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French, American Researchers Sequence Giant Virus Found Inside Amoeba

NEW YORK (GenomeWeb News) – In a paper appearing online this week in the Proceedings of the National Academy of Sciences, French and American researchers reported that they have sequenced the genome of a giant virus found inside the amoeba Acanthamoeba polyphaga.

Using Roche 454 sequencing, mass spectrometry, and other methods, the team isolated and characterized a giant virus from inside A. polyphaga cells collected from a Paris water cooling tower. Dubbed the Marseillevirus for its place of discovery, the virus contains sequences similar to those found in a range of other organisms — from bacteria and other viruses to eukaryotes. Based on the finding and others before it, the researchers noted, it seems amoebas are a hotspot for incubating previously unknown viral forms.

"We propose that amoebae are 'melting pots' of microbial evolution, where diverse forms emerge, including giant viruses with complex gene repertoires of various origins," senior author Didier Raoult, an infectious and tropical disease researcher at the Université de la Méditerranée in Marseille, and his co-authors wrote.

Very large viruses have been largely overlooked in the past, Raoult and his team explained, in part due to some of the filtering techniques used to find viruses. Nevertheless, recent studies have turned up enormous viruses — including giant viruses called Mimivirus and Mamavirus — from inside amoebas in the Acanthamoeba genus.

And because such organisms engulf fairly large particles, Raoult and his colleagues reasoned, it's possible other large viruses remain undiscovered inside amoebas. Indeed, they saw Marseillevirus when they used electron microscopy to examine burst A. polyphaga cells cultured from a biofilm collected in a Paris water cooling tower.

The researchers used the Roche 454 GS FLX platform to sequence the 368,454 base, double-stranded DNA genome of Marseillevirus. Their analysis suggests the genome — the fifth largest viral genome sequenced to date — contains 457 open reading frames coding for proteins in around 28 families.

Meanwhile, their gel electrophoresis and matrix assisted laser desorption/ionization time-of-flight mass spec studies detected at least 49 proteins in Marseillevirus virions, including both structural proteins and proteins involved in the virus' life cycle. Of these, ten appear to be glycosylated and 19 phosphorylated.

The team's subsequent analyses suggest Marseillevirus is related to other known viruses, but probably belongs to a new family of nucleocytoplasmic large DNA viruses.

Almost a third of Marseillevirus' predicted genes resembled sequences found in the Global Ocean Survey data, a collection of metagenomic sequences from ocean water.

Because many of its predicted proteins resemble those found in viruses, bacteria, and eukaryotes, the researchers concluded that Marseillevirus has likely snatched genes from a range of other organisms through processes such as horizontal gene transfer.

The team also speculated that living inside amoeba hosts may contribute to such processes, since the organism consumes an array of other organisms. If so, they added, it's likely other large viruses remain undiscovered.

"Given the diversity of phagocytic unicellular eukaryotes, it seems certain that the discovery of Mimivirus, Mamavirus, and Marseillevirus is only the first narrow window into a wondrous world of giant viruses, some of which could be even bigger and more complex than the current record holder, Mamavirus," the researchers concluded.

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