The Archaeal Legacy of Eukaryotes: a Phylogenomic Perspective

Overview

Journal Cold Spring Harb Perspect Biol

Specialties Biology
Molecular Biology

Date 2014 Jul 5

PMID 24993577

Citations 38

Authors

Lionel Guy

Jimmy H Saw

Thijs J G Ettema

Affiliations

Soon will be listed here.

Abstract

The origin of the eukaryotic cell can be regarded as one of the hallmarks in the history of life on our planet. The apparent genomic chimerism in eukaryotic genomes is currently best explained by invoking a cellular fusion at the root of the eukaryotes that involves one archaeal and one or more bacterial components. Here, we use a phylogenomics approach to reevaluate the evolutionary affiliation between Archaea and eukaryotes, and provide further support for scenarios in which the nuclear lineage in eukaryotes emerged from within the archaeal radiation, displaying a strong phylogenetic affiliation with, or even within, the archaeal TACK superphylum. Further taxonomic sampling of archaeal genomes in this superphylum will certainly provide a better resolution in the events that have been instrumental for the emergence of the eukaryotic lineage.

Citing Articles

Chimeric origins and dynamic evolution of central carbon metabolism in eukaryotes.

Santana-Molina C, Williams T, Snel B, Spang A Nat Ecol Evol. 2025; .

PMID: 40033103 DOI: 10.1038/s41559-025-02648-0.

The emerging view on the origin and early evolution of eukaryotic cells.

Vosseberg J, van Hooff J, Kostlbacher S, Panagiotou K, Tamarit D, Ettema T Nature. 2024; 633(8029):295-305.

PMID: 39261613 DOI: 10.1038/s41586-024-07677-6.

On the origin of the nucleus: a hypothesis.

Baum B, Spang A Microbiol Mol Biol Rev. 2023; 87(4):e0018621.

PMID: 38018971 PMC: 10732040. DOI: 10.1128/mmbr.00186-21.

ATP synthase evolution on a cross-braced dated tree of life.

Mahendrarajah T, Moody E, Schrempf D, Szantho L, Dombrowski N, Davin A Nat Commun. 2023; 14(1):7456.

PMID: 37978174 PMC: 10656485. DOI: 10.1038/s41467-023-42924-w.

Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere.

Spang A, Mahendrarajah T, Offre P, Stairs C Genome Biol Evol. 2022; 14(6).

PMID: 35218347 PMC: 9169541. DOI: 10.1093/gbe/evac034.

References

Martin W, Muller M . The hydrogen hypothesis for the first eukaryote. Nature. 1998; 392(6671):37-41. DOI: 10.1038/32096. View

Reynaud E, Devos D . Transitional forms between the three domains of life and evolutionary implications. Proc Biol Sci. 2011; 278(1723):3321-8. PMC: 3177640. DOI: 10.1098/rspb.2011.1581. View

Foster P, Cox C, Embley T . The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods. Philos Trans R Soc Lond B Biol Sci. 2009; 364(1527):2197-207. PMC: 2873002. DOI: 10.1098/rstb.2009.0034. View

Makarova K, Yutin N, Bell S, Koonin E . Evolution of diverse cell division and vesicle formation systems in Archaea. Nat Rev Microbiol. 2010; 8(10):731-41. PMC: 3293450. DOI: 10.1038/nrmicro2406. View

Zillig W, Schnabel R, Stetter K . Archaebacteria and the origin of the eukaryotic cytoplasm. Curr Top Microbiol Immunol. 1985; 114:1-18. DOI: 10.1007/978-3-642-70227-3_1. View

Forterre P . The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells. Biochimie. 2005; 87(9-10):793-803. DOI: 10.1016/j.biochi.2005.03.015. View

Zillig W, Klenk H, Palm P, Puhler G, Gropp F, Garrett R . The phylogenetic relations of DNA-dependent RNA polymerases of archaebacteria, eukaryotes, and eubacteria. Can J Microbiol. 1989; 35(1):73-80. DOI: 10.1139/m89-011. View

Olsen G, Woese C . Archaeal genomics: an overview. Cell. 1997; 89(7):991-4. DOI: 10.1016/s0092-8674(00)80284-6. View

Nunoura T, Takaki Y, Kakuta J, Nishi S, Sugahara J, Kazama H . Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res. 2010; 39(8):3204-23. PMC: 3082918. DOI: 10.1093/nar/gkq1228. View

10.

Ettema T, de Vos W, van der Oost J . Discovering novel biology by in silico archaeology. Nat Rev Microbiol. 2005; 3(11):859-69. DOI: 10.1038/nrmicro1268. View

11.

Bult C, White O, Olsen G, Zhou L, Fleischmann R, Sutton G . Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science. 1996; 273(5278):1058-73. DOI: 10.1126/science.273.5278.1058. View

12.

Cavalier-Smith T . The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int J Syst Evol Microbiol. 2002; 52(Pt 1):7-76. DOI: 10.1099/00207713-52-1-7. View

13.

Williams T, Foster P, Nye T, Cox C, Embley T . A congruent phylogenomic signal places eukaryotes within the Archaea. Proc Biol Sci. 2012; 279(1749):4870-9. PMC: 3497233. DOI: 10.1098/rspb.2012.1795. View

14.

Bernander R, Lind A, Ettema T . An archaeal origin for the actin cytoskeleton: Implications for eukaryogenesis. Commun Integr Biol. 2012; 4(6):664-7. PMC: 3306326. DOI: 10.4161/cib.16974. View

15.

Wolf Y, Makarova K, Yutin N, Koonin E . Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer. Biol Direct. 2012; 7:46. PMC: 3534625. DOI: 10.1186/1745-6150-7-46. View

16.

Elkins J, Podar M, Graham D, Makarova K, Wolf Y, Randau L . A korarchaeal genome reveals insights into the evolution of the Archaea. Proc Natl Acad Sci U S A. 2008; 105(23):8102-7. PMC: 2430366. DOI: 10.1073/pnas.0801980105. View

17.

Ettema T, Lindas A, Bernander R . An actin-based cytoskeleton in archaea. Mol Microbiol. 2011; 80(4):1052-61. DOI: 10.1111/j.1365-2958.2011.07635.x. View

18.

Lake J, Henderson E, Oakes M, Clark M . Eocytes: a new ribosome structure indicates a kingdom with a close relationship to eukaryotes. Proc Natl Acad Sci U S A. 1984; 81(12):3786-90. PMC: 345305. DOI: 10.1073/pnas.81.12.3786. View

19.

Embley T, Martin W . Eukaryotic evolution, changes and challenges. Nature. 2006; 440(7084):623-30. DOI: 10.1038/nature04546. View

20.

Forterre P . Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain. Proc Natl Acad Sci U S A. 2006; 103(10):3669-74. PMC: 1450140. DOI: 10.1073/pnas.0510333103. View