Actin cytoskeleton and complex cell architecture in an Asgard archaeon

Abstract

Asgard archaea are considered to be the closest known relatives of eukaryotes. Their genomes contain hundreds of eukaryotic signature proteins (ESPs), which inspired hypotheses on the evolution of the eukaryotic cell1–3. A role of ESPs in the formation of an elaborate cytoskeleton and complex cellular structures has been postulated4–6, but never visualized. Here we describe a highly enriched culture of ‘Candidatus Lokiarchaeum ossiferum’, a member of the Asgard phylum, which thrives anaerobically at 20 °C on organic carbon sources. It divides every 7–14 days, reaches cell densities of up to 5 × 107 cells per ml and has a significantly larger genome compared with the single previously cultivated Asgard strain7. ESPs represent 5% of its protein-coding genes, including four actin homologues. We imaged the enrichment culture using cryo-electron tomography, identifying ‘Ca. L. ossiferum’ cells on the basis of characteristic expansion segments of their ribosomes. Cells exhibited coccoid cell bodies and a network of branched protrusions with frequent constrictions. The cell envelope consists of a single membrane and complex surface structures. A long-range cytoskeleton extends throughout the cell bodies, protrusions and constrictions. The twisted double-stranded architecture of the filaments is consistent with F-actin. Immunostaining indicates that the filaments comprise Lokiactin—one of the most highly conserved ESPs in Asgard archaea. We propose that a complex actin-based cytoskeleton predated the emergence of the first eukaryotes and was a crucial feature in the evolution of the Asgard phylum by scaffolding elaborate cellular structures.

Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes

“…P. syntrophicum strain MK-D1’ 43 and ‘ Ca. Lokiarchaeum ossiferum’ 44 , whose cells both displayed unique morphological complexity including long and often branching protrusions facilitated by a dynamic actin cytoskeleton. Thus far no 43 , or only limited 44 visible endomembrane structures were observed in these first cultured representatives of Asgard archaea.…”

“…Lokiarchaeum ossiferum’ 44 , whose cells both displayed unique morphological complexity including long and often branching protrusions facilitated by a dynamic actin cytoskeleton. Thus far no 43 , or only limited 44 visible endomembrane structures were observed in these first cultured representatives of Asgard archaea. However, it is important to restate here that, being separated by some 2 Gya of evolution, the cellular features of present-day Asgard archaeal lineages do not necessarily resemble those of LAECA.…”

“…The analysis of Asgard archaeal genome data obtained through metagenomics, combined with the insights derived from cytological observations of the first two cultured Asgard archaea ‘ Candidatus Prometheoarchaeum syntrophicum’ 43 and ‘ Candidatus Lokiarchaeum ossiferum’ 44 , have generated new hypotheses about the nature of the archaeal ancestor of eukaryotes 43, 45–48 . However, these theories are mostly based on a limited number of features displayed by a single, or a few Asgard archaeal lineages.…”

Identification and characterization of structural and regulatory cell-shape determinants inHaloferax volcanii

“…While knowledge about archaeal cell-shape determinants is limited, the few components identified include the actin homolog crenactin in Pyrobaculum calidifontis, which is correlated with rod-shape in this species (25). Moreover, a recently characterized Asgard archaeon Candidatus Lokiarchaeum ossiferum contains Lokiactin, a highly conserved actin homolog hypothesized to provide a scaffold for the maintenance of the archaeon's network of protrusions (26). Some archaeal species change cell shape in response to specific environmental cues.…”

Salactin, a dynamically unstable actin homolog in Haloarchaea

“…Bioinformatics identified multiple actins in the TACK and Asgard families with high sequence similarity to eukaryotic actin (Cai et al, 2020;Imachi et al, 2020;Liu et al, 2021;Seitz et al, 2019;Spang et al, 2015;Zaremba-Niedzwiedzka et al, 2017;Zhang et al, 2021), and the Asgard genomes also encode multiple eukaryotic-like actin-modulating proteins (Akıl et al, 2020(Akıl et al, , 2022Akıl & Robinson, 2018;Eme et al, 2017;Stairs & Ettema, 2020;Survery et al, 2021). Accordingly, cryo-electron microscopy of Loki Asgard archaea revealed long eukaryotic-like actin filaments enriched within cellular protrusions (Rodrigues-Oliveira et al, 2022).…”