Microbe with bizarrely tiny genome may be evolving into a virus

Amazing stuff! Marvelous indeed (mirabile)!

"The newly discovered microbe provisionally known as Sukunaarchaeum isn’t a virus. But like viruses, it seemingly has one purpose: to make more of itself.

As far as scientists can tell from its genome—the only evidence of its existence so far—it’s a parasite that provides nothing to the single-celled creature it calls home. Most of Sukunaarchaeum’s mere 189 protein-coding genes are focused on replicating its own genome; it must steal everything else it needs from its host Citharistes regius, a dinoflagellate that lives in ocean waters all over the world. Adding to the mystery of the microbe, some of its sequences identify it as archaeon, a lineage of simple cellular organisms more closely related to complex organisms like us than to bacteria like Escherichia  coli.

The discovery of Sukunaarchaeum’s bizarrely viruslike way of living, reported last month in a bioRxiv preprint, “challenges the boundaries between cellular life and viruses,” ... “This organism might be a fascinating living fossil—an evolutionary waypoint that managed to hang on.”

Sukunaarchaeum was found by chance. Researchers ... were trying to sequence all the DNA inside of C. regius cells because the dinoflagellate was already known to harbor symbiotic cyanobacteria. Yet alongside the expected dinoflagellate and cyanobacteria DNA, and genomes of what may be bacterial parasites, they spotted a strange circle of DNA only 238,000 base pairs long, just 5% the length of the genome of E. coli. “Initially, we suspected this tiny circular genome might be some kind of artifact,” ...

But when ... used several methods for sequencing and assembling the genome, they kept coming across this DNA loop. The team was forced to conclude that some other entity, seemingly an archaeon, was living inside C. regius.

By contrast, ... Sukunaarchaeum lacks “virtually all recognizable metabolic pathways.” That means it likely can’t make essential molecules—such as amino acids that make up proteins, or the nucleotides that make up DNA—on its own, suggesting the microbe has a “parasitic or unilaterally exploitative relationship” with its dinoflagellate host. He adds that like viruses, Sukunaarchaeum has a “near-total reliance” on C. regius’s cellular machinery.

However, Sukunaarchaeum stands apart from viruses in one notable way: It can replicate its own genetic material. Typically, viruses must hijack their hosts to make more of themselves. But almost all of Sukunaarchaeum’s identified genes are involved in DNA replication, transcription, and translation. Still, Nakayama says the microbe’s “intense focus on self-propagation, even at the expense of nearly all metabolic capabilities, resembles viral strategies.” ..."

From the abstract:

"Defining the minimal genetic requirements for cellular life remains a fundamental question in biology. Genomic exploration continually reveals novel microbial lineages, often exhibiting extreme genome reduction, particularly within symbiotic relationships.

Here, we report the discovery of Candidatus Sukunaarchaeum mirabile, a novel archaeon with an unprecedentedly small genome of only 238 kbp —less than half the size of the smallest previously known archaeal genome— from a dinoflagellate-associated microbial community.

Phylogenetic analyses place Sukunaarchaeum as a deeply branching lineage within the tree of Archaea, representing a novel major branch distinct from established phyla.

Environmental sequence data indicate that sequences closely related to Sukunaarchaeum form a diverse and previously overlooked clade in microbial surveys.

Its genome is profoundly stripped-down, lacking virtually all recognizable metabolic pathways, and primarily encoding the machinery for its replicative core: DNA replication, transcription, and translation. This suggests an unprecedented level of metabolic dependence on a host, a condition that challenges the functional distinctions between minimal cellular life and viruses.

The discovery of Sukunaarchaeum pushes the conventional boundaries of cellular life and highlights the vast unexplored biological novelty within microbial interactions, suggesting that further exploration of symbiotic systems may reveal even more extraordinary life forms, reshaping our understanding of cellular evolution."

Microbe with bizarrely tiny genome may be evolving into a virus | Science | AAAS "With DNA focused almost entirely on replication, newly discovered organism blurs the line between cells and viruses"

A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome (open access)

Graphical Abstract