The expanding Asgard archaea invoke novel insights into Tree of Life and eukaryogenesis DOI Creative Commons
Zhichao Zhou, Yang Liu, Karthik Anantharaman

et al.

mLife, Journal Year: 2022, Volume and Issue: 1(4), P. 374 - 381

Published: Dec. 1, 2022

Abstract The division of organisms on the Tree Life into either a three‐domain (3D) tree or two‐domain (2D) has been disputed for long time. Ever since discovery Archaea by Carl Woese in 1977 using 16S ribosomal RNA sequence as evolutionary marker, there great advance our knowledge not only growing diversity but also relationships between different lineages living organisms. Here, we present this perspective to summarize progress archaeal and changing notion Life. Meanwhile, provide latest genomics/physiology‐based Asgard closest relative Eukaryotes. Furthermore, propose three major directions future research exploring “next one” Eukaryote relative, deciphering function eukaryotic signature proteins eukaryogenesis from both genomic physiological aspects, understanding roles horizontal gene transfer, viruses, mobile elements eukaryogenesis.

Language: Английский

Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes DOI Creative Commons
Laura Eme, Daniel Tamarit, Eva Caceres

et al.

Nature, Journal Year: 2023, Volume and Issue: 618(7967), P. 992 - 999

Published: June 14, 2023

Abstract In the ongoing debates about eukaryogenesis—the series of evolutionary events leading to emergence eukaryotic cell from prokaryotic ancestors—members Asgard archaea play a key part as closest archaeal relatives eukaryotes 1 . However, nature and phylogenetic identity last common ancestor remain unresolved 2–4 Here we analyse distinct marker datasets an expanded genomic sampling evaluate competing scenarios using state-of-the-art phylogenomic approaches. We find that are placed, with high confidence, well-nested clade within sister lineage Hodarchaeales, newly proposed order Heimdallarchaeia. Using sophisticated gene tree species reconciliation approaches, show analogous evolution genomes, genome in involved significantly more duplication fewer loss compared other archaea. Finally, infer was probably thermophilic chemolithotroph which evolved adapted mesophilic conditions acquired genetic potential support heterotrophic lifestyle. Our work provides insights into prokaryote-to-eukaryote transition platform for better understanding cellular complexity cells.

Language: Английский

Citations

133
Actin cytoskeleton and complex cell architecture in an Asgard archaeon DOI Creative Commons
Thiago Rodrigues-Oliveira, Florian Wollweber,

Rafael I. Ponce-Toledo

et al.

Nature, Journal Year: 2022, Volume and Issue: 613(7943), P. 332 - 339

Published: Dec. 21, 2022

Abstract Asgard archaea are considered to be the closest known relatives of eukaryotes. Their genomes contain hundreds eukaryotic signature proteins (ESPs), which inspired hypotheses on evolution cell 1–3 . A role ESPs in formation an elaborate cytoskeleton and complex cellular structures has been postulated 4–6 , but never visualized. Here we describe a highly enriched culture ‘ Candidatus Lokiarchaeum ossiferum’, member phylum, thrives anaerobically at 20 °C organic carbon sources. It divides every 7–14 days, reaches densities up 5 × 10 7 cells per ml significantly larger genome compared with single previously cultivated strain represent 5% its protein-coding genes, including four actin homologues. We imaged enrichment using cryo-electron tomography, identifying Ca L. ossiferum’ basis characteristic expansion segments their ribosomes. Cells exhibited coccoid bodies network branched protrusions frequent constrictions. The envelope consists membrane surface structures. long-range extends throughout bodies, twisted double-stranded architecture filaments is consistent F-actin. Immunostaining indicates that comprise Lokiactin—one most conserved archaea. propose actin-based predated emergence first eukaryotes was crucial feature phylum by scaffolding

Language: Английский

Citations

111
The Asgard archaeal origins of Arf family GTPases involved in eukaryotic organelle dynamics DOI
Romana Vargová,

Roxanne Chevreau,

Marine Alves

et al.

Nature Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 23, 2025

Language: Английский

Citations

2
Unique mobile elements and scalable gene flow at the prokaryote–eukaryote boundary revealed by circularized Asgard archaea genomes DOI Creative Commons
Fabai Wu, Daan R. Speth, Alon Philosof

et al.

Nature Microbiology, Journal Year: 2022, Volume and Issue: 7(2), P. 200 - 212

Published: Jan. 13, 2022

Eukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led complex gene repertoire eukaryotes is largely unresolved. Here, through enrichment hydrothermal vent microorganisms, we recovered two circularized Heimdallarchaeum species belong an Asgard archaea clade phylogenetically closest eukaryotes. These reveal diverse mobile elements, including integrative viral genome bidirectionally replicates in a circular form aloposons, transposons encode 5,000 amino acid-sized proteins Otus Ephialtes. Heimdallaechaeal elements various genes bacteria bacteriophages, likely playing role shuffling functions across domains. The number archaea- bacteria-related follow strikingly different scaling laws archaea, exhibiting size-dependent ratio functional division resembling bacteria- archaea-derived Bacterial import has thus been continuous process unaltered by eukaryogenesis scaled up expansion. Our data further highlight importance viewing pan-Asgard context, which proposal conceptual framework, is, Heimdall nucleation-decentralized innovation-hierarchical model accounts for emergence eukaryotic complexity.

Language: Английский

Citations

54
Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes DOI
Adair L. Borges, Yue Clare Lou, Rohan Sachdeva

et al.

Nature Microbiology, Journal Year: 2022, Volume and Issue: 7(6), P. 918 - 927

Published: May 26, 2022

Language: Английский

Citations

45
Analysis of nearly 3000 archaeal genomes from terrestrial geothermal springs sheds light on interconnected biogeochemical processes DOI Creative Commons

Yanling Qi,

Yating Chen, Yuan-Guo Xie

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: May 14, 2024

Abstract Terrestrial geothermal springs are physicochemically diverse and host abundant populations of Archaea. However, the diversity, functionality, geological influences these Archaea not well understood. Here we explore genomic diversity in 152 metagenomes from 48 Tengchong, China, collected 2016 to 2021. Our dataset is comprised 2949 archaeal metagenome-assembled genomes spanning 12 phyla 392 newly identified species, which increases known species by ~48.6%. The structures potential functions communities strongly influenced temperature pH, with high-temperature acidic alkaline favoring abundance over Bacteria. Genome-resolved metagenomics metatranscriptomics provide insights into ecological niches their roles carbon, sulfur, nitrogen, hydrogen metabolism. Furthermore, our findings illustrate interplay competition cooperation among biogeochemical cycles, possibly arising overlapping functional metabolic handoffs. Taken together, study expands inhabiting provides a foundation for more incisive processes mediated ecosystems.

Language: Английский

Citations

12
The emerging view on the origin and early evolution of eukaryotic cells DOI
Julian Vosseberg, Jolien J. E. van Hooff, Stephan Köstlbacher

et al.

Nature, Journal Year: 2024, Volume and Issue: 633(8029), P. 295 - 305

Published: Sept. 11, 2024

Language: Английский

Citations

12
Three families of Asgard archaeal viruses identified in metagenome-assembled genomes DOI
Sofia Medvedeva, Jiarui Sun, Natalya Yutin

et al.

Nature Microbiology, Journal Year: 2022, Volume and Issue: 7(7), P. 962 - 973

Published: June 27, 2022

Language: Английский

Citations

38
A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses DOI Creative Commons
Daniel Tamarit, Eva Caceres, Mart Krupovìč

et al.

Nature Microbiology, Journal Year: 2022, Volume and Issue: 7(7), P. 948 - 952

Published: June 27, 2022

Asgard archaea have recently been identified as the closest archaeal relatives of eukaryotes. Their ecology, and particularly their virome, remain enigmatic. We reassembled closed chromosome Candidatus Odinarchaeum yellowstonii LCB_4, through long-range PCR, revealing CRISPR spacers targeting viral contigs. found related viruses in genomes diverse prokaryotes from geothermal environments, including other archaea. These open research avenues into ecology evolution

Language: Английский

Citations

37
Integrating Phylogenetics With Intron Positions Illuminates the Origin of the Complex Spliceosome DOI Creative Commons
Julian Vosseberg,

Daan Stolker,

Samuel H. A. von der Dunk

et al.

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(1)

Published: Jan. 1, 2023

Eukaryotic genes are characterized by the presence of introns that removed from pre-mRNA a spliceosome. This ribonucleoprotein complex is comprised multiple RNA molecules and over hundred proteins, which makes it one most molecular machines originated during prokaryote-to-eukaryote transition. Previous works have established these spliceosomal core self-splicing in prokaryotes. Yet, how expanded recruiting many additional proteins remains largely elusive. In this study, we use phylogenetic analyses to infer evolutionary history 145 could trace back spliceosome last eukaryotic common ancestor. We found an overabundance derived ribosome-related processes was added prokaryote-derived core. Extensive duplications substantially increased complexity emerging By comparing intron positions between paralogs, postdates spread through proto-eukaryotic genome. The reconstruction early evolution provides insight into driving forces behind emergence complexes with eukaryogenesis.

Language: Английский

Citations

17