Molecular Evolution of the Histone Deacetylase Family: Functional Implications of Phylogenetic Analysis

https://doi.org/10.1016/j.jmb.2004.02.006Get rights and content

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.

Introduction

Histone deacetylases (HDACs) reverse the regulatory acetylation of histone proteins, influencing nucleosome structure and altering gene transcription. Histone acetylation is often correlated with gene activation, suggesting that histone deacetylases act to silence genes, but genetic experiments in Drosophila and the yeast Saccharomyces cerevisiae have indicated that deacetylase activity can contribute to gene activation as well.1., 2., 3., 4. Acetylation of core histones has also been correlated with cellular processes, including chromatin assembly, DNA repair, and recombination (reviewed by Yang et al.5).

HDACs are members of an ancient enzyme family found in plants, animals, and fungi, as well as archaebacteria and eubacteria.6 Thus far, eukaryotic HDACs have been classified into two groups (class 1 and class 2) on the basis of sequence similarity. Recently, a pair of HDAC-related proteins from Arabidopsis and humans have been reported to be more similar to each other than to either class 1 or class 2 enzymes,7 possibly representing an additional class. In addition, a group of unrelated NAD-dependent deacetylase enzymes related to the yeast protein Sir2 have sometimes been called class 3 HDACs.3., 4., 8., 9. To reduce confusion, we refer to these NAD-dependent enzymes as sirtuins (see Grozinger & Schreiber4). The domain structures and class affiliation of human HDACs, as well as representative fungal and prokaryotic proteins, are shown in Figure 1.

As is obvious from their name, it has generally been assumed that the activity of HDACs is directed at histones. However, many HDACs are at least partially cytoplasmic,10., 11., 12., 13. and evidence is accumulating that some fraction of these proteins can act on non-histone substrates, including the cytoskeletal protein tubulin and transcription factors such as p53.10., 14., 15. Indeed, it has been suggested that regulatory acetylation/deacetylation is considerably more widespread than presently appreciated, acting in a manner similar to phosphorylation and dephosphorylation.16

HDACs have recently enjoyed increased attention because HDAC inhibitors (e.g. hydroxamic acids, depsipeptide) act as efficient anti-proliferative agents in tissue culture and inhibit tumor progression in rodent models. Several HDAC inhibitors are now in phase I and II human trials.2., 17., 18. Most of the known HDAC inhibitors have broad specificity for both class 1 and class 2 deacetylases, although some (e.g. trapoxin) exhibit some specificity.2., 19. Large synthetic efforts are now focused on developing new inhibitors, with particular interest on development of isoform-specific inhibitors.4

Although understanding of HDAC activity and function is growing rapidly, most members of this family have received only initial characterization. A classic way to enhance understanding of one HDAC is to use information gained from study of related HDACs. However, maximal use of this information requires a detailed understanding of the evolutionary relationships within the HDAC family. More specifically, making useful functional predictions about human HDACs based on those from model systems depends on our ability to establish which HDACs are “orthologs” (diverged as a result of species divergence) or “paralogs” (diverged by gene duplication). Orthologs are generally expected to have similar functions and characteristics because of the constancy of basic cell biological processes between organisms (even divergent ones). Paralogs are expected to be functionally differentiated because the initial duplication releases evolutionary constraint, giving the duplicated genes the opportunity to acquire new functions, partition old functions, or gain tissue-specific distributions.20., 21. Phylogenetic trees also provide other types of functional information: conserved proteins with ancient origins are expected to participate in basic processes conserved across organisms, while recent origins suggest organism or tissue-specific functional specialization. Observation that some proteins exhibit unusually rapid rates of evolution indicates that these proteins have undergone a change in selection pressure relative to other members of the family, likely correlated with loss or change of function.

Phylogenetic analyses have been included in other studies of HDAC structure and function,6., 7., 22. but limited sequence diversity and statistical analysis have restricted interpretation of these studies. To address these issues as they relate to the HDAC family, we undertook the following analysis of evolutionary relationships between all recognizable HDAC relatives in all fully sequenced free-living organisms, eukaryotic and prokaryotic.

Section snippets

Phylogenetic analysis: alignment and tree building

We have used two phylogenetic methods, neighbor joining (as implemented by ClustalX),23., 24. and Bayesian analysis (as implemented by the program MrBayes)25 to determine evolutionary relationships between recognizable HDAC-related proteins in fully sequenced free-living organisms. Figure 2 shows the inferred relationships between eukaryotic sequences, with selected prokaryotic proteins included, and Figure 4 shows the relationships between prokaryotic sequences, with selected eukaryotic

Concluding Discussion

Whatever their ultimate origin, the observation that all three types of histone deacetylase exist in eubacteria demonstrates that these proteins have functions in the absence of histone proteins. The analysis above suggests that they predate the evolution of histones. These conclusions are significant for the function of eukaryotic HDAC proteins because it is unlikely that all three HDAC classes would lose activity on their ancestral substrates (whatever they are) and become uniquely directed

Database searching and alignment

NCBI nucleotide and protein sequence databases for fully sequenced genomes (November 2002) were scanned for proteins related to human HDAC1 using either PSI-BLAST (protein databases) or tBLASTn (nucleotide databases).26 After initial sequence collection, the full NCBI database was probed with individual human and yeast HDAC sequences to enhance the chances of finding sequences related to particular divergent HDACs and better define the range of organisms containing these proteins. Sequences

Acknowledgements

The authors thank Martin Tenniswood and the Goodson laboratory for insightful critique of the manuscript, and Paul Helquist, Joakim Lofstedt and Norbert Wiech for fruitful discussions about HDAC function and inhibition. This work was supported by grants from the American Heart Association and Norbert L. & Linda N. Wiech Research Support fund to H.V.G.

References (79)

  • G.W Humphrey et al.

    Stable histone deacetylase complexes distinguished by the presence of SANT domain proteins CoREST/kiaa0071 and Mta-L1

    J. Biol. Chem.

    (2001)
  • W.M Yang et al.

    Isolation and characterization of cDNAs corresponding to an additional member of the human histone deacetylase gene family

    J. Biol. Chem.

    (1997)
  • E Hu et al.

    Cloning and characterization of a novel human class I histone deacetylase that functions as a transcription repressor

    J. Biol. Chem.

    (2000)
  • W Fischle et al.

    Enzymatic activity associated with class II HDACs is dependent on a multiprotein complex containing HDAC3 and SMRT/N-CoR

    Mol. Cell

    (2002)
  • Y Takami et al.

    N-terminal region, C-terminal region, nuclear export signal, and deacetylation activity of histone deacetylase-3 are essential for the viability of the DT40 chicken B cell line

    J. Biol. Chem.

    (2000)
  • D Kadosh et al.

    Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters

    Cell

    (1997)
  • J Taplick et al.

    Homo-oligomerisation and nuclear localisation of mouse histone deacetylase 1

    J. Mol. Biol.

    (2001)
  • E Verdin et al.

    Class II histone deacetylases: versatile regulators

    Trends Genet.

    (2003)
  • K Petrie et al.

    The histone deacetylase 9 gene encodes multiple protein isoforms

    J. Biol. Chem.

    (2003)
  • C Lemercier et al.

    mHDA1/HDAC5 histone deacetylase interacts with and represses MEF2A transcriptional activity

    J. Biol. Chem.

    (2000)
  • U Dressel et al.

    A dynamic role for HDAC7 in MEF2-mediated muscle differentiation

    J. Biol. Chem.

    (2001)
  • H.Y Kao et al.

    Isolation and characterization of mammalian HDAC10, a novel histone deacetylase

    J. Biol. Chem.

    (2002)
  • A Verdel et al.

    Active maintenance of mHDA2/mHDAC6 histone-deacetylase in the cytoplasm

    Curr. Biol.

    (2000)
  • D.D Fischer et al.

    Isolation and characterization of a novel class II histone deacetylase, HDAC10

    J. Biol. Chem.

    (2002)
  • K Fujishiro et al.

    Crystallization and some properties of acetylpolyamine amidohydrolase from Mycoplana bullata

    Biochem. Biophys. Res. Commun.

    (1988)
  • H.Y Kao et al.

    Mechanism for nucleocytoplasmic shuttling of histone deacetylase 7

    J. Biol. Chem.

    (2001)
  • Y.I Wolf et al.

    Genome trees and the tree of life

    Trends Genet.

    (2002)
  • M.F White et al.

    Holding it together: chromatin in the Archaea

    Trends Genet.

    (2002)
  • J Ramstein et al.

    Evidence of a thermal unfolding dimeric intermediate for the Escherichia coli histone-like HU proteins: thermodynamics and structure

    J. Mol. Biol.

    (2003)
  • S.K Kurdistani et al.

    Histone acetylation and deacetylation in yeast

    Nature Rev. Mol. Cell. Biol.

    (2003)
  • R.W Johnstone

    Histone-deacetylase inhibitors: novel drugs for the treatment of cancer

    Nature Rev. Drug Discov.

    (2002)
  • D.D Leipe et al.

    Histone deacetylases, acetoin utilization proteins and acetylpolyamine amidohydrolases are members of an ancient protein superfamily

    Nucl. Acids Res.

    (1997)
  • C.M Grozinger et al.

    Three proteins define a class of human histone deacetylases related to yeast Hda1p

    Proc. Natl Acad. Sci. USA

    (1999)
  • D Shore

    The Sir2 protein family: a novel deacetylase for gene silencing and more

    Proc. Natl Acad. Sci. USA

    (2000)
  • C Hubbert et al.

    HDAC6 is a microtubule-associated deacetylase

    Nature

    (2002)
  • A Ito et al.

    MDM2-HDAC1-mediated deacetylation of p53 is required for its degradation

    EMBO J.

    (2002)
  • Y.L Yao et al.

    Regulation of transcription factor YY1 by acetylation and deacetylation

    Mol. Cell. Biol.

    (2001)
  • T Kouzarides

    Acetylation: a regulatory modification to rival phosphorylation?

    EMBO J.

    (2000)
  • S.W Remiszewski

    Recent advances in the discovery of small molecule histone deacetylase inhibitors

    Curr. Opin. Drug Discov. Dev.

    (2002)
  • Cited by (0)

    Present address: Y. -M. Lee, Department of Biotechnology, Royal Institute of Technology, SE-106 91 Stockholm, Sweden.

    View full text