Researchers have discovered what may be a novel form of giant, extrachromosomal DNA in mud-dwelling archaea, according to a preprint posted on bioRxiv last week (July 12).
They’re “not like anything that’s been seen before,” University of Texas microbiologist Brett Baker, who was not involved in the study, tells Nature.
Extrachromosomal elements (ECE) include structures such as viruses, plasmids, and megaplasmids, and contribute to features such as antibiotic resistance in bacteria. But according to the paper, the newly discovered structures, which the researchers call Borgs, weigh in at between 600,000 and more than 1 million base pairs—far too big to fit into any of these known ECE categories. According to University of California, Berkeley, geomicrobiologist Jill Banfield, who led the study, that’s about one-third the size of the host genome. Additionally, the Borgs lack characteristic elements that would fit them into existing archaeal ECE categories, such as genes coding for viral proteins or ribosomal RNA.
According to Science, Banfield came upon the Borgs while looking for viruses that infect anaerobic, mud-dwelling archaea. After pulling samples from a meter or even deeper in mud, she and her colleagues sequenced DNA they recovered and searched for viral-specific sequences.
In one mud sample, recovered from Banfield’s own property, they discovered a colossal linear stretch of DNA: nearly 1 million base pairs long and carrying mostly genes previously unreported in the literature. The sequence had unique characteristics, including distinct base pair patterns on both ends and sites for DNA replication, leading the authors to conclude the genetic behemoth might be playing some sort of functional role.
The researchers used these characteristics to scan other metagenomic datasets from similar muddy environments in the United States, including California wetlands and a Colorado riverbed. From these datasets, they identified 19 distinct Borgs and assigned each of them a color name, including ochre, apricot, rose, and lilac.
Besides their linearity, large size, and characteristic genetic patterns, all the Borgs shared something else in common: they all coexisted with and replicated within a family of methane-metabolizing archaea called Methanoperedens. Additionally, of the 21 percent of identifiable genes within the Borgs, most of them match Methoanoperedens genes, including an RNA-targeting CRISPR-Cas system, as well as genes controlling nitrogen fixation and methane metabolism.
In the paper, the researchers conclude the Borgs acquired these genes through horizontal gene transfer from Methanoperedens. The name Borg comes from Star Trek aliens who could assimilate traits and technology from other space communities, not unlike how the Borgs may have assimilated methane-metabolizing genes from Methanoperedens. They suggest that the genes carried on the Borgs may help the archaea adapt to changing environmental conditions or augment their ability to metabolize methane.
“We expect that Borgs increase the overall amount of methane that a Methanoperedens can oxidize,” Banfield tells Vice, “in part by making them more able to adapt to changing conditions.”
The authors note that they didn’t not find Borgs in all the samples, even those where Methanoperedens were highly abundant.
Whether or not Borgs are truly novel remains to be seen. Systems biologist Nitin Baliga tells Nature that the structural features of Borgs resemble large ECEs in other archaea, such as halophiles, and Julián Rafael Dib, a microbiologist at the Pilot Plant for Microbiological Industrial Processes in Tucamán, Argentina, says they’re similar to giant linear plasmids in Actinobacteria. Neither Baliga nor Dib were involved in the study. Methanoperedens can’t be cultured in the lab, which makes studying them difficult, although the team is continuing to comb through existing genomic datasets to find more Borgs.
The Borgs’ origin remains a mystery, but Banfield and her team have a few ideas. In their paper, they postulate that they may have originated as large linear viruses or plasmids—or even a formerly free-living Methanoperedens lineage that developed a symbiotic relationship with other Methanoperedens and eventually became assimilated into them—similar to the prokaryotic precursors of modern-day mitochondria.
Besides being a scientific curiosity, Banfield tells Vice this research could lead to the discovery of “new mechanisms for processes that as yet, we don’t even know exist.”
“I haven’t been this excited about a discovery since CRISPR,” Banfield writes on Twitter.