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Cited by 18Chromosomal and Genetic VariationsGenomics and Chromatin DynamicsMicrotubule and mitosis dynamics

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Repeated duplications and losses shaped SMC complex evolution from archaeal ancestors to modern eukaryotes

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van Hooff, Jolien J.E., Raas, Maximilian W.D., Tromer, Eelco C., Eme, Laura·2025·Cell Reports
DOI 10.1016/j.celrep.2025.115855

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Abstract

Across life, structural maintenance of chromosomes (SMC) complexes organize chromosomes. While most prokaryotes have one, eukaryotes usually possess four (condensin I, condensin II, cohesin, and SMC5/6), shaping their considerably larger genomes. Although essential, SMC complexes differ among model eukaryotes, suggesting underexplored diversity. Here, we reconstruct eukaryotic SMC complex evolution, revealing that the last eukaryotic common ancestor (LECA) had all four complexes, supporting a sophisticated LECA. Subsequently, condensin II was lost at least 30 times, making it one of the most frequently lost eukaryotic machineries. Moreover, multiple SMC complex components are more ancient and widespread than previously appreciated. Tracing prokaryotic origins, we propose that the SMC complex was already duplicated in the Thaumarchaeota-Aigarchaeota-Crenarchaeota-Korarchaeota (TACK) and Asgard archaeal ancestor, suggesting sophisticated chromosome organization in eukaryotes' archaeal ancestor. Gene duplications further expanded the eukaryotic SMC complex inventory, highlighting their significance in establishing eukaryotic complexity. Altogether, our work suggests major shifts in genome organization throughout eukaryote history.

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Metadata

Authors
van Hooff, J. J. E., Raas, M. W. D., Tromer, E. C., & Eme, L.
Affiliations
  • Centre National de la Recherche Scientifique (FR)
  • Royal Netherlands Academy of Arts and Sciences (NL)
  • University of Groningen (NL)
Corresponding author
  • van Hooff, Jolien J.E.
  • Eme, Laura
ORCID
Venue
Cell Reports
Publisher
Elsevier BV
Published
2025-07
Volume
44
Issue
7
Pages
115855
ISSN
2211-1247 (ISSN-L)
DOI
10.1016/j.celrep.2025.115855
OpenAlex
W4411445485
Cited by
18
References
9
Citations by year
2026: 8 · 2025: 5
FWCI
7.08
Type
journal article
Language
en
Open access
Licence
Locations
  • Cell Reports (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • University of Groningen research database (University of Groningen / Centre for Information Technology) (publishedVersion, cc-by)
  • HAL (submittedVersion)
  • HAL (submittedVersion, cc-by)
  • Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
  • Socio-Environmental Systems Modeling (submittedVersion, cc-by)
Funders
  • HORIZON EUROPE European Research Council (803151)
  • Dutch Research Council (VI.Veni.212.099, VI.Veni.202.223)
  • University of Rhode Island
  • Okinawa Institute of Science and Technology Graduate University
  • European Research Council
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Microtubule and mitosis dynamics
Keywords
structural maintenance of chromosomes, SMC complex, condensin II, cohesin, gene duplication, gene loss, eukaryotic evolution, last eukaryotic common ancestor, Asgard archaea, chromosome organization, genome organization
MeSH terms
Adenosine Triphosphatases, Archaea, Chromosomal Proteins, Non-Histone, DNA-Binding Proteins, Phylogeny, Cell Cycle Proteins, Evolution, Molecular, Gene Duplication, Multiprotein Complexes, Eukaryota

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