Sequence and annotation of the 369-kb NY-2A and the 345-kb AR158 viruses that infect Chlorella NC64A

Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
Virology (Impact Factor: 3.32). 03/2007; 358(2):472-84. DOI: 10.1016/j.virol.2006.08.033
Source: PubMed


Viruses NY-2A and AR158, members of the family Phycodnaviridae, genus Chlorovirus, infect the fresh water, unicellular, eukaryotic, chlorella-like green alga, Chlorella NC64A. The 368,683-bp genome of NY-2A and the 344,690-bp genome of AR158 are the two largest chlorella virus genomes sequenced to date; NY-2A contains 404 putative protein-encoding and 7 tRNA-encoding genes and AR158 contains 360 putative protein-encoding and 6 tRNA-encoding genes. The protein-encoding genes are almost evenly distributed on both strands, and intergenic space is minimal. Two of the NY-2A genes encode inteins, the large subunit of ribonucleotide reductase and a superfamily II helicase. These are the first inteins to be detected in the chlorella viruses. Approximately 40% of the viral gene products resemble entries in the public databases, including some that are unexpected for a virus. These include GDP-d-mannose dehydratase, fucose synthase, aspartate transcarbamylase, Ca(++) transporting ATPase and ubiquitin. Comparison of NY-2A and AR158 protein-encoding genes with the prototype chlorella virus PBCV-1 indicates that 85% of the genes are present in all three viruses.

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    • "This conclusion was supported by finding that an extract from yeast cells that were transformed with another Kcv channel protein (Kcv AR158 ) did not cross-react with anti-Kcv-8D6 (Fig. 3). Kcv AR158 is from a chlorovirus that encodes a truncated Kcvtype channel (Fig. 2; Fitzgerald et al. 2007b); its expression in yeast was not recognized by the antibody (Fig. 3). "
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    ABSTRACT: Most chloroviruses encode small K(+) channels, which are functional in electrophysiological assays. The experimental finding that initial steps in viral infection exhibit the same sensitivity to channel inhibitors as the viral K(+) channels led to the hypothesis that the channels are structural proteins located in the internal membrane of the virus particles. This hypothesis was questioned recently because proteomic studies failed to detect the channel protein in virions of the prototype chlorovirus Paramecium bursaria chlorella virus-1 (PBCV-1). Here we use a monoclonal antibody raised against the functional K(+) channel from chlorovirus MA-1D to search for the viral K(+) channel in the virus particle. The results show that the antibody is specific and binds to the tetrameric channel on the extracellular side. The antibody reacts in a virus specific manner with protein extracts from chloroviruses that encode channels similar to the one from virus MA-1D. There is no cross-reactivity with chloroviruses that encode more diverse channels or with a chlorovirus that lacks a K(+) channel gene. Together with electron microscopic imaging, which reveals labeling of individual virus particles with the channel antibody, the results establish that the viral particles contain an active K(+) channel, presumably located in the lipid membrane that surrounds DNA in the mature virions.
    Journal of General Virology 08/2013; 94(Pt_11). DOI:10.1099/vir.0.055251-0 · 3.18 Impact Factor
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    • "Since the initial sequencing of the prototype CV, Paramecium bursaria chlorella virus 1 [13,14], more than 15 years ago, only 5 more whole-genome sequences of CVs have been reported [15-17]. These 6 sequences reveal many features that distinguish them from other NCLDV including genes encoding a translation elongation factor EF-3, enzymes required to glycosylate proteins [18], enzymes required to synthesize the polysaccharides hyaluronan and chitin, polyamine biosynthetic enzymes, proteins that are ion transporters and ones that form ion channels including a virus-encoded K+ channel (designated Kcv) [19], a SET domain-containing protein (referred to as vSET) that dimethylates Lys27 in histone 3 [20,21], and many DNA methyltransferases and DNA site-specific endonucleases [22,23]. "
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    ABSTRACT: Background Giant viruses in the genus Chlorovirus (family Phycodnaviridae) infect eukaryotic green microalgae. The prototype member of the genus, Paramecium bursaria chlorella virus 1, was sequenced more than 15 years ago, and to date there are only 6 fully sequenced chloroviruses in public databases. Presented here are the draft genome sequences of 35 additional chloroviruses (287 – 348 Kb/319 – 381 predicted protein encoding genes) collected across the globe; they infect one of three different green algal species. These new data allowed us to analyze the genomic landscape of 41 chloroviruses, which revealed some remarkable features about these viruses. Results Genome colinearity, nucleotide conservation and phylogenetic affinity were limited to chloroviruses infecting the same host, confirming the validity of the three previously known subgenera. Clues for the existence of a fourth new subgenus indicate that the boundaries of chlorovirus diversity are not completely determined. Comparison of the chlorovirus phylogeny with that of the algal hosts indicates that chloroviruses have changed hosts in their evolutionary history. Reconstruction of the ancestral genome suggests that the last common chlorovirus ancestor had a slightly more diverse protein repertoire than modern chloroviruses. However, more than half of the defined chlorovirus gene families have a potential recent origin (after Chlorovirus divergence), among which a portion shows compositional evidence for horizontal gene transfer. Only a few of the putative acquired proteins had close homologs in databases raising the question of the true donor organism(s). Phylogenomic analysis identified only seven proteins whose genes were potentially exchanged between the algal host and the chloroviruses. Conclusion The present evaluation of the genomic evolution pattern suggests that chloroviruses differ from that described in the related Poxviridae and Mimiviridae. Our study shows that the fixation of algal host genes has been anecdotal in the evolutionary history of chloroviruses. We finally discuss the incongruence between compositional evidence of horizontal gene transfer and lack of close relative sequences in the databases, which suggests that the recently acquired genes originate from a still largely un-sequenced reservoir of genomes, possibly other unknown viruses that infect the same hosts.
    BMC Genomics 03/2013; 14(1):158. DOI:10.1186/1471-2164-14-158 · 3.99 Impact Factor
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    • "Acanthocystis turfacea chlorella virus 1 NC_008724 ATCV-1 Fitzgerald et al. (2007) 288,047 Bathycoccus sp. RCC1105 virus BpV1 NC_014765 BpV1 Moreau et al. (2010) 198,519 Bathycoccus sp. "
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    ABSTRACT: Viruses in Earth's aquatic environment outnumber all other forms of life and carry a vast reservoir of genetic information. A large proportion of the characterized viruses infecting eukaryotic algae are large double-stranded DNA viruses, each of their genomes carrying more than a hundred genes, but only a minority of their genes resemble genes with known biological functionalities. Unusual forms of single-stranded DNA and single- and double-stranded RNA viral genomes have been characterized over the last 10 years, and the number of novel taxa of viruses being discovered continues to increase. Although viral infections are usually specific to certain host strains in a species, lytic viral infections nevertheless affect a large proportion of algae and have a global impact, for example in the termination of blooms. Resistance to viruses is thus subject to strong selection, but little is known about its mechanism. Lateral gene transfer between host and virus has been shown by comparisons between their complete genomes and must play an important role in coevolution in the microbial world. Recent advances in bioinformatics and the possibility of amplifying complete genomes from single cells promise to revolutionize analyses of viral genomes from environmental samples.
    Advances in Botanical Research volume 64: Genomic Insights into the Biology of Algae, 1 edited by Gwenael Piganeu, 10/2012: chapter 9: pages 343-381; Academic Press Inc.., ISBN: 978-0-12-391499-6
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