Plasmid, Virus or Other? DNA 'Borgs' Blur Boundaries. - Quanta Magazine
Jul 21, 2021 2 mins, 22 secs
Just as the alien species in Star Trek “assimilates” individuals into a hive mind, these unknown elements may integrate genes from their host cells into their own DNA, according to Basem Al-Shayeb, a graduate student in Banfield’s lab.

When Banfield and her team first stumbled upon the unfamiliar DNA sequences, they were “stunned to find these elements that were over 900,000 bases long,” Al-Shayeb said.

“And the majority of the genes that were encoded on there were completely unknown.” This left the researchers relatively few genetic clues to what the Borgs were, or what they might be doing.

In fact, the sequences were almost a third the size of the genomes of their host archaea.

None of this seemed to align with what Banfield and her colleagues expected to see in known genetic elements like chromosomes, viruses or plasmids.

They seemed to carry genes from the archaea they inhabited — including genes involved in methane metabolism, ribosomal protein synthesis, cell wall structure, nitrogen utilization and extracellular electron transfer.

Genes for many of these functions aren’t usually located in marginal elements outside the chromosomes of cells.

The researchers even saw hints that Borgs might sometimes get transferred between different archaea, which would allow them to carry genes from one host to another.

While Banfield has not yet ruled out the possibility that Borgs are a very large virus or plasmid, she hypothesizes that they could represent an entirely new type of genetic element — “not because they have any single feature that’s unique, but because of the combination of features,” she said.

“A new type of plasmid, and maybe a very exciting type of plasmid, but a plasmid nevertheless.” Linear plasmids have not been previously found in archaea, but in their size and genetic composition, Borgs look a lot like some massive linear plasmids discovered a decade ago in bacteria.

Given their size, the Borgs “might be on the way to becoming additional chromosomes for these archaea,” Krupovic said.

Yet regardless of what Borgs turn out to be, their real significance is in underscoring “that the boundary between these different genetic entities is actually fluid,” Feschotte said.

“They add to our understanding of how diverse [genetic] elements can be, in terms of genome structure, in terms of size, in terms of organisms where they can be found,” he said.

In fact, part of why it has taken so long to uncover Borgs is that their host archaea, like nearly all known archaeal species, have never been cultured in a laboratory.

Banfield, Al-Shayeb and their colleagues speculated in their paper that, because some Borgs carry genes for methane oxidation, the genetic elements might one day be useful for modifying cells to remove methane from the environment and help curb climate change.

“There’s a huge inventory of genes that remain to be explored” in the Borgs, Banfield said

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