Sequence analysis of malacoherpesvirus proteins: Pan-herpesvirus capsid module and replication enzymes with an ancient connection to “Megavirales”

Mushegian, Arcady; Karin, Eli Levy; Pupko, Tal

doi:10.1016/j.virol.2017.10.009

Cited by 21 publications

(32 citation statements)

References 72 publications

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“…Although there were multiple recent attempts to build phylogenies of PolBs ( 3 , 24 , 28 ), our current work differs from the previous analyses in two major ways. First, our dataset was enriched by metagenomic sequences and contained nearly 3000 sequences (see Materials and Methods).…”

Section: Resultsmentioning

confidence: 94%

“…PolBs are also encoded by many DNA viruses with larger genomes, mainly belonging to the order Caudovirales (head-tailed viruses of Archaea and Bacteria), Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) and several other families of eukaryotic viruses such as baculoviruses and herpesviruses. In a recent study, Mushegian and colleagues showed that PolBs encoded by eukaryotic viruses form two clades, one including NCLDVs (excluding Poxviridae and Asfarviridae ), Hytrosaviridae and Herpesviridae and the other one containing Alloherpesviridae , Malacoherpesviridae , Poxviridae , Baculoviridae and Nimaviridae ( 28 ).…”

Section: Introductionmentioning

confidence: 99%

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Diversity and evolution of B-family DNA polymerases

Kazlauskas

Krupovìč

Guglielmini

et al. 2020

Nucleic Acids Research

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B-family DNA polymerases (PolBs) represent the most common replicases. PolB enzymes that require RNA (or DNA) primed templates for DNA synthesis are found in all domains of life and many DNA viruses. Despite extensive research on PolBs, their origins and evolution remain enigmatic. Massive accumulation of new genomic and metagenomic data from diverse habitats as well as availability of new structural information prompted us to conduct a comprehensive analysis of the PolB sequences, structures, domain organizations, taxonomic distribution and co-occurrence in genomes. Based on phylogenetic analysis, we identified a new, widespread group of bacterial PolBs that are more closely related to the catalytically active N-terminal half of the eukaryotic PolEpsilon (PolEpsilonN) than to Escherichia coli Pol II. In Archaea, we characterized six new groups of PolBs. Two of them show close relationships with eukaryotic PolBs, the first one with PolEpsilonN, and the second one with PolAlpha, PolDelta and PolZeta. In addition, structure comparisons suggested common origin of the catalytically inactive C-terminal half of PolEpsilon (PolEpsilonC) and PolAlpha. Finally, in certain archaeal PolBs we discovered C-terminal Zn-binding domains closely related to those of PolAlpha and PolEpsilonC. Collectively, the obtained results allowed us to propose a scenario for the evolution of eukaryotic PolBs.

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Section: Resultsmentioning

confidence: 94%

Section: Introductionmentioning

confidence: 99%

Diversity and evolution of B-family DNA polymerases

Kazlauskas

Krupovìč

Guglielmini

et al. 2020

Nucleic Acids Research

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“…The power of multi-parameter classifications described in the current study and elsewhere [ 32 ] is that outputs from improved structure modelling methods can be directly slotted into the processing pipeline and virus relationships re-evaluated within the same overall computational framework. Such methods may greatly expand the depth of phylogenetic trees constructed from CGJ distances and reveal considerably more about their deeper evolutionary relationships, perhaps including those currently apparent by morphology alone [ 36 , 43 , 44 , 47 , 48 ].…”

Section: Discussionmentioning

confidence: 99%

The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

Aiewsakun

Simmonds

2018

Microbiome

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BackgroundThe 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.ResultsThe 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.ConclusionsA 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.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0422-7) contains supplementary material, which is available to authorized users.

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“…Our search for OsHV-1-encoded miRNAs suggested that OsHV-1 does not utilize miRNAs. This was not self-evident since other viruses related to OsHV-1 [ 6 ], as well as WSSV [ 16 , 63 ] can encode miRNAs. However, the OsHV-1 sncRNA reads showed a size distribution lacking abundant size classes typical of miRNAs.…”

Section: Discussionmentioning

confidence: 99%

Parallel analysis of miRNAs and mRNAs suggests distinct regulatory networks in Crassostrea gigas infected by Ostreid herpesvirus 1

et al. 2020

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Background Since 2008, the aquaculture production of Crassostrea gigas was heavily affected by mass mortalities associated to Ostreid herpesvirus 1 (OsHV-1) microvariants worldwide. Transcriptomic studies revealed the major antiviral pathways of the oyster immune response while other findings suggested that also small non-coding RNAs (sncRNA) such as microRNAs might act as key regulators of the oyster response against OsHV-1. To explore the explicit connection between small non-coding and protein-coding transcripts, we performed paired whole transcriptome analysis of sncRNA and messenger RNA (mRNA) in six oysters selected for different intensities of OsHV-1 infection. Results The mRNA profiles of the naturally infected oysters were mostly governed by the transcriptional activity of OsHV-1, with several differentially expressed genes mapping to the interferon, toll, apoptosis, and pro-PO pathways. In contrast, miRNA profiles suggested more complex regulatory mechanisms, with 15 differentially expressed miRNAs (DE-miRNA) pointing to a possible modulation of the host response during OsHV-1 infection. We predicted 68 interactions between DE-miRNAs and oyster 3′-UTRs, but only few of them involved antiviral genes. The sncRNA reads assigned to OsHV-1 rather resembled mRNA degradation products, suggesting the absence of genuine viral miRNAs. Conclusions We provided data describing the miRNAome during OsHV-1 infection in C. gigas. This information can be used to understand the role of miRNAs in healthy and diseased oysters, to identify new targets for functional studies and, eventually to disentangle cause and effect relationships during viral infections in marine mollusks.

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Sequence analysis of malacoherpesvirus proteins: Pan-herpesvirus capsid module and replication enzymes with an ancient connection to “Megavirales”

Cited by 21 publications

References 72 publications

Diversity and evolution of B-family DNA polymerases

Diversity and evolution of B-family DNA polymerases

The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

Parallel analysis of miRNAs and mRNAs suggests distinct regulatory networks in Crassostrea gigas infected by Ostreid herpesvirus 1

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