Functional Divergence and Structural Changes of class IV Histone Deacetylases (HDACs) Across the Tree of Life

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ID: 317690
2026
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Abstract
Abstract Class IV histone deacetylases (HDACs) are the least understood branch of the classical zinc-dependent HDAC family with HDAC11 standing out as the sole member of class IV HDACs. Using a broad phylogenetic dataset spanning bacteria, archaea, and eukaryotes, we identified two deeply conserved HDAC11 lineages, clades A and B, that differ in evolutionary origin, predicted subcellular localization, and enzymatic properties. Clade A is enriched in phototrophic eukaryotes and targeted to mitochondria or plastids, whereas clade B predominates in heterotrophs and localizes mainly to the cytoplasm or nucleus. High-resolution crystal structures of selected representatives from each clade revealed a conserved catalytic core but distinct structural features—including electrostatic surface profiles, loop architectures, and foot-pocket geometries—that clearly separate the two lineages and act as sequential “selectivity filters” shaping substrate specificity. Biochemical assays show robust long-chain fatty-acid deacylase activity in clade B enzymes, but no detectable activity for any of clade A representatives against peptide substrates, suggesting adaptation to alternative, non-peptidic targets. Together, these findings define a revised evolutionary framework for HDAC11 and provide structural and functional insights into the diversification of this ancient enzyme family.
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Authors Zora Nováková, Pavla Bartošová‐Sojková, Julia Kudlacova, Fady Baselious, Zsófia Kutil, Pavlína Jaklová, Marat Meleshin, L. Motlova, Andrea Schenkmayerová, Vladimír Vrkoslav, Štěpán Strnad, Natan Horáček, Ansgar Gruber, Petr Žáček, Sebastian Kroll, Barbora Havlínová, Marketa Ondrakova, Ruzena Tuckova, Tereza Krunclová, Josef Cvačka, Miroslav Obornı́k, Mike Schutkowski, Wolfgang Sippl, Cyril Bařinka
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Journal molecular biology and evolution
Year 2026
DOI
10.1093/molbev/msag150
URL
https://doi.org/10.1093/molbev/msag150
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