On the Origins of Viruses

Wired has an interesting article from Ars Technica on the questions raised by recent discoveries of some huge viruses (“huge” relative to other viruses of course). The characterization of viruses themselves challenged biologists’ definition of life, and these giant viruses do so even more. They’re as large as some bacteria, contain genes previously thought to be specific to cells, and one virus (mamavirus) even gets infected by a small virus – the first known virophage, a virus that infects a virus.

This article, though, is about their origins; when did these giant viruses originate, and are they the ancestors or descendants of cellular life?

The unusual size and gene content of the virus led one scientist to suggest that viruses could explain the origin of DNA-based life. If viruses carried all these genes, then it’s possible to imagine that one could set up shop in a cell and simply never leave, gradually taking over the remaining functions once performed by its host’s genetic material. This would explain the origin of DNA, which would distinguish the virus from its host’s genetic material, a holdover from the RNA world. It could also explain the existence of a distinct nucleus within Eukaryotic cells.

Eukaryotic cells (like those found in plants and animals) have a nucleus; prokaryotic cells (like bacteria) do not. The “origin of DNA-based life” is a reference to the fact that it’s theorized that life used to rely on RNA as its chief genetic code, the job DNA does now. And the idea of a virus “setting up shop” in a cell and forming a nucleus is similar to mitochondria and chloroplasts, organelles (cellular compartments) in eukaryotic cells that used to be bacteria, and still have their own DNA and everything. 

A paper is being released today, however, that argues that this scenario has things exactly backwards. Giant viruses, its authors argue, have all these genes normally associated with cells because, in their distant evolutionary past, they were once cells…

And what they find supports the view that the virus started out with a much larger complement of genes… Both viruses share an identical set of genes involved in transcribing their DNA into RNA, and use an identical set of signals to indicate where the transcripts should start and stop…

Clearly, the common genes suggest that the viruses share a common ancestor. This leaves two possibilities for the novel ones: either the ancestral virus had a larger collection and its descendants have lost different ones, or each virus picked up different genes from its hosts through a process called horizontal gene transfer. The authors favor the former explanation, because most of the genes specific to one of the two viruses don’t look like any gene present in their hosts (or any other gene we’ve ever seen, for that matter).

So, when did the common ancestor exist? The authors line up a few of the conserved megavirus genes (including those of a more distantly related giant virus, CroV) with the equivalents in other eukaryotic species, and find that they branch off right at the base of the the eukaryotic lineage. In other words, the viruses seem to have had a common ancestor with eukaryotes, but it split off right after the eukaryotes diverged from bacteria and archaea…

To the authors, this suggests that the viruses are the evolutionary descendants of an ancient, free-living eukaryotic cell. Various genes and structures from that organism have gradually been lost over its long history as a parasite, leaving something that propagates like a virus, but belongs to a distinct lineage from all other viruses that we’re aware of.

The authors make a reasonably compelling case against the megaviruses getting their complex genomes via horizontal gene transfer, although it would be good to see a similar analysis for a lot more of the shared genes. What they don’t do, however, is rule out the initial alternative: it’s still technically possible that the megaviruses and eukaryotes share an ancient common ancestor because all eukaryotes are descendants of the virus’ genome. At the moment, I’m not sure it’s possible to distinguish between these alternative explanations.

If this is true, that would mean we’re more recently related to these viruses than to bacteria or archaea. It’d also imply that a living species evolved into non-life. I bet Darwin wasn’t counting on that.

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