Borg's massive DNA structures baffle scientists

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Borg's massive DNA structures baffle scientists
Borg's massive DNA structures baffle scientists

The Borgs have landed - or at least researchers have found their counterpart on Earth. Scientists analyzing samples from muddy areas in the western United States have discovered new DNA structures that appear to collect and "assimilate" microbial genes in the environment, much like the fictional aliens from Star Trek, the Borg, who assimilate knowledge and technology from other species.

These extra-long strands of DNA, which scientists named after aliens, join a diverse collection of genetic structures - such as circular plasmids - known as extrachromosomal elements (ECEs). Most microbes have one or two chromosomes that code for their basic genetic blueprint. But they can contain and often share many different IQEs. They carry non-essential but useful genes, such as antibiotic resistance genes.

Borghi are a previously unknown, unique and "absolutely stunning" type of ECE, says Jill Banfield, a geomicrobiologist at the University of California, Berkeley. She and her colleagues described the structures they discovered in a preprint hosted on the bioRxiv1 server. The work has not yet been reviewed.

Unlike everything previously seen

Borges are DNA structures "unlike anything we've seen before," says Brett Baker, a microbiologist at the University of Texas at Austin.

In recent years, "people have become accustomed to ESE surprises," says Huang Li, a microbiologist at the Chinese Academy of Sciences in Beijing. "However, the discovery of the Borgs, which undoubtedly enriches the concept of IVF, has delighted many experts in this field."

Their sheer size - from 600,000 to 1 million DNA base pairs in length - is one of the features that sets the Borgs apart from many other ECEs. Borgs are so huge that they are up to one-third the length of the host microbes' main chromosome, Banfield said.

Banfield is studying the effects of microbes on the carbon cycle, including the production and decomposition of methane, a potent greenhouse gas, and in October 2019, she and her colleagues set out to search for ECEs containing genes involved in the carbon cycle in California's swamps. There they discovered the first Borgs, and later identified 19 different types from this and similar locations in Colorado and California.

Borges appear to be related to archaea, which are single-celled microorganisms other than bacteria. In particular, the Borgs discovered by Banfield and her team are associated with the Methanoperedens species, which digest and break down methane. And the Borg genes seem to be involved, says Banfield.

Scientists are not yet able to cultivate Methanoperedens in the laboratory, which is a persistent problem for many microbes, so the team's conclusions that archaea can use the borghi to process methane are based only on sequence data.

Costs and Benefits

If the Borgs exist, maintaining such a massive ESE would be costly for the Methanoperedens, Banfield and colleagues say, so DNA structures must be of some benefit. To find out what it might be, the researchers analyzed the sequences of hundreds of Borg genes and compared them with known genes.

Borgs appear to contain a variety of genes required for entire metabolic processes, including the digestion of methane, Banfield said. She calls these collections a "toolbox" that can extend the capabilities of Methanoperedens.

What makes a Borg a Borg?

Aside from their striking size, the Borgs share several structural features in common: they are linear rather than circular like many ECEs; they have mirrored repeating sequences at each end of the strand; and they have many other repetitive sequences both within and between putative genes.

Borges also resemble the giant linear plasmids found in soil-dwelling actinobacteria, says Julian Rafael Deeb, a microbiologist at the Experimental Plant for Microbiological Industrial Processes in Tucuman, Argentina.

Banfield argues that while individual traits of the Borg have been encountered before, they are distinguished by "the size, combination and metabolic load of genes." She suggests that they were once whole microbes and were assimilated by methanoperenes in much the same way that eukaryotic cells received energy-generating mitochondria by assimilating free-living bacteria.

Now that scientists know what to look for, they can find more Borgs by sifting through old data, says Baker, who used to work at Banfield's lab. He believes that he may have already discovered several candidates in his own genetic database after the publication of the preprint.

Resistance is futile

By analyzing the Borg genome, Banfield and his colleagues also saw signs that the Borgs were assimilating genes from various sources, including the Methanoperedens main chromosome, Banfield says. This potential for "assimilation" of genes led her son to suggest the name "Borg" at Thanksgiving dinner in 2020.

The Banfield team is currently studying the function of the Borgs and the role of their DNA replicas. Repetitions are important for microbes: repetitions of different structure, called CRISPR, are fragments of the genetic code of viruses that microbes insert into their own DNA in order to "remember" pathogens and protect themselves from them in the future.

CRISPR and its associated proteins have become a boon to biotechnology as they have been adapted into powerful gene editing techniques - a hint that Borg genomes could be useful tools as well. "It may be as important and interesting as CRISPR, but I think it will be a new thing," says Banfield, who is collaborating on future research with preprint co-author Jennifer Doudna, a pioneer of CRISPR-based gene editing at the University of California.

One potential application the researchers see for the Borgs could be to help fight climate change. Stimulating the growth of microbes that contain them could possibly reduce the methane emissions of soil-dwelling archaea, which amount to about 1 gigaton annually globally.

It would be risky to do this in natural wetlands, Banfield said, but it might be appropriate in agricultural areas. So as a first step, her group is now hunting Borgs in California's rice paddies.