Giant virus with a remarkable complement of genes infects marine zooplankton

Fischer, Matthias; Allen, Michael J.; Wilson, William H.; Suttle, Curtis A.

doi:10.1073/pnas.1007615107

Cited by 321 publications

(354 citation statements)

References 48 publications

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“…A total of 796 pair-end reads were found to meet these criteria, suggesting a multiplicity of integration sites. Close to 50% of PgV predicted proteins do not exhibit a significant match (E < 10 −5 ) in the NCBI NR protein database, as is typical for viruses belonging to a newly explored lineage with no other sequenced representatives (2,6). (B) Surprisingly, for 77% of the PgV predicted proteins exhibiting a viral protein as their best match, this homolog is found in the partially sequenced OLPV1 or -2.…”

Section: Resultsmentioning

confidence: 99%

Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes

Santini

Jeudy

Bartoli

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

176

213

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Large dsDNA viruses are involved in the population control of many globally distributed species of eukaryotic phytoplankton and have a prominent role in bloom termination. The genus Phaeocystis ( Haptophyta , Prymnesiophyceae ) includes several high-biomass-forming phytoplankton species, such as Phaeocystis globosa , the blooms of which occur mostly in the coastal zone of the North Atlantic and the North Sea. Here, we report the 459,984-bp-long genome sequence of P. globosa virus strain PgV-16T, encoding 434 proteins and eight tRNAs and, thus, the largest fully sequenced genome to date among viruses infecting algae. Surprisingly, PgV-16T exhibits no phylogenetic affinity with other viruses infecting microalgae (e.g., phycodnaviruses), including those infecting Emiliania huxleyi , another ubiquitous bloom-forming haptophyte. Rather, PgV-16T belongs to an emerging clade (the Megaviridae) clustering the viruses endowed with the largest known genomes, including Megavirus, Mimivirus (both infecting acanthamoeba), and a virus infecting the marine microflagellate grazer Cafeteria roenbergensis . Seventy-five percent of the best matches of PgV-16T–predicted proteins correspond to two viruses [Organic Lake phycodnavirus (OLPV)1 and OLPV2] from a hypersaline lake in Antarctica (Organic Lake), the hosts of which are unknown. As for OLPVs and other Megaviridae, the PgV-16T sequence data revealed the presence of a virophage-like genome. However, no virophage particle was detected in infected P. globosa cultures. The presence of many genes found only in Megaviridae in its genome and the presence of an associated virophage strongly suggest that PgV-16T shares a common ancestry with the largest known dsDNA viruses, the host range of which already encompasses the earliest diverging branches of domain Eukarya.

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Section: Resultsmentioning

confidence: 99%

Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes

Santini

Jeudy

Bartoli

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

176

213

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“…The significance of this finding is twofold: first, it demonstrates that viral AARS are not limited to class-I enzymes, and second, it makes the scenario of independent acquisition of these genes by HGT increasingly unlikely. Interestingly, the 730-kb genome of the Cafeteria roenbergensis virus, a very distant relative of Mimivirus, also encodes an IleRS (25). Both of these viral IleRS sequences are from the cytoplasmic archaeal/eukaryotic type, but do not exhibit phylogenetic affinity with a known eukaryotic clade (Fig.…”

Section: Resultsmentioning

confidence: 99%

Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae

Arslan

Legendre

Seltzer

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

312

334

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Mimivirus, a DNA virus infecting acanthamoeba, was for a long time the largest known virus both in terms of particle size and gene content. Its genome encodes 979 proteins, including the first four aminoacyl tRNA synthetases (ArgRS, CysRS, MetRS, and TyrRS) ever found outside of cellular organisms. The discovery that Mimivirus encoded trademark cellular functions prompted a wealth of theoretical studies revisiting the concept of virus and associated large DNA viruses with the emergence of early eukaryotes. However, the evolutionary significance of these unique features remained impossible to assess in absence of a Mimivirus relative exhibiting a suitable evolutionary divergence. Here, we present Megavirus chilensis, a giant virus isolated off the coast of Chile, but capable of replicating in fresh water acanthamoeba. Its 1,259,197-bp genome is the largest viral genome fully sequenced so far. It encodes 1,120 putative proteins, of which 258 (23%) have no Mimivirus homologs. The 594 Megavirus/Mimivirus orthologs share an average of 50% of identical residues. Despite this divergence, Megavirus retained all of the genomic features characteristic of Mimivirus, including its cellular-like genes. Moreover, Megavirus exhibits three additional aminoacyl-tRNA synthetase genes (IleRS, TrpRS, and AsnRS) adding strong support to the previous suggestion that the Mimivirus/Megavirus lineage evolved from an ancestral cellular genome by reductive evolution. The main differences in gene content between Mimivirus and Megavirus genomes are due to (i) lineages specific gains or losses of genes, (ii) lineage specific gene family expansion or deletion, and (iii) the insertion/migration of mobile elements (intron, intein).Mimiviridae | DNA virus phylogeny | girus | viral translation | tree of life

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“…These mega-viruses infect amoeba, algae and an unknown array of other cell types [152]. Their genomes contain sequences from all three domains of life [153].…”

Section: The Roles Of Viruses and The Virospherementioning

confidence: 99%

How life changes itself: The Read–Write (RW) genome

Shapiro

2013

Physics of Life Reviews

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The genome has traditionally been treated as a Read-Only Memory (ROM) subject to change by copying errors and accidents. In this review, I propose that we need to change that perspective and understand the genome as an intricately formatted Read-Write (RW) data storage system constantly subject to cellular modifications and inscriptions. Cells operate under changing conditions and are continually modifying themselves by genome inscriptions. These inscriptions occur over three distinct time-scales (cell reproduction, multicellular development and evolutionary change) and involve a variety of different processes at each time scale (forming nucleoprotein complexes, epigenetic formatting and changes in DNA sequence structure). Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.

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Giant virus with a remarkable complement of genes infects marine zooplankton

Cited by 321 publications

References 48 publications

Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes

Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes

Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae

How life changes itself: The Read–Write (RW) genome

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