Molecular evolution of the histone deacetylase family: functional implications of phylogenetic analysis

Gregoretti, IvanV; Lee, Yun-Mi; Goodson, Holly V

doi:10.1016/j.jmb.2004.02.006

Cited by 1,456Histone Deacetylase Inhibitors ResearchGenomics and Chromatin DynamicsEpigenetics and DNA Methylation

Molecular evolution of the histone deacetylase family: functional implications of phylogenetic analysis

Gregoretti, IvanV, Lee, Yun-Mi, Goodson, Holly V·2004·Journal of Molecular Biology

DOI 10.1016/j.jmb.2004.02.006

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Abstract

Histone deacetylases (HDACs) modify core histones and participate in large regulatory complexes that both suppress and enhance transcription. Recent studies indicate that some HDACs can act on non-histone proteins as well. Interest in these enzymes is growing because HDAC inhibitors appear to be promising therapeutic agents against cancer and a variety of other diseases. Thus far, 11 members of the HDAC family have been identified in humans, but few have been characterized in detail. To better define the biological function of these proteins, make maximal use of studies performed in other systems, and assist in drug development efforts, we have performed a phylogenetic analysis of all HDAC-related proteins in all fully sequenced free-living organisms. Previous analyses have divided non-sirtuin HDACs into two groups, classes 1 and 2. We find that HDACs can be divided into three equally distinct groups: class 1, class 2, and a third class consisting of proteins related to the recently identified human HDAC11 gene. We term this novel group "class 4" to distinguish it from the unrelated "class 3" sirtuin deacetylases. Analysis of gene duplication events indicates that the common ancestor of metazoan organisms contained two class 1, two class 2, and a single class 4 HDAC. Examination of HDAC characteristics in light of these evolutionary relationships leads to functional predictions, among them that self-association is common among HDAC proteins. All three HDAC classes (including class 4) exist in eubacteria. Phylogenetic analysis of bacterial HDAC relatives suggests that all three HDAC classes precede the evolution of histone proteins and raises the possibility that the primary activity of some "histone deacetylase" enzymes is directed against non-histone substrates.

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The eleven zinc-dependent HDACs are categorized in class I (HDACs 1-3 and 8), class IIa (HDACs 4, 5, 7, and 9), class IIb (HDACs 6 and 10), and class IV (HDAC11).
“the eleven zinc-dependent HDACs, which are categorized in class I (HDACs 1-3 and 8), class IIa (HDACs 4, 5, 7, and 9), class IIb (HDACs 6 and 10), and class IV (HDAC11) (Fig. 1A) (Marmorstein, 2001; Gregoretti et al., 2004).”
From Histone deacetylase 11 is an ε-N-Myristoyllysine hydrolase (2018) · cites this paper as Gregoretti et al., 2004

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Authors: Gregoretti, I., Lee, Y.-M., & Goodson, H. V.
Affiliations: University of Notre Dame (US)
Corresponding author: Goodson, Holly V
ORCID: Goodson, Holly V
Venue: Journal of Molecular Biology
Publisher: Elsevier BV
Published: 2004-04
Volume: 338
Issue: 1
Pages: 17-31
ISSN: 0022-2836 (ISSN-L)
DOI: 10.1016/j.jmb.2004.02.006
OpenAlex: W2112351720
Cited by: 1,456
References: 80
Citations by year: 2026: 28 · 2025: 51 · 2024: 64 · 2023: 70 · 2022: 56 · 2021: 95 · 2020: 85 · 2019: 76 · 2018: 85 · 2017: 77 · 2016: 81 · 2015: 96 · 2014: 83 · 2013: 83 · 2012: 75
FWCI: 12.00
Type: journal article
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Journal of Molecular Biology (publishedVersion)
PubMed (publishedVersion)
Funders: American Heart Association
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Histone Deacetylase Inhibitors Research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords: histone deacetylase, phylogenetic classification, HDAC11, sirtuin deacetylase, gene duplication, protein self-association, non-histone substrates, histone deacetylase inhibitors, histone modifications
MeSH terms: Eukaryotic Cells, Multigene Family, Histone Deacetylases, Histones, Phylogeny, Prokaryotic Cells, Genome, Evolution, Molecular

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Molecular evolution of the histone deacetylase family: functional implications of phylogenetic analysis

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