Asgard archaeal origin of microtubules

bioRxiv (Cold Spring Harbor Laboratory) · 2026-02-16

ABSTRACT Eukaryotic cells change their shapes, actively segregate their DNA and contain membrane networks, facilitated by a complex cytoskeleton containing actin filaments, microtubules made from tubulin, and other components. These filaments have ancient evolutionary origins since actin- and tubulin-like proteins form prokaryotic cytoskeletons in archaea and bacteria. Bona fide eukaryotic F-actin can be traced back to crenarchaea and Asgard archaea, which are the closest known relatives of eukaryotes. A possible Asgard archaeal origin of microtubules was suggested recently with the discovery of a lokiarchaeon containing AtubAB mini microtubules that share architectural features with their eukaryotic counterparts. Using phylogenetic analyses of metagenomic data, here we report the broad occurrence of tubulins in Asgard archaea. Biochemical and structural analyses showed that one of our newly discovered heimdallarchaeial AtubAB tubulin pairs forms four-protofilament mini-microtubules that show dynamic instability and are inhibited by the tubulin drug maytansine. Our work raises the possibility that microtubule architecture and dynamics evolved in Asgard archaea prior to eukaryogenesis.

Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling

Nature Microbiology · 2026-03-05 · 2 citations

Asgard archaea played a key role in the origin of the eukaryotic cell, with extant genomes encoding relatives of diverse eukaryotic signature proteins (ESPs) involved in cellular organization. However, their often punctuated distribution and the absence of detectable homologues for many eukaryotic proteins limit our ability to reconstruct the cellular complexity of the Asgard archaeal ancestor of eukaryotes. Here we used de novo protein structure modelling and sequence similarity detection across an expanded Asgard archaeal genomic dataset to build a structural catalogue of the Asgard archaeal pangenome. We identified 908 'isomorphic' ESPs-Asgard archaeal proteins with statistically enriched structural matches to eukaryotic proteins, often bridging deep sequence divergence. These isomorphic ESPs are enriched in information storage and processing roles and contain key components of the eukaryotic Vault (MVP) and Commander (COMMD) complexes, with potential roles in cellular compartmentalization and endosomal processing. These findings expand the repertoire of eukaryotic-like proteins in Asgard archaea and suggest a higher degree of eukaryote-like cellular complexity in the archaeal ancestor of eukaryotes.

Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor

Nature · 2026-02-18 · 8 citations

Author Correction: Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes (Nature, (2023), 618, 7967, (992-999), 10.1038/s41586-023-06186-2)

Utrecht University Repository (Utrecht University) · 2026-01-01

Correction to: Naturehttps://doi.org/10.1038/s41586-023-06186-2 Published online 14 June 2023 Our manuscript included a phylogenomic study of the evolutionary relationship between eukaryotes and Asgard archaea, showing that eukaryotes likely emerged from a bona fide Asgard archaeal ancestor. Our results suggested that eukaryotes and the heimdallarchaeial order Hodarchaeales form a monophyletic group. A set of 57 phylogenetic markers (NM57) was central to reach these conclusions. After the publication of our study, we noticed that three of these markers were partially redundant, as they belong to paralogous families. We have therefore reduced this dataset to 54 non-redundant markers (NM54; we removed markers M127, M028, and MA54) and used the same methodology to re-run all phylogenomic analyses presented in the paper. The results of the analyses of the corrected dataset are consistent with the original findings: while we observe small variations in statistical support, the overall trends support that eukaryotes are placed within Heimdallarchaeia, as sister-group to the order Hodarchaeales when both Susko-Roger-4 (SR4)-recoding and Fast-site removal (FSR) treatments were combined. A full discussion of changes to the article is available as Supplementary information accompanying this amendment. Text, figures and Supplementary information have been amended in the HTML and PDF versions of the article. Supplementary information is available in the online version of this amendment.

Mapping environmental microbiomes across an entire country

Trends in Microbiology · 2026-03-18

Evolution and diversity of oxidoreductases involved in redox balance and energy conservation

Nature Ecology & Evolution · 2026-02-03

The archaeal roots of eukaryotic life

Proceedings of the National Academy of Sciences · 2026-03-13

Resolving the biological and geological events that led to the origin of eukaryotes is an ongoing challenge in biology. A major step in the evolution of complex cellular life was the merger between an ancestral host cell and a bacterium (that became the mitochondrion) some two billion years ago. Recently, metagenomics has enabled the reconstruction of a broad diversity of genomes, referred to as the Asgard Archaea. The Asgards are monophyletic with eukaryotes on the tree of life. Asgards have an array of genes, previously thought exclusive to eukaryotes, involved in cellular trafficking, the ubiquitin system, endosomal sorting, and cytoskeleton formation, with growing evidence demonstrating the functions of these proteins mirror those in eukaryotes. This gene repertoire suggests that these Archaea are descendants of the archaeal host from which eukaryotes evolved. Increased sampling has revealed that Asgard lineages are metabolically versatile and play key roles in various ecosystems and uncovered evolutionary transitions between Archaea and eukaryotes, such as innovations in eukaryotic defense systems. The positioning of eukaryotes in the Asgards is debated, but eukaryotes appear to branch within the Heimdallarchaeia. Lineages within this group, particularly Hodarchaeales and Kariarchaeaceae, contain a broad repertoire of eukaryote-like traits, including high-energy yielding metabolisms. Observing and studying Asgard interactions with bacterial descendants of mitochondria in a modern setting will transform our understanding of the origin of complex cellular life.

Author Correction: Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes

Nature · 2026-02-11

Correction to: Naturehttps://doi.org/10.1038/s41586-023-06186-2 Published online 14 June 2023 Our manuscript included a phylogenomic study of the evolutionary relationship between eukaryotes and Asgard archaea, showing that eukaryotes likely emerged from a bona fide Asgard archaeal ancestor. Our results suggested that eukaryotes and the heimdallarchaeial order Hodarchaeales form a monophyletic group. A set of 57 phylogenetic markers (NM57) was central to reach these conclusions. After the publication of our study, we noticed that three of these markers were partially redundant, as they belong to paralogous families. We have therefore reduced this dataset to 54 non-redundant markers (NM54; we removed markers M127, M028, and MA54) and used the same methodology to re-run all phylogenomic analyses presented in the paper. The results of the analyses of the corrected dataset are consistent with the original findings: while we observe small variations in statistical support, the overall trends support that eukaryotes are placed within Heimdallarchaeia, as sister-group to the order Hodarchaeales when both Susko-Roger-4 (SR4)-recoding and Fast-site removal (FSR) treatments were combined. A full discussion of changes to the article is available as Supplementary information accompanying this amendment. Text, figures and Supplementary information have been amended in the HTML and PDF versions of the article. Supplementary information is available in the online version of this amendment.

Microcompartments in archaeal ancestors of eukaryotes: a bioenergetic engine that could have fuelled eukaryogenesis

bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-09

Eukaryotic intracellular compartmentalization is a key innovation in the evolution of complex cellular life. While microcompartments enable metabolic specialization in many bacteria, to our knowledge, no analogous systems have been identified in Archaea. Here, we report the discovery of archaeal microcompartments (AMCs) in Hodarchaeales, an order within the phylum Promethearchaeati (Asgard archaea) that includes the closest known archaeal relatives of eukaryotes. Phylogenetic and structural analyses indicate that these catabolic AMCs, which are specialized for sugar-phosphate metabolism, were acquired by horizontal gene transfer from deep-rooted bacteria of the phylum Myxococcota. The shell pentamers of AMCs are fused to lysine/arginine-rich intrinsically disordered regions that capture cytosolic DNA, facilitating nutrient scavenging. Reaction-diffusion modelling predicts that enzyme colocalization and substrate channelling within AMCs can increase the NADH flux approximately 100-fold. Thus, the AMCs substantially boost energy production in the cell and might have primed the archaeal host for eukaryogenesis.

Plastic degradation by enzymes from uncultured deep sea microorganisms

The ISME Journal · 2025-01-01 · 5 citations

Polyethylene terephthalate (PET)-hydrolyzing enzymes (PETases) are a recently discovered enzyme class capable of plastic degradation. PETases are commonly identified in bacteria; however, pipelines for discovery are often biased to recover highly similar enzymes. Here, we searched metagenomic data from hydrothermally impacted deep sea sediments in the Guaymas Basin (Gulf of California) for PETases. A broad diversity of potential proteins were identified and 22 were selected based on their potential thermal stability and phylogenetic novelty. Heterologous expression and functional analysis of these candidate PETases revealed three candidates capable of depolymerizing PET or its byproducts. One is a PETase from a Bathyarchaeia archaeon (dubbed GuaPA, for Guaymas PETase Archaeal) and two bishydroxyethylene terephthalate-hydrolyzing enzymes (BHETases) from uncultured bacteria, Poribacteria, and Thermotogota. GuaPA is the first archaeal PETase discovered that is able to depolymerize PET films and originates from a specific enzyme class which has endowed it with predicted novel structural features. Within 48 h, GuaPA released ~3-5 mM of terephthalic acid and mono-(2-hydroxyethyl) terephthalate from low crystallinity PET. PET co-hydrolysis containing GuaPA and one of the newly discovered BHETases further improves the hydrolysis of untreated PET film by 68%. Genomic analysis of the PETase- and BHETase-encoding microorganisms reveals that they likely metabolize the products of enzymatic PET depolymerization, suggesting an ecological role in utilizing anthropogenic carbon sources. Our analysis reveals a previously uncharacterized ability of these uncultured microorganisms to catabolize PET, suggesting that the deep ocean is a potential reservoir of biocatalysts for the depolymerization of plastic waste.