Borgs: Giant Extrachromosomal Elements found in mud Archaea

Supriyo Mukherjee, Kalyani Mahavidyalaya

Scientific researches have unveiled a novel conformation of gigantic, extrachromosomal DNA in mud-dwelling archaea, as stated in a preprint posted on July 10, 2021, on bioRxiv.

Extrachromosomal elements (ECE) comprise structures such as plasmids, megaplasmids, viruses, etc. which give rise to attributes like antibiotic resistance in bacteria. However, as reported in the preprint, borgs are the recently discovered structures, weight in between 600,000 and above one million base pairs, are huge to insert into any of these proclaimed ECE categories. Per Jill Banfield, a renowned microbiologist at UC Berkeley, that’s approximately ⅓ the amplitude of the host genome.

The interesting discovery:

According to Science, Banfield came across the Borgs when gazing for viruses that infect mud-dwelling, anaerobic archaea. Later than extracting the samples from approximately a couple of meters deep in mud, they sequenced DNA that they retrieved and looked for viral-specific sequences.

In one mud sample, retrieved from Banfield’s property, they disclosed a colossal linear stretch of DNA: almost 1 million base pairs long and conveying mainly genes formerly unrecorded in the literature. The sequence had distinctive attributes, including different base pair patterns on both the sites and ends of DNA replication, which assisted the authors to culminate the genetic behemoth might be involved in some sort of functional role.

The researchers utilized the attributes to examine other metagenomic datasets from alike muddy environments in the United States, along with a Colorado riverbed and California wetlands. From these datasets, they recognized 19 discrete Borgs and allocated each of them a color name, along with rose, apricot, ochre, and lilac.

The notable findings of the study:

Apart from their characteristic genetic patterns, large size, linearity, all the Borgs dispensed something else in common: they concurred with and reproduced within a family of methane-metabolizing archaea called Methanoperedans. Furthermore, of the 21 percent of recognizable genes within the Borgs, principally match Methanoperedens genes, together with an RNA-targeting CRISPR-Cas system, moreover, genes directing nitrogen fixation and methane metabolism.

The researchers proposed with evidence that the Borgs obtained these genes via horizontal gene transfer from Methanoperedens. The term Borg derives from Star Trek aliens who could comprehend traits and technology from other space sections, not distant from how the Borgs may have comprehended methane-metabolizing genes from Methanoperedens. They propose that the genes kept on the Borgs may assist the archaea to modify to changing environmental circumstances or increase their capability to metabolize methane.

The authors observe that they didn’t discover Borgs in all the samples, even where the Methanoperedens were exceedingly proliferated. Certainly, Borgs are precisely novel remains to be seen. Nitin Baliga, a systems biologist, brief Nature that the structural characteristics of Borgs come across large ECEs in other archaea, like halophiles, and microbiologist Julian Rafael Dib at the Microbiological Industrial Processes pilot plant in Tucaman, Argentina, tells they are alike to gigantic linear plasmids in Actinobacteria. Neither Dib nor Baliga was incorporated in the study. Methanoperedans can’t be cultivated in the lab, which creates examining them difficult. Even though the team is unrelenting to dig through existing genomic datasets to observe more Borgs.

Significance of the study:

  The Borg’s origin endures an enigma, but Banfield and her team have a few proposals. In their paper, they hypothesized that they may have derived as huge linear plasmids or viruses or even earlier free-living Methanoperedens lineage that evolved a symbiotic relationship with other Methanoperedens and ultimately became incorporated alike prokaryotic precursors of mitochondria studied in recent days.

Also read: Can shingles develop without chickenpox?

References:

1. Al-Shayeb, B., Schoelmerich, M. C., West-Roberts, J., Valentin-Alvarado, L. E., Sachdeva, R., Mullen, S., Crits-Christoph, A., Wilkins, M. J., Williams, K. H., Doudna, J. A., & Banfield, J. F. (2021). Borgs are giant extrachromosomal elements with the potential to augment methane oxidation [Preprint]. Microbiology. https://doi.org/10.1101/2021.07.10.451761
2. Pennisi, E. (2021, July 15). Mysterious DNA sequences, known as ‘Borgs,’ recovered from California mud. Science | AAAS. https://www.sciencemag.org/news/2021/07/mysterious-dna-sequences-known-borgs-recovered-california-mud

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Author info:

Supriyo Mukherjee is an undergraduate student in Microbiology. His areas of interest are Spectroscopy, Immunology, Microbiology, and Bioinformatics.

Previous Publications:

1. A Viral DNA-packaging Motor Mechanism: https://bioxone.in/news/worldnews/a-viral-dna-packaging-motor-mechanism/
2. The Ancient Koji Mold: A Modern Biotechnological Tool: https://bioxone.in/news/worldnews/the-ancient-koji-mold-a-modern-biotechnological-tool/