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A hypothesis for nucleosome evolution based on mutational analysis.

Yu Nakabayashi1, Masayuki Seki1

  • 1Division of Biochemistry, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University.

Genes & Genetic Systems
|December 18, 2024
PubMed
Summary
This summary is machine-generated.

The evolution of eukaryotic nucleosomes involved histone proteins from archaeal ancestors, with giant viruses playing a role in establishing key features in the last eukaryotic common ancestor (LECA). This research models nucleosome emergence and histone evolution in early eukaryotes.

Keywords:
H2A.ZLECAgiant virushistonenucleosome

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Area of Science:

  • Molecular Biology
  • Evolutionary Biology
  • Genetics

Background:

  • Nucleosomes, composed of DNA and histone proteins, are fundamental to eukaryotic chromatin structure.
  • The evolutionary origins of eukaryotic histones from archaeal homologs are not fully understood.
  • Previous studies identified conserved histone residues in yeast and trypanosomes, with some conservation in giant viruses.

Purpose of the Study:

  • To model the emergence of the eukaryotic nucleosome and trace the evolutionary path of histone proteins.
  • To investigate the role of giant viruses in the establishment of histone features in the last eukaryotic common ancestor (LECA).
  • To propose a hypothesis for the origin of histone H3 variants and their role in chromosome segregation.

Main Methods:

  • Comparative genetic analysis of histone residues in Saccharomyces cerevisiae, Trypanosoma brucei, and giant viruses.
  • Development of a model for eukaryotic nucleosome emergence based on conserved histone residues and viral nucleosome structures.
  • Phylogenetic analysis to infer the evolutionary history of histone proteins and their domains.

Main Results:

  • Identified 26 conserved histone residues, with 15 being essential and 11 synthetically lethal with FEN1 deletion in yeast.
  • Proposed a model where histone doublets in giant viruses facilitated the formation of eukaryotic nucleosome features like the acidic patch and entry sites.
  • Demonstrated that splitting of histone doublets led to the H2A variant H2A.Z and a eukaryote-specific domain for H2A.Z chromatin binding.
  • Hypothesized horizontal gene transfer of an N-tail to H3 in the LECA, preceding CENP-A evolution.

Conclusions:

  • The evolution of the eukaryotic nucleosome involved contributions from archaeal ancestors and giant viruses, shaping key structural and functional components.
  • The model suggests a stepwise evolution of histone complexity, including the emergence of H2A.Z and specific chromatin binding domains.
  • The proposed evolutionary timeline places the emergence of CENP-A and related processes after the LECA, suggesting Euglenida as the root of eukaryotes.