Genetic elements and defense systems drive diversification and evolution in Asgard archaea DOI Open Access
Luis E. Valentin-Alvarado, Ling-Dong Shi, Kathryn E. Appler

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 23, 2024

Abstract Asgard Archaea are of great interest as the progenitors Eukaryotes, but little is known about mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs replicate in Atabeyarchaeia, wetland archaea phylum represented by two complete genomes. We used soil depth-resolved population metagenomic datasets to track 18 for which genome structures were defined and precise chromosome integration sites could be identified confident host linkage. Additionally, a 20.67 kilobase pair (kbp) circular plasmid (the first reported archaea) groups viruses linked via CRISPR spacer targeting. Closely related 40 kbp possess hypervariable genomic region encoding combinations specific genes small cysteine-rich proteins structurally similar restriction-homing endonucleases. One 10.9 circularizable plasmid-like MGE integrates genomically into an Atabeyarchaeia has 2.5 element integrated within it. The encodes highly expressed methylase with sequence specificity matching active methylation motif PacBio sequencing. Restriction-modification differs from another coexisting Freyarchaeia few possesses diverse defense mechanisms, including DISARM Hachiman not found Atabeyarchaeia. Overall, systems mechanisms likely modulate interactions MGEs, integration/excision copy number variation turn enable versatility.

Language: Английский

Description of Asgardarchaeum abyssi gen. nov. spec. nov., a novel species within the class Asgardarchaeia and phylum Asgardarchaeota in accordance with the SeqCode DOI Creative Commons
Daniel Tamarit, Stephan Köstlbacher, Kathryn E. Appler

et al.

Systematic and Applied Microbiology, Journal Year: 2024, Volume and Issue: 47(4), P. 126525 - 126525

Published: June 15, 2024

Asgardarchaeota, commonly referred to as Asgard archaea, is a candidatus phylum-rank archaeal clade that includes the closest relatives of eukaryotes. Despite their prevalence in scientific literature, name Asgardarchaeota lacks nomenclatural validation. Here, we describe novel high-quality metagenome-assembled genome (MAG), AB3033_2

Language: Английский

Citations

7
Arf family GTPases are present in Asgard archaea DOI Creative Commons
Romana Vargová,

Roxanne Chevreau,

Marine Alves

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 1, 2024

Summary The emergence of eukaryotes from their prokaryotic ancestors is one the most fundamental evolutionary events in history life. Little robustly known about how eukaryogenesis occurred, but a major breakthrough came with identification Asgardarchaeota, closest lineage to yet discovered. Endomembrane organelles, and capacity transport material between them, are hallmarks eukaryotic cells. Arf family GTPases crucial regulators organelle dynamics eukaryotes, functioning vesicle budding, membrane tethering membrane-cytoskeleton interactions. Although an expanded GTPase complement has been reported specific origins remain elusive. Here we report new group GTPases, ArfRs. Widely present Asgardarchaeota almost exclusive it clade which all proteins derived. Heterologous expression representative ArfR model eukaryote Saccharomyces cerevisiae X-ray crystallographic studies demonstrate that possess mechanism binding structural features unique proteins. Our results show strongly suggest they originated archaeal contributor eukaryogenesis, providing support for nascent endomembrane system evolving early eukaryogenesis.

Language: Английский

Citations

1
Methanotrophic Methanoperedens archaea host diverse and interacting extrachromosomal elements DOI
Ling-Dong Shi, Jacob West-Roberts, Marie C. Schoelmerich

et al.

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(9), P. 2422 - 2433

Published: June 25, 2024

Language: Английский

Citations

1
Structure-based inference of eukaryotic complexity in Asgard archaea DOI
Stephan Köstlbacher, Jolien J. E. van Hooff, Kassiani Panagiotou

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 5, 2024

Abstract Asgard archaea played a key role in the origin of eukaryotic cell. While previous studies found that genomes encode diverse signature proteins (ESPs), representing homologs play important roles complex organization cells, cellular characteristics and complexity archaeal ancestor eukaryotes remain unclear. Here, we used de novo protein structure modeling sensitive sequence similarity detection algorithms within an expanded genomic dataset to build structural catalogue pangenome identify 908 new ‘isomorphic’ ESPs (iESPs), clusters structures most similar likely underwent extensive divergence. previously identified were involved processes signaling, iESPs are enriched information storage processing functions, with several being potentially implicated facilitating complexity. By expanding complement archaea, this study indicates was more than assumed.

Language: Английский

Citations

1
Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor DOI
Kathryn E. Appler, James P. Lingford, Xianzhe Gong

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 4, 2024

Abstract Asgard archaea were pivotal in the origin of complex cellular life. Hodarchaeales (Asgardarchaeota class Heimdallarchaeia) recently shown to be closest relatives eukaryotes. However, limited sampling these constrains our understanding their ecology and evolution 1–3 , including anticipated role eukaryogenesis. Here, we nearly double number Asgardarchaeota metagenome-assembled genomes (MAGs) 869, 136 new Heimdallarchaeia (49 Hodarchaeales) several novel lineages. Examining global distribution revealed Hodarcheales are primarily found coastal marine sediments. Detailed analysis metabolic capabilities guilds distinct from other Asgardarchaeota. These encode hallmarks aerobic eukaryotes, electron transport chain complexes (III IV), biosynthesis heme, response reactive oxygen species (ROS). The predicted structural architecture membrane-bound hydrogenases includes additional Complex-I-like subunits potentially increasing proton motive force ATP synthesis. CoxD, which regulates (ETC) Thus, key for respiration may have been present Asgard-eukaryotic ancestor. Moreover, that is a variety oxic environments. This expanded diversity reveals Archaea likely conferred energetic advantages during early stages eukaryogenesis, fueling complexity.

Language: Английский

Citations

1
Genetic elements and defense systems drive diversification and evolution in Asgard archaea DOI Open Access
Luis E. Valentin-Alvarado, Ling-Dong Shi, Kathryn E. Appler

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 23, 2024

Abstract Asgard Archaea are of great interest as the progenitors Eukaryotes, but little is known about mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs replicate in Atabeyarchaeia, wetland archaea phylum represented by two complete genomes. We used soil depth-resolved population metagenomic datasets to track 18 for which genome structures were defined and precise chromosome integration sites could be identified confident host linkage. Additionally, a 20.67 kilobase pair (kbp) circular plasmid (the first reported archaea) groups viruses linked via CRISPR spacer targeting. Closely related 40 kbp possess hypervariable genomic region encoding combinations specific genes small cysteine-rich proteins structurally similar restriction-homing endonucleases. One 10.9 circularizable plasmid-like MGE integrates genomically into an Atabeyarchaeia has 2.5 element integrated within it. The encodes highly expressed methylase with sequence specificity matching active methylation motif PacBio sequencing. Restriction-modification differs from another coexisting Freyarchaeia few possesses diverse defense mechanisms, including DISARM Hachiman not found Atabeyarchaeia. Overall, systems mechanisms likely modulate interactions MGEs, integration/excision copy number variation turn enable versatility.

Language: Английский

Citations

0