The Progress of Histone Deacetylase and Its Regulation

doi:10.11924/j.issn.1000-6850.2014-0697

Abstract

Abstract: Histone deacetylation played an important role in epigenetic, and histone deacetylase, which acted in concert with histone acetyltransferase, was a target to develop new medicine of tumor inhibitor. This paper reviewed recent findings of histone deacetylase in animal and yeast, and analyzed their homology of amino acid sequence and conserved domains with Arabidopsis thaliana, summarized their function of regulation, aimed to predict its function in plant development. It is concluded that, from its response to hormone stimulation and abiotic stress, HDACs widely participates in plants’development. The function of Plant’s HDACs may differ from animal and yeast because of their different conserved domains distribution in protein sequences. Although HDACs’function in Non-histone acetylation is still unknown, Non-histone acetylation actually exists.

References

[1] Anna P, Manel E. Epigenetic modifications and human disease[J]. Nature biotechnology,2010,28:1057-1068.
[2] Taunton J, Hassig C A, Schreiber S L. A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p[J]. Science,1996,272:408-411.
[3] De Ruijter A J, van Gennip A H, Caron H N, et al. Histone deacetylases (HDACs): characterization of the classical HDAC family[J]. Biochem J,2003,370:737-749.
[4] Hollender C, Liu Z. Histone deacetylase genes in Arabidopsis development[J]. J Integr Plant Biol,2008,50:875-885.
[5] Dangl M, Brosch G, Haas H, et al. Comparativeanalysis of HD2 type histone deacetylases in higher plants[J].Planta,2001,213:280- 285.
[6] Lopez-Rodas G, Georgieva E I, Sendra R, et al. Histone acetylation in Zea mays.I. Activities of histone acetyltransferases and histone deacetylases[J]. J Biol Chem,1991,266:18745-18750.
[7] Brosch G, Lusser A, Goralik- Schramel M, et al. Purification and characterization of a high molecular weight histone deacetylase complex (HD2) of maize embryos[J]. Biochemistry,1996,35:15907- 15914.
[8] Jung M, Hoffmann K, Brosch G, et al. Analogues of trichostatin A and trapoxin B as histone deacetylase inhibitors[J]. Bioor.Med. Chemm. Lett.,1997,7,1655-1658.
[9] Grozinger C M, Chao E D, Blackwell H E, et al. Identification of a class of small molecule inhibitors ofthe sirtuin family of NADdependent deacetylases by phenotypic screening[J]. J. Biol. Chem., 2001,276,38837-38843.
[10] Kaeberlein M. McVey M, Guarente L. The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms[J]. Genes Dev,1999,13,2570-2580.
[11] van der Horst A, Tertoolen LG, de Vries-Smits LM, et al. Burgering BM FOXO4 is acetylated upon peroxide stress and deacetylated by the longevity protein hSir2(SIRT1) [J]. J Biol Chem,2004,279: 28873-28879.
[12] Pandey R, Muller A, Napoli C A, et al. Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes[J].Nucleic Acids Res., 2002,30,5036-5055.
[13] Wang C, Gao F, Wu J, et al. Arabidopsis putative deacetylase AtSRT2 regulates basal defense by suppressing PAD4, EDS5 and SID2 expression. [J]Plant Cell Physiol,2010,51:1291-1299.
[14] Hollender C, Liu Z C. Histone Deacetylase and Their Function in Plant Development[J]. Journal of Integrative Plant Biology,2008,50 (7):875-885.
[15] Luger K, Mader A W, Richmond R K, et al .Crystal structure of the nucleosome core particle at 2.8 A resolution[J]. Nature,1997,389, 251-260.
[16] Turner B M. Histone acetylation and an epigenetic code[J]. Bioessays,2000,22:836-845.
[17] Turner B M. Cellular memory and the histone code[J]. Cell,2002, 111:285-291.
[18] Strahl B D, Allis C D. The language of covalent histone modifications[J].Nature,2000,403: 41-45.
[19] Schreiber S L, Bernstein B E. Signaling network model of chromatin[J]. Cell,2002,111:771-778.
[20] Kurdistani S K, Grunstein M. Histone acetylation and deacetylation in yeas[J]t. Nat Rev Mol Cell Biol,2003,4:276-284.
[21] Berger S L. Histone modifications in transcriptional regulation[J]. Curr Opin Genet Dev,2002, 12: 142-148.
[22] Jackson V, Shires A, Tanphaichitr N, et al. Modifications to histones immediately after synthesis[J]. J. Mol. Biol,1976,104,471-483.
[23] Louie A J, Candido E P, Dixon G H. Enzymatic modifications and their possible roles in regulating the binding of basic proteins to DNA and in controlling chromosomal structure[J]. Cold Spring Harb. Symp. Quant. Biol,1974,38,803-819.
[24] Ruiz- Carillo A, Wangh L J, Allfry V. Processing of newly synthesized histone molecule[J]. Science,1975,190,117-128.
[25] R Sogo J M. Replication of transcriptionally active chromatinLucchini[J].Nature,1995,374:276-80.
[26] Ruiz- Carrillo A, Wangh L J, Allfrey V G. Selective synthesis and modification of nuclear proteins during maturation of avian erythroid cells[J]. Science,1976,190:117-28
[27] Jackson V, Shires A, Tanphaichitr N. Modifications to histones immediately after synthesis[J] J. Mol. Biol,1976,104:471-83.
[28] Sobel R E, Cook R G, Perry CA. Conservation of deposition-related acetylation sites in newly synthesized histones H3 and H4[J].Proc. Natl. Acad. Sci.USA,1995,92:1237-41.
[29] Ma X J, Wu J, Altheim B A, et al. Deposition-related sites K5/K12 in histone H4 are not required for nucleosome deposition in yeast [J]. Proc. Natl. Acad. Sci. USA,1998,95:6693-98.
[30] Siino J S, Yau P M, Imai B S, et al. Effect of DNA length and H4 acetylation on the thermal stability of reconstituted nucleosome particles[J]. Biochem. Biophys. Res.Commun.,2003,302:885-91.
[31] Dorigo B, Schalch T, Bystricky K, et al. Chromatin Fiber Folding . Requirement for the Histone H4 N- terminal Tail[J]. J. Mol. Biol., 2003,327:85-96.
[32] Shogren-Knaak M, Ishii H, Sun JM, et al. Peterson CL.Histone H4- K16 Acetylation Controls Chromatin Structure and Protein Interactions[J]. Science,2006,311:844-47.
[33] Buchman A R, Kimmerly W J, Rine J, et al. Two DNA- binding factors recognize specific sequences at silencers, upstream activating sequences, autonomously replicating sequences, and telomeres in Saccharomyces cerevisiae[J].Mol. Cell. Biol,1988,8: 210-25.
[34] Moretti P, Freeman K, Coodly L, et al. Evidence that a complex of SIR proteins interacts with the silencer and telomere- binding protein RAP1[J]. Genes Dev.,1994,8:2257-69.
[35] Moretti P, Shore D. Evidence that a complex of SIR proteins interacts with the silencer and telomere- binding protein RAP1[J]. Mol. Cell. Biol,2001,21:8082-94.
[36] Imai S, Armstrong C M, Kaeberlein M, et al. Transcriptional silencing and longevity protein Sir2 is an NAD- dependent histone deacetylase[J]. Nature,2000,403:795-800.
[37] Cubizolles F, Martino F, Perrod S, et al. A HomotrimerHeterotrimer Switch in Sir2 Structure Differentiates rDNA and Telomeric SilencingMol[J]. Cell,2006,21:825-36.
[38] Johnson L M, Fisher- Adams G, Grunstein M. Identification of a non- basic domain in the histone H4 N- terminus required for repression of the yeast silent mating loci[J]. EMBO J.,1992,11: 2201-9.
[39] Thompson J S, Ling X, Grunstein M. Histone H3 amino terminus is required for telomeric and silent mating locus repression in yeast[J] Nature,1994,369:245-47.
[40] Kurdistani S K, Tavazoie S, Grunstein M. Mapping global histone acetylation patterns to gene expression[J]. Cell,2004,117:721-733.
[41] Luo M, Yu C W, Chen F F. Histone Deacetylase HDA6 Is Functionally Associated with AS1 in Repression of KNOX Genes in Arabidopsis[J]. Plos Genetics,2012,8:1-10.
[42] Kim S C, Sprung R, Chen Y, et al. Substrate and functional diversity of lysine acetylation revealed by a proteomics survey[J]. Mol Cell,2006,23:607-18.
[43] Wu X, Oh M H, Schwarz E M, et al. Lysine acetylation is a widespread protein modification for diverse proteins in Arabidopsis [J]. Plant Physiol,2011,155:1769-1778.