Borgs - a novel type of extrachromosomal elements

On July 10, a preprint of an article devoted to a new type of extrachromosomal (this type includes, for example, plasmids) elements was published on the bioRxiv.  The rising star of microbiology Basem Al-Shayeb, the 2020 Nobel laureate in chemistry Jennifer A. Doudna and the undisputed authority in the scientific world Jillian Banfield are among the authors of the article. Jillian Banfield stated on her Twitter that she “hasn’t been this excited about a new discovery since CRISPR

Let's try to figure out what exactly this scientific team discovered.

Methane (CH4) is a greenhouse gas roughly 30 times more potent than carbon dioxide (CO2) Approximately gigaton is produced annually by methanogenic (methane-producing) archaea that inhabit anoxic environments. Methanoperedens (ANME-2d, phylum Euryarchaeota) can directly couple CH4 oxidation to the reduction of iron, nitrate or manganese. Of all of Earth’s biogeochemical cycles, the methane cycle may be most tightly linked to climate. For example, some phages can decrease methane oxidation rates by infection and lysis of methane-oxidizing bacteria and others with the critical subunit of methane monooxygenase likely increase the ability of their host bacteria to generate energy during phage replication.

By analysis of whole-community metagenomic data from saturated vernal pool (wetland) soils in California, scientists discovered enigmatic genetic elements, the genomes for three of which were carefully manually curated to completion. The genome sizes range from 661,708 to 918,293 kbp. Authors rule out the possibility that these sequences represent genomes of novel Archaea, as they lack almost all of the single-copy genes found in archaeal genomes and sets of ribosomal proteins that are present even in obligate symbionts. Authors refer to these elements as “Borgs”. Authors refer to them as Borgs since many of the known genes they encode include metabolic, ribosomal, extra-cellular electron transfer, and other genes they've likely "assimilated" from their hosts via horizontal gene transfer as well as recombination among each other. This name is a reference to the Star Trek universe. The Borg co-opt the technology and knowledge of other alien species to the Collective. The Borg's ultimate goal is "achieving perfection".

A few percent of the genes in the Borgs genomes have locally elevated GC contents that approach, and in some cases match, those of coexisting Methanoperedens. This, and the very high similarity of some protein sequences to those of Methanoperedens, indicate that these genes were acquired by lateral gene transfer from them. Given all of these observations, authors conclude that the genomes represent novel archaeal extrachromosomal elements that occur in association with, but not as part of, Methanoperedens genomes. 
Many Borg genomes encode mobile element defense systems, including RNA-targeting type III-A CRISPR-Cas systems that lack spacer acquisition machinery, a feature previously noted in huge bacterial viruses. At least seven Borgs carry a nifHDK operon for nitrogen fixation. Intriguingly, all Borgs carry large FtsZ-tubulin homologs that may be involved in membrane remodeling or division, and proteins that resemble.

Borgs are enigmatic extrachromosomal elements that can reach (and likely exceed) 1 Mbp in length. The existence of Borgs encoding methyl-CoM reductase (MCR) demonstrates for the first time that MCR and MCR-like proteins for the metabolism of methane and short-chain hydrocarbons can exist on extrachromosomal elements and thus could potentially be dispersed across lineages, as is inferred to have occurred several times throughout archaeal evolution.

It was the metagenomic approach to the study of microbiota that made it possible to identify the Borgs. The SciBear team is always happy to help analyze your metagenomic sequencing data for your breakthroughs.

Al-Shayeb, Basem, et al. "Borgs are giant extrachromosomal elements with the potential to augment methane oxidation." bioRxiv (2021).

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