Borg (microbiology) explained

A borg is a "giant extrachromosomal element with the potential to augment methane oxidation", described by Basem Al-Shayeb and Jill Banfield. Borgs are long DNA sequences existing alongside the main chromosome^[1] in the archaea Methanoperedens, in oxygen-starved environments such as deep mud.^{[2] [3]} Borgs were discovered by Professor Jill Banfield and her team in the soil of a wetland, an aquifer, a riverbed, and a deserted mercury mine in the states of California and Colorado.

Borgs are considered to be a new form of "giant linear plasmids" or giant viruses rather than unknown DNA elements.^[4] They co-occur within a species of archaea which likely hosts them and shares many of their genes. The archaeon's main chromosome is only three times larger, and their capacity for anaerobic oxidation of methane as well as other biological functions – such as production of proteins – may be augmented by borgs.^{[5] [6] [7]}

Features

They were discovered in March 8 2020 by Banfield and others. The structure of Borg genomes are conserved and are distinguished from the plasmids and chromosomes of Methanoperedens, as well as other archaeal genomes. Borgs do not possess discernible proteins that are associated with plasmids or viruses, rRNA loci, origins of replication, or vital genes that are commonly found within minichromosomes, also known as megaplasmids, of archaea. A sample of borg genomes have been found to measure between 0.66-0.92 Mbp long, which is beyond the genome length of archaea viruses currently known.^[8] Instead, the size of Borg genomes are characteristic of eukaryote-specific double-stranded DNA viruses from the phylum Nucleocytoviricota, also known as nucleocytoplasmic large DNA viruses (NCLDV), which can surpass 2.5 Mbp.^[9] Tandem direct repeat sequences are prevalent throughout a Borg's genome, and long inverted repeats terminate the genome. This differs from the megaplasmids of some bacteria, which carry interspaced repeats and usually are not responsible for encoding necessary genes.

Functions (Gene list)

Below are some of the reported genes that are encoded via Borg genomes:

Note that not every Borg genome contains the same genes.

• Mobile or transposable element defense systems
• Anaerobic oxidation of Methane (AOM)
• Type III-A CRISPR-Cas system (No spacer acquisition machinery and primarily targets RNA)
• RPL11 - Ribosomal protein L11
• Glycosyltransferase
• DNA and RNA manipulation
• Transport genes
• Energy metabolism
• Cell surface proteins
  • PEGA
  • S-layer
• Membrane-associated proteins (unknown functions that possibly affect host's membrane properties)
• Nitrogen fixation (nifHDK operon)
• Polyhydroxyalkanoate synthesis (Carbon storage) - Possibly used for when resources are low
• Tellurium resistance proteins
• FtsZ (tabulin homolog)
• Proteins that favor Major Vault Proteins
• TCA cycle genes
  • citrate synthase
  • aconitase
• cfbB and cfbC
• Coenzyme F420:L-glutamate ligase - cofE
• Electron bifurcating complexes
  • D-Lactate dehydrogenase
• Tetrahydromethanopterin synthesis
• Ferredoxin proteins
• 5,6,7,8-tetrahydromethanopterin hydro-lyase (Fae) - Involved in formaldehyde detoxification
• Carbon monoxide dehydrogenase (CODH)
• Plastocyanin
• Cupredoxins
• Multiheme cytochromes (MHC)

Trivia

Their name was chosen as a reference to the Star Trek species of the same name due to their propensity to assimilate genes from organisms, most notably Methanoperedens.

Notes and References

1. Rinke C . Mystery find of microbial DNA elements called Borgs . Nature . 610 . 7933 . 635–637 . October 2022 . 36261713 . 10.1038/d41586-022-02975-3 . 253020155 . 2022Natur.610..635R .
2. Web site: Pennisi E . Mysterious DNA sequences, known as 'Borgs,'recovered from California mud. . Science . 15 July 2021 .
3. Web site: Rayne E . 2021-08-03. Resistance is futile, because Star Trek's Borg are real and can assimilate DNA from microbes. 2021-08-05. SYFY WIRE. en.
4. News: Cepelewicz J, Whitten A . Plasmid, Virus or Other? DNA 'Borgs' Blur Boundaries. . 13 August 2021 . Quanta Magazine . 21 July 2021 . en.
5. Dance A . Massive DNA 'Borg' structures perplex scientists . Nature . 16 July 2021 . 595 . 7869 . 636 . en . 10.1038/d41586-021-01947-3. 2021Natur.595..636D . free .
6. News: Sandoval J . Previously undiscovered DNA 'borgs' found on California wetlands . 13 August 2021 . The Independent . 30 July 2021 . en.
7. Al-Shayeb B, Schoelmerich MC, West-Roberts J, Valentin-Alvarado LE, Sachdeva R, Mullen S, Crits-Christoph A, Wilkins MJ, Williams KH, Doudna JA, Banfield JF . 6 . Borgs are giant extrachromosomal elements with the potential to augment methane oxidation . bioRxiv . 13 August 2021 . 2021.07.10.451761 . en . 10.1101/2021.07.10.451761 . 10 July 2021. 235812990 .
8. Schoelmerich MC, Sachdeva R, West-Roberts J, Waldburger L, Banfield JF . Tandem repeats in giant archaeal Borg elements undergo rapid evolution and create new intrinsically disordered regions in proteins . PLOS Biology . 21 . 1 . e3001980 . January 2023 . 36701369 . 9879509 . 10.1371/journal.pbio.3001980 . free .
9. Xian Y, Xiao C . Current capsid assembly models of icosahedral nucleocytoviricota viruses . Advances in Virus Research . 108 . 275–313 . 2020-01-01 . 33837719 . 8328511 . 10.1016/bs.aivir.2020.09.006 . Virus Assembly and Exit Pathways . Kielian M, Mettenleiter TC, Roossinck MJ . Academic Press . 9780128207611 .