New giant viruses suggest their genomes expanded like an accordion

Viruses tend to have stripped-down genomes, carrying just enough genes to take over a cell and make lots more copies. Ebola, for example, carries a total of just seven genes, allowing new copies to be made with little fuss. There are a few exceptions—viruses like herpes with complex life cycles—but even the biggest of the viruses we knew about had only a few hundred genes.

All that changed a bit more than a decade ago, when researchers discovered the Mimivirus, which had a genome bigger than some bacteria and carried many genes for functions that are normally provided by host proteins. The huge genomes and strange behavior of the viruses led their discoverers to propose that they weren’t just odd offshoots that preyed upon life—rather, they might have played a critical role in boosting life’s complexity.

Now, researchers have discovered a new family of giant viruses, related to the Mimiviruses but distinct in a number of ways. And a careful analysis of their genes suggests they, and all other giant viruses, have been put together through relatively recent evolution. The work argues very strongly against these viruses playing a key role in life’s diversification.

Viruses and you

The Mimiviruses contain many of the genes needed to read DNA and use the information to make proteins; most other viruses rely entirely on the system that their host cells use. They also set up an odd “virus factory” inside cells they infect, which appears physically distinct from the rest of the cell’s contents.

To the people that discovered the virus, this looked almost as if the virus were setting up its own nucleus, the place where cells normally store their DNA. So they suggested this might be how cells ended up with a nucleus in the first place: a virus set up shop in what had been a simple cell, and never left. Additional complexity evolved over time, but many of the virus’ genes are still around in complex cells like our own.

While intriguing, the proposal rested on the idea that the giant viruses are a distinct lineage that has been around since the main branches of the tree of life first started. And, from a genetic standpoint, this seemed plausible; many of the genes the viruses carry were either previously unknown or not closely related to the genes of the host they preyed upon.

The new giants

That idea was put to a test by the combination of an Austrian-US research collaboration and a sewage plant. Samples from the wastewater treatment plant at Klosterneuburg, Austria were subjected to what’s called metagenome analysis. Rather than trying to culture everything that grew in the waste, the authors simply isolated DNA from it and started sequencing. Computers can then search for pieces that overlap, gradually building up individual genomes out of the random parts.

This turned up Klosneuvirus, another giant virus with a genome 1.6 million base pairs long. Electron microscopy of the sewage water then revealed giant viruses were present. Struck by this success, the authors then started searching through other metagenome data sets. This search put together three additional giant virus genomes, belonging to Catovirus, Hokovirus, and Indivirus. Combined, the new viruses add 2,500 additional gene families to the ones previously found in giant viruses.

An evolutionary comparison showed that these viruses were closely related to the Mimivirus family but formed a distinct branch. And compared to the Mimiviruses, they had an even larger collection of genes needed for protein manufacture, being able to incorporate 14 of the 20 different amino acids into proteins without any help from the host.

Origins

If giant viruses were involved in the origin of life, then the new sequences should shed some light on that. The hypothesis has some consequences—the viruses should share a core set of genes that are distinct, forming its own domain on the tree of life.

The new study finds very little evidence of that. Instead, as noted above, the new viruses have a lot more protein-manufacturing genes than the Mimiviruses. When the authors analyzed each of these genes individually, they were typically most closely related to a species with a complex cell, rather than another virus. Most of these branches were fairly recent, as well.