Recently, researchers have discovered an ultra-long DNA structure in the dirt of their backyard, presumably an extrachromosome element (ECE). One of their miraculous properties is that they can "assimilate" the DNA structural forms of other species, and scientists have discovered that it contains key genes from other organisms. This ability is comparable to the alien race "Borg" in the famous science fiction work "Star Trek", so this DNA is also called "Borg". Regarding the Borg, there are still many questions worth exploring.
Written by | Gu Shuchen
In the science fiction film Star Trek, there is an evil alien race called the Borg, who are extremely adaptable and can maintain their own race by assimilating other races, although they cannot reproduce on their own. They want to make their race perfect by assimilating all the races they can encounter. When confronted with resistance from other races, the Borg take out their mantra: Resistance is futile. However, you certainly can't imagine that this kind of alien race "Borg" also has an Earth variant that is "lurking" around us!
Captain Picard, assimilated by the Borg 丨 Image source: CBS
Recently, the team of Professor Jill Banfield of the University of California, Berkeley, published a research paper entitled "Borgs are giant extrachromosomal elements with the potential to augment methane oxidation" on the preprint platform bioRxiv. Professor Banfiled's research team discovered a new form of DNA structure that can "assimilate" different microbial genes in the environment from soil samples in the western United States, which has aroused widespread concern in the academic community, including journals such as Science and Nature. Interestingly, the name "Borg" was proposed at Thanksgiving dinner by Professor Banfield's sci-fi-loving son.
Professor Jillian Banfield received the 2011 World Outstanding Women Scientist Award for her research on the behavior of bacteria and matter in the extreme environments of the Earth. Her main research interests are the relationship between microorganisms and minerals, and from these two fields of research that are very different at first glance, Professor Banfield has discovered the mystery of the interaction between the two fields, and has made many unique insights, and she has even cited the fact that microorganisms have large-scale geological changes such as influencing erosion, as well as the ability to construct special substances from stones. Therefore, the discovery of "Borg" DNA this time has also triggered a hot discussion, and everyone is looking forward to Professor Banfield to bring new research breakthroughs to the academic community.
Professor Banfield's group originally planned to study archaea that can degrade methane, as well as viruses that can infect such archaea and affect their ability to degrade methane. Archaea mostly live in anaerobic environments, and researchers need to dig pits more than a meter deep to obtain the samples they need. These dirt samples will be taken back to the laboratory for sequencing analysis, and then computer calculations will be used to obtain each DNA sequence and find DNA from the virus.
The discovery of the Borg DNA was purely accidental. In a dirt sample from the researchers' own backyard, they found an extra-long stretch of DNA with a large number of new genes that had never been seen before. Not only that, but this piece of DNA also has a very special structure, with near-mirror DNA sequences at the head and tail, and special repetitive sequences between genes. There are also sequences that allow DNA to initiate replication, indicating that such DNA has the potential to replicate itself. Combining these findings, the scientists believe that this DNA is not randomly generated. And after searching a large number of databases, the researchers found 23 potential "Borg" DNA, 19 of which have the same characteristics as the first "Borg" DNA discovered, all from the wetland soil of Colorado and California.
Researchers collect DNA samples from soil 丨 Image source: JILL BANFIELD
Through further research, the researchers believe that "Borg" DNA is extrachromosomal DNA, an extrachromosomal element (ECE). The so-called extrasomal elements are extrachromosome DNA, which are present in many host microorganisms. Most microbes have one or two chromosomes for genetic coding, but in addition to the DNA in the chromosomes, there are also the presence of extrasomal DNA, such as mitochondrial DNA, and plasmids that have become important scientific tools, carrying certain non-essential but beneficial genes to coexist with the host microbe. ECE is mostly circular, bare, and a few are linear and can be independently replicated within cells. Some of them are necessary for the life activities of cells, such as mitochondria and chloroplasts; some can give cells certain characteristics, such as resistance genes of bacterial plasmids, carba grains of poisonous grasshoppers, etc.
As for what the role of the "Borg" DNA is, the researchers speculate that it can be involved in metabolizing methane. Sequence analysis revealed that the "Borg" DNA appeared to be associated with a type of archaea called Methanoperedens, and that some of the genes in the "Borg" DNA assimilation genes came from the chromosomes of this archaea. These archaea are able to digest and metabolize methane, and Borg DNA appears to be involved in the process. As a result, scientists believe that Borg DNA may also help fight climate change — methane is the second largest human greenhouse gas after carbon dioxide, accounting for about 20 percent of global greenhouse gas emissions — and that the growth of microbes containing Borg DNA will be able to break down large amounts of methane. However, because scientists have not yet been able to grow this archaea in the laboratory, the conclusion that the "Borg" structure may be used by archaea to process methane is only speculation based on genetic sequencing data.
In addition to many genes associated with Methanoperedens archaea, Borg DNA contains many other important genes, such as some that are essential for metabolism. In addition, Borg DNA has some unique properties. First of all, as mentioned earlier, it is huge in size, its length is between 60-1 million pairs of DNA bases, which is close to one-third of the length of eukaryote chromatin, and it is important to know that the average ECE is only between 50 and 1000 pairs of bases. This is an important feature that distinguishes it from other fragments. Second, "Borg" DNA is linear, not circular as many ECEs do. Finally, there are mirror repeats at both ends of the Borg DNA, and there are many other repeats inside and between genes.
Scanning electron microscopy images show that Burgergella appears to be associated with single-celled microorganisms called archaea
丨图源：Eye of Science/SPL
While the discovery of the Borg DNA has left some researchers extremely excited, the work has not yet been peer-reviewed for publication in a formal journal. Therefore, the researchers believe we need to be more cautious about this finding and suggest a number of other possibilities. Nitin Baliga, a biologist at the Institute for Systems Biology in Seattle, Washington, thinks there's a risk of error when researchers, like Banfield's team, sift through fragments of many genomes and piece them together. He believes that "Borg" DNA can only be confirmed if it is found in cultured Methanoperedens archaea. In addition, from the structural characteristics of the "Borg" DNA alone, it may overlap with the characteristics of other large ECEs, such as elements in some salt-loving archaea. Therefore, Bagliga believes that the novelty of the "Borg" DNA structure is still debatable at this stage. Julian Rafael Dib, a microbiologist at the Pilot Plant for Microbiological Industrial Processes in Tucuman, Argentina, believes the Borg structure is similar to the giant mitoplasmids found in actinomycetes that inhabit the soil. There are other seemingly crazy explanations, such as the fact that the "Borg" DNA originated from some unknown microorganism and was subsequently assimilated by other archaea, just as mitochondria are assimilated by eukaryotic cells. Or maybe this "Borg DNA" is a giant virus in itself...
Currently, the research team is studying the function of the "Borg" DNA and the role of its DNA repeats. DNA repeats are very important for microorganisms, such as the CRISPR-Cas system, the immune defense system of bacteria and archaea against viruses. The repeating structure in the system, known as the CRISPR array, comes from fragments of the virus's genetic code that microbes integrate into their own DNA to "remember" pathogens in order to fend off them in the future. CRISPR has become a powerful gene-editing technology that is transforming the life sciences research field and even the human world. Professor Banfield's preprint co-author Professor Jennifer Doudna, who also won the 2020 Nobel Prize in Chemistry for his research on CRISPR gene editing, will also work on their future collaboration to investigate the similar instrumentalization potential of "Borg" DNA.
Although so far, we still do not know what the "Borg" DNA is, what its function is, but it is worth noting that the researchers found that the "Borg" DNA can assimilate genes from different sources, and the existence of "Borg" DNA shows the fact that many genetic elements can "jump" between different chromosomes and even between different species, so that life can better adapt to the environment. This also reflects the wonder of life. The charm of science lies in exploring the unknown, discovering the unknown, and hopefully in the near future we will know when Borg DNA will say the classic line "Resistance is ineffective" to other species.
Resources
[1] Basem Al-Shayeb et al., (2021), Borgs are giant extrachromosomal elements with the potential to augment methane oxidation, bioRxiv, DOI: https://doi.org/10.1101/2021.07.10.451761
[2] Mysterious DNA sequences, known as ‘Borgs,’ recovered from California mud, Retrieved July 19, 2021, from https://www.sciencemag.org/news/2021/07/mysterious-dna-sequences-known-borgs-recovered-california-mud
[3] Massive DNA ‘Borg’ structures perplex scientists, Retrieved July 19, 2021, from https://www.nature.com/articles/d41586-021-01947-3