Paramecium bursaria Chlorella Virus 1 Proteome Reveals Novel Architectural and Regulatory Features of a Giant Virus

The functional diversity of eukaryotic viruses infecting a single host strain from seawater samples originating from distant marine locations is unknown. To estimate this diversity, we used lysis plaque assays to detect viruses that infect the widespread species Ostreococcus lucimarinus, which is found in coastal and mesotrophic systems, and O. tauri, which was isolated from coastal and lagoon sites from the northwest Mediterranean Sea. Detection of viral lytic activities against O. tauri was not observed using seawater from most sites, except those close to the area where the host strain was isolated. In contrast, the more cosmopolitan O. lucimarinus species recovered viruses from locations in the Atlantic and Pacific Oceans and the Mediterranean Sea. Six new O. lucimarinus viruses (OlVs) then were characterized and their genomes sequenced. Two subgroups of OlVs were distinguished based on their genetic distances and on the inversion of a central 32-kb-long DNA fragment, but overall their genomes displayed a high level of synteny. The two groups did not correspond to proximity of isolation sites, and the phylogenetic distance between these subgroups was higher than the distances observed among viruses infecting O. tauri. Our study demonstrates that viruses originating from very distant sites are able to infect the same algal host strain and can be more diverse than those infecting different species of the same genus. Finally, distinctive features and evolutionary distances between these different viral subgroups does not appear to be linked to biogeography of the viral isolates. IMPORTANCEMarine eukaryotic phytoplankton virus diversity has yet to be addressed, and more specifically, it is unclear whether diversity is connected to geographical distance and whether differential infection and lysis patterns exist among such viruses that infect the same host strain. Here, we assessed the genetic distance of geographically segregated viruses that infect the ubiquitous green microalga Ostreococcus. This study provides the first glimpse into the diversity of predicted gene functions in Ostreococcus viruses originating from distant sites and provides new insights into potential host distributions and restrictions in the world oceans.

Section: Discussionmentioning

confidence: 61%

Section: Fig 1 Locations Of the Sampling Sites The Type Of Ostreococmentioning

confidence: 99%

Diversity of Viruses Infecting the Green Microalga Ostreococcus lucimarinus

Derelle

Monier

Cooke

et al. 2015

“…(iv) The NY-2A virion protein sample lacked SOD activity, which provides indirect evidence that the PBCV-1 activity was virus encoded. (v) Finally, a PBCV-1 proteome study reported that the cvSOD protein was packaged in the virion (27). Therefore, the SOD activity detected in the PBCV-1 virion is the virus-encoded protein and not from the host.…”

Section: Resultsmentioning

confidence: 99%

“…The chloroviruses are proposed to have a common evolutionary ancestor with some other large DNA viruses, including the poxviruses, asfarviruses, iridoviruses, ascoviruses, mimiviruses, and marseilleviruses, and collectively are often referred to as nucleocytoplasmic large DNA viruses (NCLDVs) (24,25,26). The 331-kb linear genome of the chlorovirus type species, Paramecium bursaria chlorella virus 1 (PBCV-1), has 416 predicted protein coding sequences (CDSs) (27). About 40% of the predicted CDSs resemble those for known proteins (23), including a gene, a245r, which encodes a putative Cu-Zn SOD.…”

mentioning

confidence: 99%

Chlorovirus PBCV-1 Encodes an Active Copper-Zinc Superoxide Dismutase

Kang

Duncan

Kuszynski

et al. 2014

Self Cite

Superoxide dismutases (SODs) are metalloproteins that protect organisms from toxic reactive oxygen species by catalyzing the conversion of superoxide anion to hydrogen peroxide and molecular oxygen. Chlorovirus PBCV-1 encodes a 187-amino-acid protein that resembles a Cu-Zn SOD with all of the conserved amino acid residues for binding copper and zinc (named cvSOD). cvSOD has an internal Met that results in a 165-amino-acid protein (named tcvSOD). Both cvSOD and tcvSOD recombinant proteins inhibited nitroblue tetrazolium reduction of superoxide anion generated in a xanthine-xanthine oxidase system in solution. tcvSOD was chosen for further characterization because it was easier to produce. Recombinant tcvSOD also inhibited a riboflavin photochemical reduction system in a polyacrylamide gel assay, which was blocked by the Cu-Zn SOD inhibitor cyanide but not by azide, which inhibits Fe and Mn SODs. A k cat /K m value for cvSOD was determined by stop-flow spectrophotometry as 1.28 ؋ 10 8 M ؊1 s ؊1 , suggesting that cvSOD-catalyzed O 2 ؊ dismutation was not a diffusion controlled encounter. The cvsod gene was expressed as a late gene, and cvSOD activity was detected in purified virions. Superoxide accumulated rapidly during virus infection, and circumstantial evidence indicates that cvSOD aids its decomposition to benefit virus replication. Cu-Zn SOD homologs have been described to occur in 3 other families of large DNA viruses, poxviruses, baculoviruses, and mimiviruses, which group as a clade. Interestingly, cvSOD does not group in the same clade as the other virus SODs but instead groups in an expanded clade that includes Cu-Zn SODs from many cellular organisms. IMPORTANCEVirus infection often leads to an increase in toxic reactive oxygen species in the host, which can be detrimental to virus replication. Viruses have developed various ways to overcome this barrier. As reported in this article, the chloroviruses often encode and package a functional Cu-Zn superoxide dismutase in the virion that presumably lowers the concentration of reactive oxygen induced early during virus infection.

“…The large number of proteins in PBCV-1 raised the issue of why giant viruses contain so many genes (45). We propose that a partial answer is provided by the current report, which highlights the elaborate and highly dynamic protein composition of VFs.…”

Section: Figmentioning

confidence: 80%

Efficiency in Complexity: Composition and Dynamic Nature of Mimivirus Replication Factories

Fridmann-Sirkis

Milrot

Mutsafi

et al. 2016

The recent discovery of multiple giant double-stranded DNA (dsDNA) viruses blurred the consensual distinction between viruses and cells due to their size, as well as to their structural and genetic complexity. A dramatic feature revealed by these viruses as well as by many positive-strand RNA viruses is their ability to rapidly form elaborate intracellular organelles, termed "viral factories," where viral progeny are continuously generated. Here we report the first isolation of viral factories at progressive postinfection time points. The isolated factories were subjected to mass spectrometry-based proteomics, bioinformatics, and imaging analyses. These analyses revealed that numerous viral proteins are present in the factories but not in mature virions, thus implying that multiple and diverse proteins are required to promote the efficiency of viral factories as "production lines" of viral progeny. Moreover, our results highlight the dynamic and highly complex nature of viral factories, provide new and general insights into viral infection, and substantiate the intriguing notion that viral factories may represent the living state of viruses. IMPORTANCELarge dsDNA viruses such as vaccinia virus and the giant mimivirus, as well as many positive-strand RNA viruses, generate elaborate cytoplasmic organelles in which the multiple and diverse transactions required for viral replication and assembly occur. These organelles, which were termed "viral factories," are attracting much interest due to the increasing realization that the rapid and continuous production of viral progeny is a direct outcome of the elaborate structure and composition of the factories, which act as efficient production lines. To get new insights into the nature and function of viral factories, we devised a method that allows, for the first time, the isolation of these organelles. Analyses of the isolated factories generated at different times postinfection by mass spectrometry-based proteomics provide new perceptions of their role and reveal the highly dynamic nature of these organelles.A n exciting recent development in cellular biology is the realization that intracellular organelles previously considered to be randomly organized are in fact exquisitely ordered and that this order crucially affects their function. A prominent example is provided by replication cycles of positive-strand RNA [(ϩ)RNA] viruses, which were shown to involve massive reorganization of the host cytoskeleton and membrane networks into well-defined cytoplasmic platforms, termed "viral factories" (VFs), within which genome replication and virion assembly are effectively coordinated (1-4). An additional example of highly ordered virus-generated intracellular organelles is the replication cycle of nucleocytoplasmic large DNA viruses (NCLDVs), which include Poxviridae, Phycodnaviridae, Iridoviridae, Asfarviridae, Mimiviridae, and Marseilleviridae (5-7). Specifically, these viruses were shown to partially or exclusively replicate within large and elaborate cytoplasmic ...