Common Origin of Four Diverse Families of Large Eukaryotic DNA Viruses

Iyer, Lakshminarayan M.; Aravind, L.; Koonin, Eugene V.

doi:10.1128/jvi.75.23.11720-11734.2001

Cited by 501 publications

(533 citation statements)

References 79 publications

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“…There were 36 NCLDV genes identified in the genome, including nine conserved orthologs found in all NCLDV (19) and seven that were present in all four families but that are missing from some lineages within those families. IIV-9 057R, 076R, and 164L were most closely related to predicted pro- Combined analysis for pre-miRNA sequences using VMir and MiPred generated seven possible pre-miRNAs (Table 3).…”

Section: Resultsmentioning

confidence: 99%

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Genomic and Proteomic Analysis of Invertebrate Iridovirus Type 9

Wong

Young

Kleffmann

et al. 2011

J Virol

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Iridoviruses (IV) are nuclear cytoplasmic large DNA viruses that are receiving increasing attention as sublethal pathogens of a range of insects. Invertebrate iridovirus type 9 (IIV-9; Wiseana iridovirus) is a member of the major phylogenetic group of iridoviruses for which there is very limited genomic and proteomic information. The genome is 205,791 bp, has a G؉C content of 31%, and contains 191 predicted genes, with approximately 20% of its repeat sequences being located predominantly within coding regions. The repeated sequences include 11 proteins with helix-turn-helix motifs and genes encoding related tandem repeat amino acid sequences. Of the 191 proteins encoded by IIV-9, 108 are most closely related to orthologs in IIV-3 (Chloriridovirus genus), and 114 of the 126 IIV-3 genes have orthologs in IIV-9. In contrast, only 97 of 211 IIV-6 genes have orthologs in IIV-9. There is almost no conservation of gene order between IIV-3, IIV-6, and IIV-9. Phylogenetic analysis using a concatenated sequence of 26 core IV genes confirms that IIV-3 is more closely related to IIV-9 than to IIV-6, despite being from a different genus of the Iridoviridae. An interaction between IIV and small RNA regulatory systems is supported by the prediction of seven putative microRNA (miRNA) sequences combined with XRN exonuclease, RNase III, and double-stranded RNA binding activities encoded on the genome. Proteomic analysis of IIV-9 identified 64 proteins in the virus particle and, when combined with infected cell analysis, confirmed the expression of 94 viral proteins. This study provides the first full-genome and consequent proteomic analysis of group II IIV.

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Section: Resultsmentioning

confidence: 99%

“…Iridoviruses (IV) are members of the nucleocytoplasmic large DNA viruses (NCLDV) (19). They possess a linear double-stranded DNA (dsDNA) genome with circular permutation and terminal redundancy (6,13), and replication of the viral genome includes distinct nuclear and cytoplasmic phases (12).…”

mentioning

confidence: 99%

Genomic and Proteomic Analysis of Invertebrate Iridovirus Type 9

Wong

Young

Kleffmann

et al. 2011

J Virol

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“…Viruses within this family are some of the largest known, with genomes up to 560 kbp in length and particles up to 220 nm in size (Dunigan et al, 2006). Comparative genomic studies suggest that phycodnaviruses are ancient, predating the diversification of the eukaryote lineage (Iyer et al, 2001(Iyer et al, , 2006. The large genomes of phycodnaviruses harbor genes that are unusual for viruses.…”

Section: Introductionmentioning

confidence: 99%

Detection of inteins among diverse DNA polymerase genes of uncultivated members of the Phycodnaviridae

2008

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Viruses in the family Phycodnaviridae infect autotrophic protists in aquatic environments. Application of a PCR assay targeting the DNA polymerase of viruses in this family has revealed that phycodnaviruses are quite diverse and appear to be widespread, but a limited number of environments have been examined so far. In this study, we examined the sequence diversity among viral DNA pol genes amplified by PCR from subtropical coastal waters of O'ahu, Hawai'i. A total of 18 novel prasinovirus-like sequences were detected along with two other divergent sequences that differ at the genus-level relative to other sequences in the family. Of the 20 new sequence types reported here, three were serendipitously found to contain protein introns, or inteins. Sequence analysis of the inteins suggested that all three have self-splicing domains and are apparently capable of removing themselves from the translated polymerase protein. Two of the three also appear to be 'active', meaning they encode all the motifs necessary for a complete dodecapeptide homing endonuclease, and are therefore capable of horizontal transfer. A subsequent PCR survey of our samples with intein-specific primers suggested that intein-containing phycodnaviruses are common in this environment. A search for similar sequences in metagenomic data sets from other oceans indicated that viral inteins are also widespread, but how these genetic parasites might be influencing the ecology and evolution of phycodnaviruses remains unclear.

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“…For example, algal viruses (family Phycodnaviridae), African swine fever virus (family Asfarviridae) and iridoviruses (family Iridoviridae) all produce large icosahedral virions containing an internal lipid membrane between the core and the capsid and a linear dsDNA genome (Dixon et al, 2000;Goorha & Murti, 1982;Heppel & Bethiaume, 1992;van Etten, 2000;Ward & Kalmakoff, 1991;Williams et al, 2000). Phylogenetic analyses of their DNA polymerase, major capsid protein and several other virally encoded structural proteins and enzymes suggest these viruses originated from a common ancestral icosahedral nucleocytoplasmic DNA virus (He et al, 2002;Iyer et al, 2001;Knopf, 1998;Stasiak et al, 2000), which also may be the evolutionary source of poxviruses (Iyer et al, 2001;Salas et al, 1999). There is little evidence, however, that two virus families that produce virions with markedly different structural properties are closely related and evolved from a common ancestor, or that one evolved from another.…”

Section: Introductionmentioning

confidence: 99%

Evidence for the evolution of ascoviruses from iridoviruses

Stasiak

Renault

Demattei

et al. 2003

Journal of General Virology

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Ascoviruses (family Ascoviridae) are large, enveloped, double-stranded (ds)DNA viruses that attack lepidopteran larvae and pupae, and are unusual in that they are transmitted by parasitic wasps during oviposition. Previous comparisons of DNA polymerase sequences from vertebrate and invertebrate viruses suggested that ascoviruses are closely related to iridoviruses. This relationship was unexpected because these viruses differ markedly in virion symmetry, genome configuration and cellular pathology. Here we present evidence based on sequence comparisons and phylogenetic analyses of a greater range of ascovirus proteins and their homologues in other large dsDNA viruses that ascoviruses evolved from iridoviruses. Consensus trees for the major capsid protein, DNA polymerase, thymidine kinase and ATPase III from representative ascoviruses, algal viruses (family Phycodnaviridae), vertebrate and invertebrate iridoviruses (family Iridoviridae) and African swine fever virus (ASFV; family Asfarviridae) showed that ascovirus proteins clustered most closely with those of the lepidopteran iridovirus Chilo iridescent virus (CIV) (Invertebrate iridescent virus 6). Moreover, analysis of the presence or absence of homologues of an additional 50 proteins encoded in the genome of Spodoptera frugiperda ascovirus showed that about 40 % occurred in CIV, with lower percentages encoded by the genomes of, respectively, vertebrate iridoviruses, phycodnaviruses and ASFV. The occurrence of three of these genes in SfAV-1a but not CIV was indicative of the evolutionary differentiation of ascoviruses from invertebrate iridoviruses.

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Common Origin of Four Diverse Families of Large Eukaryotic DNA Viruses

Cited by 501 publications

References 79 publications

Genomic and Proteomic Analysis of Invertebrate Iridovirus Type 9

Genomic and Proteomic Analysis of Invertebrate Iridovirus Type 9

Detection of inteins among diverse DNA polymerase genes of uncultivated members of the Phycodnaviridae

Evidence for the evolution of ascoviruses from iridoviruses

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