Researchers Discover Self-Mutating Archaea


Judy Lau
Staff Writer

While searching the depths off the coast of Santa Monica, a research team from the University of California, Santa Barbara discovered a new virus that infects methane-eating archaea living beneath the ocean’s floor.

Archaea, a type of single-celled microorganism, go to great lengths to thrive in the most extreme environments on the planet. However, it was recently discovered that a virus is capable of selectively targeting one of its own genes for mutation; what’s more, is that some archaea can do this as well.

Using the submarine Alvin, David Valentine, a professor in the UCSB Department of Earth and Science and Marine Science Institute (MSI), and his colleagues collected samples from a deep-ocean methane seep by pushing tubes into the ocean floor and retrieving sediments. The contents were fed methane gas to help the archaea grow. When the team checked for viral infection, they found a new virus with a distinctive genetic fingerprint that suggested a methane-eating archaea host.

“We found a partial genetic match from methane seeps in Norway and California,” said lead author Blair Paul, also of the Valentine lab. “The evidence suggests this viral type is distributed around the globe in deep ocean methane seeps.” This has likely been affecting archaea for nearly as long as they have been around.

Further investigation showed diversity-generating retroelements, which allow the virus to prompt and accelerate mutation. These retroelements are also capable of selecting what part of its genome will change. Such genetic elements have been identified in bacteria and viruses, but never among archaea or the viruses that infect them. Although the archaeal virus and bacterial elements seem to resemble each other, there is evidence of divergent evolutionary history.

“The target of guided mutation—the tips of the virus that make first contact when infecting a cell—was similar,” said Paul. “The ability to mutate those tips is an offensive countermeasure against the cell’s defenses—a move that resembles a molecular arms race.”

Researchers identified similar features in the genomes of a group of archaea known as nanoarchaea. Nanoarchaea target at least four distinct genes, while the virus uses guided mutation to alter a single gene.

“This is a new record,” said co-author Sarah Bagby, a postdoctoral scholar at the Valentine lab. “Previously, a few bacteria had been observed to target two genes with this mechanism. That may not seem like a huge difference, but targeting four is extraordinary. If they’re all firing at once, suddenly the number of combinations of protein variants in play is really massive.”

The virus tries to find its way into an archaea’s cell and engages in a “genetic arms race,” where both parties are rapidly mutating to outmatch each other. Researchers suspect that these competitors use these techniques to keep the virus at bay and adapt to its home.

“The cell is choosing to modify certain proteins,” Valentine explained. “While we don’t know what those proteins are being used for, I think learning about the process can tell us something about the environment in which these organisms thrive. Right now, we know so little about life in that environment.”

The research was supported by a National Science Foundation Dimensions of Biodiversity grant aimed at characterizing virus-mediated microbial diversity in methane seep ecosystems. The research team also included scientists from the University of California, Los Angeles, University of California, San Diego, and the Department of Energy’s Joint Genome Institute. The study was published in Nature Communications.