- and scorpion-derived sequences represent bona fide polyomavirus LT proteins.

Bottom Line: To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods.Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages.The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae.

View Article: PubMed Central - PubMed

Affiliation: Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America.

ABSTRACT
Polyomaviruses are a family of DNA tumor viruses that are known to infect mammals and birds. To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. Analyses drawing upon the divergent new sequences indicate that polyomaviruses have been gradually co-evolving with their animal hosts for at least half a billion years. Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages. The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae.

Show MeSH
Related in: MedlinePlus