Virophages to viromes: a report from the frontier of viral oceanography

Culley, Alexander I.

doi:10.1016/j.coviro.2011.05.003

Cited by 10 publications

(11 citation statements)

References 65 publications

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“…To determine which viruses SMBV is most closely related to, we performed the following analyses: [1] we constructed phylogenetic trees by aligning the ribonucleotide reductase (Figure 6B) and helicase gene (data not shown) sequences from SMBV with GenBank sequences and [2] we constructed a Venn diagram showing a presence-absence analysis of ORFs from SMBV and related viruses (Additional file 3: Figure S3). Both phylogenetic trees show that SMBV clusters with members of Megavirales order group A (MGA), which includes APMV (the prototype of the family) and ACMV (Figure 6B).…”

Section: Resultsmentioning

confidence: 99%

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Samba virus: a novel mimivirus from a giant rain forest, the Brazilian Amazon

Campos

Boratto

Assis

et al. 2014

Virol J

133

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BackgroundThe identification of novel giant viruses from the nucleocytoplasmic large DNA viruses group and their virophages has increased in the last decade and has helped to shed light on viral evolution. This study describe the discovery, isolation and characterization of Samba virus (SMBV), a novel giant virus belonging to the Mimivirus genus, which was isolated from the Negro River in the Brazilian Amazon. We also report the isolation of an SMBV-associated virophage named Rio Negro (RNV), which is the first Mimivirus virophage to be isolated in the Americas.Methods/resultsBased on a phylogenetic analysis, SMBV belongs to group A of the putative Megavirales order, possibly a new virus related to Acanthamoeba polyphaga mimivirus (APMV). SMBV is the largest virus isolated in Brazil, with an average particle diameter about 574 nm. The SMBV genome contains 938 ORFs, of which nine are ORFans. The 1,213.6 kb SMBV genome is one of the largest genome of any group A Mimivirus described to date. Electron microscopy showed RNV particle accumulation near SMBV and APMV factories resulting in the production of defective SMBV and APMV particles and decreasing the infectivity of these two viruses by several logs.ConclusionThis discovery expands our knowledge of Mimiviridae evolution and ecology.

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Section: Resultsmentioning

confidence: 99%

“…The complexity of NCLDVs in terms of genome size, particle size and metabolic capabilities (such as their role in photosynthesis and apoptosis) has challenged many concepts in virology [2]. However, it was the discovery of APMV that spotlighted NCLDVs [3].…”

Section: Introductionmentioning

confidence: 99%

Samba virus: a novel mimivirus from a giant rain forest, the Brazilian Amazon

Campos

Boratto

Assis

et al. 2014

Virol J

133

View full text Add to dashboard Cite

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“…This is partly due to the relative paucity of studies that investigate the sequences of phages when compared with their abundance and genetic diversity 29 , 30 . Furthermore, many phage sequences are not easily accessible in databases such as GenBank, but many more exist in viral metagenome or virome studies 31 . Large proportions of phage sequences have no similarity to any known phage or other sequences.…”

Section: Introductionmentioning

confidence: 99%

CRISPRTarget

et al. 2013

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The bacterial and archaeal CRISPR/Cas adaptive immune system targets specific protospacer nucleotide sequences in invading organisms. This requires base pairing between processed CRISPR RNA and the target protospacer. For type I and II CRISPR/Cas systems, protospacer adjacent motifs (PAM) are essential for target recognition, and for type III, mismatches in the flanking sequences are important in the antiviral response. In this study, we examine the properties of each class of CRISPR. We use this information to provide a tool (CRISPRTarget) that predicts the most likely targets of CRISPR RNAs (http://bioanalysis.otago.ac.nz/CRISPRTarget). This can be used to discover targets in newly sequenced genomic or metagenomic data. To test its utility, we discover features and targets of well-characterized Streptococcus thermophilus and Sulfolobus solfataricus type II and III CRISPR/Cas systems. Finally, in Pectobacterium species, we identify new CRISPR targets and propose a model of temperate phage exposure and subsequent inhibition by the type I CRISPR/Cas systems.

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“…Giant viruses and virophages are thought to be abundant in aquatic environments, infecting a variety of protists La Scola et al 2010;Culley 2011;Yau et al 2011). Consequently, virophages could play important roles in regulating the population dynamics between protists and their viruses.…”

Section: Introductionmentioning

confidence: 99%

Evolutionary dynamics of giant viruses and their virophages

Wodarz

2013

Ecology and Evolution

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Giant viruses contain large genomes, encode many proteins atypical for viruses, replicate in large viral factories, and tend to infect protists. The giant virus replication factories can in turn be infected by so called virophages, which are smaller viruses that negatively impact giant virus replication. An example is Mimiviruses that infect the protist Acanthamoeba and that are themselves infected by the virophage Sputnik. This study examines the evolutionary dynamics of this system, using mathematical models. While the models suggest that the virophage population will evolve to increasing degrees of giant virus inhibition, it further suggests that this renders the virophage population prone to extinction due to dynamic instabilities over wide parameter ranges. Implications and conditions required to avoid extinction are discussed. Another interesting result is that virophage presence can fundamentally alter the evolutionary course of the giant virus. While the giant virus is predicted to evolve toward increasing its basic reproductive ratio in the absence of the virophage, the opposite is true in its presence. Therefore, virophages can not only benefit the host population directly by inhibiting the giant viruses but also indirectly by causing giant viruses to evolve toward weaker phenotypes. Experimental tests for this model are suggested.

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Virophages to viromes: a report from the frontier of viral oceanography

Cited by 10 publications

References 65 publications

Samba virus: a novel mimivirus from a giant rain forest, the Brazilian Amazon

Samba virus: a novel mimivirus from a giant rain forest, the Brazilian Amazon

CRISPRTarget

Evolutionary dynamics of giant viruses and their virophages

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