Genome complexity: Archaea genes that attack methane (Introduction)

by David Turell , Thursday, July 15, 2021, 19:56 (1226 days ago) @ David Turell

Strange new genes found in Archaea allow methane consumption:

https://www.biorxiv.org/content/10.1101/2021.07.10.451761v1

Borgs are giant extrachromosomal elements with the potential to augment methane oxidation

"Summary
Anaerobic methane oxidation exerts a key control on greenhouse gas emissions 1, yet factors that modulate the activity of microorganisms performing this function remain little explored. In studying groundwater, sediments, and wetland soil where methane production and oxidation occur, we discovered extraordinarily large, diverse DNA sequences that primarily encode hypothetical proteins. Four curated, complete genomes are linear, up to ~1 Mbp in length and share genome organization, including replicore structure, long inverted terminal repeats, and genome-wide unique perfect tandem direct repeats that are intergenic or generate amino acid repeats. We infer that these are a new type of archaeal extrachromosomal element with a distinct evolutionary origin. Gene sequence similarity, phylogeny, and local divergence of sequence composition indicate that many of their genes were assimilated from methane-oxidizing Methanoperedens archaea. We refer to these elements as “Borgs”. We identified at least 19 different Borg types coexisting with Methanoperedens in four distinct ecosystems. Borg genes expand redox and respiratory capacity (e.g., clusters of multiheme cytochromes), ability to respond to changing environmental conditions, and likely augment Methanoperedens capacity for methane oxidation (e.g., methyl coenzyme M reductase). By this process, Borgs could play a previously unrecognized role in controlling greenhouse gas emissions."

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"Conclusions
Borgs are enigmatic extrachromosomal elements that can approach (and likely exceed) 1 Mbp in length (Table 1). We can neither prove that they are archaeal viruses or plasmids or mini-chromosomes, nor can we prove that they are not. Regardless of the name, they are clearly different from anything that has been reported previously. It is fascinating to ponder their possible evolutionary origins. Are they giant linear viruses or plasmids unlike anything previously reported? Alternatively, are they auxiliary chromosomes? Perhaps they were once a sibling Methanoperedens lineage that underwent gene loss and established a symbiotic association within Methnoperedens, as might be indicated by the monophyly of some of their Methanoperedens-like genes (Figs. S9, S10). We suspect that different Borgs tend to associate with different Methanoperedens species, yet Borg homologous recombination may indicate movement among hosts, thus their possible roles as gene transfer agents. It has been noted that Methanoperedens have been particularly open to gene acquisition from diverse bacteria and archaea 6, and Borgs may have contributed to this. The existence of Borgs encoding MCR demonstrates for the first time that MCR and MCR-like proteins for 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 over the course of archaeal evolution 17,29. Borgs carry numerous metabolic genes, some of which produce variants of Methanoperedens proteins that could have distinct biophysical and biochemical properties. Assuming that these genes extend and augment Methanoperedens energy metabolism, Borgs may have far-reaching biogeochemical consequences, including reducing methane fluxes, with important and unanticipated climate implications."

Comment: What the researchers have found is a form of genome not seen before. Archaea bacteria are the originators of life, under current theory. They are newly found and their secrets are slowly being uncovered. These extrachromosomal genes are possibly present in more advanced forms, awaiting their discovery.