Characterization of the endonuclease activity of the replication-associated protein of beak and feather disease virus

Chen, Jui-Kai; Hsiao, Chiaolong; Wu, Jian-Shin; Lin, Shin-Yi; Wang, Chi-Young

doi:10.1007/s00705-019-04292-z

Cited by 5 publications

(2 citation statements)

References 33 publications

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“…We identified 13 putative Reps in these crucivirus genomes that lack all four motifs typically found in S3H helicases (e.g., CruV-166, CruV-202, and CruV-499 [ Table S4]). Recent work has shown that the deletion of individual conserved motifs in the helicase domain of the Rep protein of beak and feather disease virus does not abolish ATPase and GTPase activity (66). The absence of all four motifs may prevent these putative Reps from performing helicase and ATPase activity using previously characterized mechanisms.…”

Section: Resultsmentioning

confidence: 99%

Unveiling Crucivirus Diversity by Mining Metagenomic Data

Higuera

Kasun

Torrance

et al. 2020

mBio

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The discovery of cruciviruses revealed the most explicit example of a common protein homologue between DNA and RNA viruses to date. Cruciviruses are a novel group of circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) viruses that encode capsid proteins that are most closely related to those encoded by RNA viruses in the family Tombusviridae. The apparent chimeric nature of the two core proteins encoded by crucivirus genomes suggests horizontal gene transfer of capsid genes between DNA and RNA viruses. Here, we identified and characterized 451 new crucivirus genomes and 10 capsid-encoding circular genetic elements through de novo assembly and mining of metagenomic data. These genomes are highly diverse, as demonstrated by sequence comparisons and phylogenetic analysis of subsets of the protein sequences they encode. Most of the variation is reflected in the replication-associated protein (Rep) sequences, and much of the sequence diversity appears to be due to recombination. Our results suggest that recombination tends to occur more frequently among groups of cruciviruses with relatively similar capsid proteins and that the exchange of Rep protein domains between cruciviruses is rarer than intergenic recombination. Additionally, we suggest members of the stramenopiles/alveolates/Rhizaria supergroup as possible crucivirus hosts. Altogether, we provide a comprehensive and descriptive characterization of cruciviruses. IMPORTANCE Viruses are the most abundant biological entities on Earth. In addition to their impact on animal and plant health, viruses have important roles in ecosystem dynamics as well as in the evolution of the biosphere. Circular Rep-encoding single-stranded (CRESS) DNA viruses are ubiquitous in nature, many are agriculturally important, and they appear to have multiple origins from prokaryotic plasmids. A subset of CRESS-DNA viruses, the cruciviruses, have homologues of capsid proteins encoded by RNA viruses. The genetic structure of cruciviruses attests to the transfer of capsid genes between disparate groups of viruses. However, the evolutionary history of cruciviruses is still unclear. By collecting and analyzing cruciviral sequence data, we provide a deeper insight into the evolutionary intricacies of cruciviruses. Our results reveal an unexpected diversity of this virus group, with frequent recombination as an important determinant of variability.

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Section: Resultsmentioning

confidence: 99%

Unveiling Crucivirus Diversity by Mining Metagenomic Data

Higuera

Kasun

Torrance

et al. 2020

mBio

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“…Table 4). Recent work has shown that the deletion of individual conserved motifs in the helicase domain of the Rep protein of beak and feather disease virus does not abolish ATPase and GTPase activity (86). The absence of all four motifs may prevent these putative Reps from performing helicase and ATPase activity using previously characterized mechanisms.…”

Section: Crucivirus Repmentioning

confidence: 99%

Unveiling Crucivirus Diversity by Mining Metagenomic Data

Higuera

Kasun

Torrance

et al. 2020

Preprint

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The discovery of cruciviruses revealed the most explicit example of a common protein homologue between DNA and RNA viruses to date. Cruciviruses are a novel group of circular Rep-encoding ssDNA (CRESS-DNA) viruses that encode capsid proteins (CPs) that are most closely related to those encoded by RNA viruses in the family Tombusviridae. The apparent chimeric nature of the two core proteins encoded by crucivirus genomes suggests horizontal gene transfer of CP genes between DNA and RNA viruses. Here, we identified and characterized 451 new crucivirus genomes and ten CP-encoding circular genetic elements through de novo assembly and mining of metagenomic data. These genomes are highly diverse, as demonstrated by sequence comparisons and phylogenetic analysis of subsets of the protein sequences they encode.Most of the variation is reflected in the replication associated protein (Rep) sequences, and much of the sequence diversity appears to be due to recombination. Our results suggest that recombination tends to occur more frequently among groups of cruciviruses with relatively similar capsid proteins, and that the exchange of Rep protein domains between cruciviruses is rarer than gene exchange. Altogether, we provide a comprehensive and descriptive characterization of cruciviruses. IMPORTANCEViruses are the most abundant biological entities on Earth. In addition to their impact on animal and plant health, viruses have important roles in ecosystem dynamics as well as in the evolution of the biosphere. Circular Rep-encoding single-stranded (CRESS) DNA viruses are ubiquitous in nature, many are agriculturally important, and are viruses that appear to have multiple origins from prokaryotic plasmids. CRESS-DNA viruses such as the cruciviruses, have homologues of capsid proteins (CPs) encoded by RNA viruses. The genetic structure of cruciviruses attests to the transfer of capsid genes between disparate groups of viruses. However, the evolutionary history of cruciviruses is still unclear. By collecting and analyzing cruciviral sequence data, we provide a deeper insight into the evolutionary intricacies of cruciviruses. Our results reveal an unexpected diversity of this virus group, with frequent recombination as an important determinant of variability. Bootstrap support 0.95 -1 0.8 -0.95 1 subs/site UF Bootstrap support 0.95 -1 0.8 -0.95 1 subs/site Rep CP A B * Endonuclease Helicase UF Bootstrap support 0.95 -1 0.8 -0.95 Cp-based clusters Endonuclease Helicase UF Bootstrap support 0.95 -1 0.8 -0.95 Endonuclease Helicase UF Bootstrap support 0.95 -1 0.8 -0.95

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