Histones predate the split between bacteria and archaea
Abstract
Motivation: Histones form octameric complexes called nucleosomes, which organize the genomic DNA of eukaryotes into chromatin. Each nucleosome comprises two copies each of the histones H2A, H2B, H3 and H4, which share a common ancestry. Although histones were initially thought to be a eukaryotic innovation, the subsequent identification of archaeal homologs led to the notion that histones emerged before the divergence of archaea and eukaryotes. Results: Here, we report the detection and classification of two new groups of histone homologs, which are present in both archaea and bacteria. Proteins in one group consist of two histone subunits welded into single-chain pseudodimers, whereas in the other they resemble eukaryotic core histone subunits and show sequence patterns characteristic of DNA binding. The sequences come from a broad spectrum of deeply-branching lineages, excluding their genesis by horizontal gene transfer. Our results extend the origin of histones to the last universal common ancestor. Supplementary information: Supplementary data are available at Bioinformatics online.
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A histone-related cluster supports the previously reported evolutionary link between eukaryotic and bacterial histones.
“However, we found exceptions including, for example, a histone-related cluster (Fig. 3c) supporting the previously reported evolutionary link between eukaryotic and bacterial histones26.”
From Clustering predicted structures at the scale of the known protein universe (2023) · cites this paper as [26]
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Clustering predicted structures at the scale of the known protein universe
Barrio-Hernandez, I., Yeo, J., Jänes, J., Mirdita, M., Gilchrist, C. L. M., Wein, T., Varadi, M., Velankar, S., Beltrao, P., & Steinegger, M. (2023) · Nature · doi:10.1038/s41586-023-06510-w · Cited by 362 · see citing works
- Authors
- Alva, V., & Lupas, A. N.
- Corresponding author
- Alva, Vikram
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-12-06
- Volume
- 35
- Issue
- 14
- Pages
- 2349-2353
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2904141395
- Cited by
- 43
- References
- 35
- Citations by year
- 2026: 4 · 2025: 12 · 2024: 11 · 2023: 8 · 2022: 3 · 2021: 3 · 2019: 2
- FWCI
- 0.45
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- Max Planck Society
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- histones, histone evolution, archaea, bacteria, last universal common ancestor, nucleosome, DNA binding, horizontal gene transfer
- MeSH terms
- Archaea, Bacteria, Histones, Nucleosomes
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