Mysterious new 'Borg' DNA seems to assimilate genes from different organisms

Mysterious strands of DNA that seemingly assimilate genes from many different organisms in their surrounding environment have been discovered in a Californian backyard.

Scientists have named these elements "Borgs", and their discovery could help us not just understand the evolution of microorganisms, but their interactions within their ecosystems, and their role in the broader environment.

According to geomicrobiologist Jill Banfield from the University of California, Berkeley, Borgs could make for a tremendously significant discovery.

"I haven't been this excited about a discovery since CRISPR," she said on Twitter. "We found something enigmatic that, like CRISPR, is associated with microbial genomes."

A paper describing the structures has been uploaded to preprint server bioRxiv, and currently awaits peer review.

The first of the Borgs was discovered in mud dredged up from Banfield's backyard. She was working with geneticist Basem Al-Shayeb of UC Berkeley to identify viruses that infect anoxic microbes known as archaea that live in wetland environments, Science Magazine reports.

Environmental DNA is an excellent way to identify the range of organisms that inhabit an ecosystem. But in their scoop of mud, Banfield and Al-Shayeb found something funny: a structure of DNA consisting of nearly a million base pairs. That's huge.

A closer look at the sequence revealed even more peculiarities: more than half of the genes were new; it had mirrored sequences at the end of each strand; and it showed structures consistent with the ability to self-replicate.

Puzzled, the researchers turned to DNA databases to see if they could find anything else that looked like their discovery. They identified 19 sequences that seemed to fit the profile.

What these DNA structures are is unclear, but they're certainly fascinating. They belong to a class of structures called extrachromosomal elements, or ECEs, which can be found outside of the chromosomes that contain most of an organism's genetic material.

ECEs are huge and self-replicating, and they can be found inside or outside of the cell nuclei; examples include plasmids and viral DNA.

"We can neither prove that they are archaeal viruses or plasmids or mini-chromosomes, nor can we prove that they are not," the researchers write in their paper.

The Borgs are much larger than other ECEs, however, according to Banfield: one-third of the size of their host microbes.

Sequencing revealed that the Borg they found have features in common with a genus of archaea called Methanoperedens that oxidize methane, suggesting that the structures could be associated with those particular microbes. In fact, the Borgs could be critically involved in that process.

This is of interest to scientists like Banfield, because the process reduces the amount of methane in the atmosphere. Since methane is a potent greenhouse gas, learning how microbes conduct this could have implications for climate science.

However, Methanoperedens can't be grown in a laboratory setting – not yet, anyway. One problem with environmental DNA is that it can be contaminated by other genetic material in the same environment.

Indeed, Borgs seem to share a lot of gene sequences from other elements and microbes; the researchers interpret this to mean that the ECEs have absorbed and assimilated these genes and elements – hence the name, after the alien hive-mind race from Star Trek.

It's possible, however, that those shared genes are evidence of environmental contamination. Until Methanoperedens can be grown in a lab, isolated from those contaminating influences, it may not be possible to definitively declare these genetic structures a new discovery.

Nevertheless, the finding is an intriguing one. If the Borgs are real, they could boost the capacity for Methanopederens' ability to oxidize methane. This suggests unknown processes could be at play, and that these ECEs play a previously unknown role in regulating the atmosphere.

"Borgs carry numerous metabolic genes, some of which produce variants of Methanoperedens proteins that could have distinct biophysical and biochemical properties," the researchers write in their paper.

"Assuming that these genes extend and augment Methanoperedens energy metabolism, Borgs may have far-reaching biogeochemical consequences, including reducing methane fluxes, with important and unanticipated climate implications."

The findings are available on preprint site bioRxiv.

#Nature | https://sciencespies.com/nature/mysterious-new-borg-dna-seems-to-assimilate-genes-from-different-organisms/