Deep RNA Sequencing Reveals Hidden Features and Dynamics of Early Gene Transcription in Paramecium bursaria Chlorella Virus 1

Blanc, Guillaume; Mozar, Michael; Agarkova, Irina V.; Gurnon, James R.; Yanai-Balser, Giane M.; Rowe, Janet M.; Xia, Yuannan; Riethoven, Jean-Jack M.; Dunigan, David D.; Etten, James L. Van

doi:10.1371/journal.pone.0090989

Cited by 35 publications

(64 citation statements)

References 45 publications

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“…The genes encoding these virion-associated proteins are dispersed throughout the virus genome, and most are transcribed late or early-late in the infection cycle. In contrast, the PBCV-1 ANK and vSkp1 genes are expressed as early genes (44,45). Western blotting confirmed the appearance of the vSkp1 PBCV-1 protein at 45 min p.i.…”

Section: Resultsmentioning

confidence: 80%

Chlorovirus Skp1-Binding Ankyrin Repeat Protein Interplay and Mimicry of Cellular Ubiquitin Ligase Machinery

Noel

Kang

Adamec

et al. 2014

J Virol

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The ubiquitin-proteasome system is targeted by many viruses that have evolved strategies to redirect host ubiquitination machinery. Members of the genus Chlorovirus are proposed to share an ancestral lineage with a broader group of related viruses, nucleo-cytoplasmic large DNA viruses (NCLDV). Chloroviruses encode an Skp1 homolog and ankyrin repeat (ANK) proteins. Several chlorovirus-encoded ANK repeats contain C-terminal domains characteristic of cellular F-boxes or related NCLDV chordopox PRANC (pox protein repeats of ankyrin at C-terminal) domains. These observations suggested that this unique combination of Skp1 and ANK repeat proteins might form complexes analogous to the cellular Skp1-Cul1-F-box (SCF) ubiquitin ligase complex. We identified two ANK proteins from the prototypic chlorovirus Paramecium bursaria chlorella virus-1 (PBCV-1) that functioned as binding partners for the virus-encoded Skp1, proteins A682L and A607R. These ANK proteins had a C-terminal Skp1 interactional motif that functioned similarly to cellular F-box domains. A C-terminal motif of ANK protein A682L binds Skp1 proteins from widely divergent species. Yeast two-hybrid analyses using serial domain deletion constructs confirmed the C-terminal localization of the Skp1 interactional motif in PBCV-1 A682L. ANK protein A607R represents an ANK family with one member present in all 41 sequenced chloroviruses. A comprehensive phylogenetic analysis of these related ANK and viral Skp1 proteins suggested partnered function tailored to the host alga or common ancestral heritage. Here, we show proteinprotein interaction between corresponding family clusters of virus-encoded ANK and Skp1 proteins from three chlorovirus types. Collectively, our results indicate that chloroviruses have evolved complementing Skp1 and ANK proteins that mimic cellular SCF-associated proteins. IMPORTANCEViruses have evolved ways to direct ubiquitination events in order to create environments conducive to their replication. As reported in the manuscript, the large chloroviruses encode several components involved in the SCF ubiquitin ligase complex including a viral Skp1 homolog. Studies on how chloroviruses manipulate their host algal ubiquitination system will provide insights toward viral protein mimicry, substrate recognition, and key interactive domains controlling selective protein degradation. These findings may also further understanding of the evolution of other large DNA viruses, like poxviruses, that are reported to share the same monophyly lineage as chloroviruses.T he ubiquitin-proteasome proteolytic pathway is an attractive target for viruses in their battle to create an intracellular environment conducive for their replication. In fact, targeting of ubiquitin-associated enzymes is a reoccurring theme in permissive viral infections (1). This eukaryotic regulatory system mediates a variety of biological processes, including protein turnover, DNA repair, trafficking, and signal transduction (2). Through sequential reactions of three enzyme types, covale...

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Section: Resultsmentioning

confidence: 80%

Chlorovirus Skp1-Binding Ankyrin Repeat Protein Interplay and Mimicry of Cellular Ubiquitin Ligase Machinery

Noel

Kang

Adamec

et al. 2014

J Virol

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“…The ratio of the mean transcript counts of the most expressed viral gene (OtV5_154c: 5,878) over that of one of the most highly expressed host genes, the ribulose bisphosphate carboxylase small subunit ( rbcS , ostta18g01880: 49,249), gives 0.12. As a comparison, the transcript abundance ratio of the corresponding genes during Paramecium bursaria chlorella Virus 1 (PBCV-1) infection of Chlorella was 37, far exceeding host transcription levels [47]. Since relative OtV5 transcription was lower than that of the host, even in R P lines with relatively higher OtV5 transcripts levels, this suggests viral activity was certainly much lower than expected during infection of susceptible O .…”

Section: Resultsmentioning

confidence: 99%

A Viral Immunity Chromosome in the Marine Picoeukaryote, Ostreococcus tauri

et al. 2016

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Micro-algae of the genus Ostreococcus and related species of the order Mamiellales are globally distributed in the photic zone of world's oceans where they contribute to fixation of atmospheric carbon and production of oxygen, besides providing a primary source of nutrition in the food web. Their tiny size, simple cells, ease of culture, compact genomes and susceptibility to the most abundant large DNA viruses in the sea render them attractive as models for integrative marine biology. In culture, spontaneous resistance to viruses occurs frequently. Here, we show that virus-producing resistant cell lines arise in many independent cell lines during lytic infections, but over two years, more and more of these lines stop producing viruses. We observed sweeping over-expression of all genes in more than half of chromosome 19 in resistant lines, and karyotypic analyses showed physical rearrangements of this chromosome. Chromosome 19 has an unusual genetic structure whose equivalent is found in all of the sequenced genomes in this ecologically important group of green algae.

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“…Chlorovirus PBCV‐1 infection of Chlorella variabilis is initiated by the ejection of its dsDNA genome into the host cytoplasm in a phage‐like process (Van Etten and Dunigan, ), which is followed by its presumed translocation into the nucleus. Early PBCV‐1 transcription was detected within 7 min post infection (PI) (Blanc et al ., ), followed by viral DNA synthesis at 60 min PI (Van Etten et al ., ). The studies reported here focus on the cytoplasmic factories generated by PBCV‐1 shortly after the release of its replicated genomes from the host nuclei into the cytoplasm.…”

Section: Resultsmentioning

confidence: 99%

Virus-host interactions: insights from the replication cycle of the largeParamecium bursaria chlorella virus

et al. 2015

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The increasing interest in cytoplasmic factories generated by eukaryotic-infecting viruses stems from the realization that these highly ordered assemblies may contribute fundamental novel insights to the functional significance of order in cellular biology. Here, we report the formation process and structural features of the cytoplasmic factories of the large dsDNA virus Paramecium bursaria chlorella virus 1 (PBCV-1). By combining diverse imaging techniques, including scanning transmission electron microscopy tomography and focused ion beam technologies, we show that the architecture and mode of formation of PBCV-1 factories are significantly different from those generated by their evolutionary relatives Vaccinia and Mimivirus. Specifically, PBCV-1 factories consist of a network of single membrane bilayers acting as capsid templates in the central region, and viral genomes spread throughout the host cytoplasm but excluded from the membrane-containing sites. In sharp contrast, factories generated by Mimivirus have viral genomes in their core, with membrane biogenesis region located at their periphery. Yet, all viral factories appear to share structural features that are essential for their function. In addition, our studies support the notion that PBCV-1 infection, which was recently reported to result in significant pathological outcomes in humans and mice, proceeds through a bacteriophage-like infection pathway.

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Deep RNA Sequencing Reveals Hidden Features and Dynamics of Early Gene Transcription in Paramecium bursaria Chlorella Virus 1

Cited by 35 publications

References 45 publications

Chlorovirus Skp1-Binding Ankyrin Repeat Protein Interplay and Mimicry of Cellular Ubiquitin Ligase Machinery

Chlorovirus Skp1-Binding Ankyrin Repeat Protein Interplay and Mimicry of Cellular Ubiquitin Ligase Machinery

A Viral Immunity Chromosome in the Marine Picoeukaryote, Ostreococcus tauri

Virus-host interactions: insights from the replication cycle of the largeParamecium bursaria chlorella virus

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