Histones and histone variant families in prokaryotes

Samuel Schwab, Yimin Hu, Bert Erp, Marc K. M. Cajili, Marcus D. Hartmann, Birte Hernandez Alvarez, Vikram Alva, Aimee L. Boyle and Remus T. Dame ()
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Samuel Schwab: Leiden University
Yimin Hu: Max Planck Institute for Biology Tübingen
Bert Erp: Leiden University
Marc K. M. Cajili: Leiden University
Marcus D. Hartmann: Max Planck Institute for Biology Tübingen
Birte Hernandez Alvarez: Max Planck Institute for Biology Tübingen
Vikram Alva: Max Planck Institute for Biology Tübingen
Aimee L. Boyle: Leiden University
Remus T. Dame: Leiden University

Nature Communications, 2024, vol. 15, issue 1, 1-13

Abstract: Abstract Histones are important chromatin-organizing proteins in eukaryotes and archaea. They form superhelical structures around which DNA is wrapped. Recent studies have shown that some archaea and bacteria contain alternative histones that exhibit different DNA binding properties, in addition to highly divergent sequences. However, the vast majority of these histones are identified in metagenomes and thus are difficult to study in vivo. The recent revolutionary breakthroughs in computational protein structure prediction by AlphaFold2 and RoseTTAfold allow for unprecedented insights into the potential function and structure of previously uncharacterized proteins. Here, we categorize the prokaryotic histone space into 17 distinct groups based on AlphaFold2 predictions. We identify a superfamily of histones, termed α3 histones, which are common in archaea and present in several bacteria. Importantly, we establish the existence of a large family of histones throughout archaea and in some bacteriophages that, instead of wrapping DNA, bridge DNA, thereby diverging from conventional nucleosomal histones.

Date: 2024
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DOI: 10.1038/s41467-024-52337-y

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