Pandoravirus: New Domain or Window into Old?
Pandoravirus (left); infected ameba (right)
Imagine that you pick up some river mud, and culture amebas in it. And the amebas implode, eaten from within by a mysterious new kind of life form. Science fiction?
Actually, that’s the everyday experience of a virus hunter. Viruses–the most abundant life form on the planet–are found everywhere, and new ones can emerge from anywhere. For example, your gut is full of coliphages (bacteriophages named for your colon). So anyone can pick out a bit of colon contents (as in sewage), filter it, and form plaques on a bacterial lawn. Yes, some lucky undergraduates get to do this. And chances are you’ll find phages never before reported.
In this case, French researchers Jean-Marie Claverie and Chantal Abergal looked at mud from an Australian pond, and from the coast of Chile. In both places they found Pandoravirus, a large virus with a genome twice as long as that of the largest viruses known to date (the Megaviruses, including Mimivirus) and longer than that of many eukaryotic parasites (parasitic cells with a nucleus). Who knew–similar Pandoraviruses (and ones new to science) were probably floating around your toes at the beach.
The Pandoravirus genome lacks basic cell functions: no ribosomal parts (to make proteins), no way to eat food (such as Krebs TCA cycle), and not even a capsid protein. Thus, the Pandoravirus (at left, D) has no geometric symmetry like Mimivirus; its asymmetric form more closely resembles that of a pox virus, such as smallpox. Also, unlike Mimivirus, Pandoravirus requires a stage of replication inside the nucleus.
What about all those new mysterious genes of Pandoravirus, found within no other known life form? Does this make Pandoravirus a “fourth domain of life” (the other three being bacteria, eukaryotes, and archaea)?
Perhaps not so fast. Pandoravirus does have several “core genes” of DNA management that are found in other large DNA viruses. The Science article shows a phylogeny tree (tree of evolutionary descent) based on the sequence of DNA polymerase common to many viruses, such as megaviruses, poxviruses, and herpesviruses. The Pandoravirus sequence for DNA polymerase actually maps close to those of phycodnaviruses (viruses of algae) and herpes (viruses of you know who). But a virus may evolve in a separate track from other life forms, constrained (and sustained) by its highly specific environment, the interior of the eukaryotic cell. Suppose its genome happened to maintain a large number of genes that got lost from other organisms? This could happen by selection, or even by chance; like when an Amish community happens to maintain the name Yoder at high frequency, but loses the name Smith. So the new genes in Pandoravirus might actually represent “living fossils” of genes from an ancestral genome that the rest of us may have lost.
At any rate, it neat to think what surprises may lie before us in the mud (for a future summer perhaps?) before we clean up and head for home, looking ahead to the new academic year.
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Ultraphyte 
I’m a little confused so I’m going to try and recap and ask if I’m being accurate. So from one perspective, Pandoravirus could belong to a separate domain of life that evolved independently of any other domain. On the other hand, it could have previously belonged to the bacteria, eukaryote, or archaea domains and then diverged. In this second scenario, does that mean that Pandoravirus would still belong to one of these domains? Or does it mean that Pandoravirus no longer belongs to the domain it derives from and instead is classified as non-life? I’m not sure in general where viruses are placed in context of domains so it might help to get some background on that.
Right, so the possibilities are:
(1) Pandoravirus belongs to a “fourth domain” in the sense that it branched earlier than (or around the same time) the three domains diverged. In that case, its core genes (such as DNA polymerase) should look more distant from the three than the three do from each other.
(2) Pandoravirus branches within one of the domains (diverged later) but because it evolved in such a unique niche, it kept some of the original ancestor’s genes that no longer exist anywhere else. In which case, its core genes should resemble those of one of the domains–Eukarya, if I read the paper right.
However, the big monkeywrench in the above is that viral genomes get so scrambled by horizontal transfer that it’s hard to even define the difference between horizontal and vertical, or core versus peripheral. Suppose Pandoravirus just picked up a huge chunk of a host genome at some point, by “transduction” or whatever. Then suppose that host went extinct.
On the other hand, it’s hard to imagine that a virus would keep that much functional genome hanging around without using it for something. And if those genes work for that virus, surely they work for other entities. I think there exist a lot more viruses out there that we haven’t dreamed of–and also lots more tiny eukaryotes.