Histone Deacetylase Genes in Arabidopsis Development

Abstract

Histone acetylation and deacetylation are directly connected with transcriptional activation and silencing in eukaryotes. Gene families for enzymes that accomplish these histone modifications show surprising complexity in domain organization, tissue-specific expression, and function. This review is focused on the family of histone deacetylases (HDACs) that remove the acetyl group from core histone tails, resulting in a "closed" chromatin and transcriptional repression. In Arabidopsis, 18 HDAC genes are divided into three different types - RPD3-like, HD-tuin and sirtuin - with two or more members in each type. The structural feature of each HDAC class, the expression profile of each HDAC gene during development and functional insights of important family members are summarized here. It is clear that HDACs are an important class of global transcriptional regulators that play crucial roles in plant development, defense, and adaptation.

The Arabidopsis Class II Sirtuin Is a Lysine Deacetylase and Interacts with Mitochondrial Energy Metabolism

“…Lys acetylation can have a strong impact on the biochemical function of proteins as the transfer of the acetyl group to Lys masks the positive charge, which is known to be important in many catalytic centers of enzymes, as well as for protein-protein and protein-DNA interactions. In plants, Lys acetylation was, until recently, mainly thought to occur on histone proteins as regulatory mechanism for transcription and chromatin functions (Hollender and Liu, 2008). However, several central metabolic enzymes of diverse subcellular compartments were recently discovered to be Lys acetylated in Arabidopsis (Arabidopsis thaliana), and in vitro deacetylation tests confirmed that Lys acetylation affects enzyme activities and protein functions (Finkemeier et al, 2011;Wu et al, 2011).…”

“…Generally, protein acetyltransferases and deacetylases are known to catalyze the reversible modification of the « N-group of Lys. In addition to the classical family of histone deacetylases, a second family of protein deacetylases exists, namely the sirtuins, which are conserved across bacteria, yeast (Saccharomyces cerevisiae), plants, and animals (Hollender and Liu, 2008). Sirtuins catalyze an NAD + -dependent deacetylation of acetyl-Lys in proteins and thereby produce a deacetylated Lys, as well as the metabolites nicotinamide and 29-Oacetyl-ADP-ribose.…”

Impact of nucleosome dynamics and histone modifications on cell proliferation during Arabidopsis development

“…Arabidopsis histone deacetylases (HDACs) have been classified into three families (Hollender and Liu, 2008;Alinsug et al, 2009). The first one contains members homologous to the yeast RPD3 (reduced potassium deficiency 3) and HDA1 proteins; the second, the HD-tuins (HDT1 through 3), appears to be plant-specific (Wu et al, 2000;Dangl et al, 2001) and the third family contains homologs of the yeast silent information regulator 2 (Sir2), a (NAD)-dependent HDAC (Pandey et al, 2002;Hollender and Liu, 2008). The main conclusion that we can extract from the data available is that a fine balance between HAT and HDAC activities is at the core of crucial processes during plant development.…”

High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns inArabidopsisand rice

“…[14][15][16][17][18] Besides its role in gene expression, plant histone acetylation plays crucial roles in the crosstalk between genomes and the environment during plant responses to diverse stresses at the cellular and organismal levels. [19][20][21][22][23][24] Acetylation occurs at many histone lysine residues and regulates chromatin activity by at least 2 different mechanisms. On the one hand, individual acetylation marks have precise function on a specific chromatin-based process independent of other acetylated residues.…”