title: Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes.
abstract: Sequence similarity and profile searching tools were used to analyze the genome sequences of Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans and Drosophila melanogaster for genes encoding three families of histone deacetylase (HDAC) proteins and three families of histone acetyltransferase (HAT) proteins. Plants, animals and fungi were found to have a single member of each of three subfamilies of the GNAT family of HATs, suggesting conservation of these functions. However, major differences were found with respect to sizes of gene families and multi-domain protein structures within other families of HATs and HDACs, indicating substantial evolutionary diversification. Phylogenetic analysis identified a new class of HDACs within the RPD3/HDA1 family that is represented only in plants and animals. A similar analysis of the plant-specific HD2 family of HDACs suggests a duplication event early in dicot evolution, followed by further diversification in the lineage leading to Arabidopsis. Of three major classes of SIR2-type HDACs that are found in animals, fungi have representatives only in one class, whereas plants have representatives only in the other two. Plants possess five CREB-binding protein (CBP)-type HATs compared with one to two in animals and none in fungi. Domain and phylogenetic analyses of the CBP family proteins showed that this family has evolved three distinct types of CBPs in plants. The domain architecture of CBP and TAF(II)250 families of HATs show significant differences between plants and animals, most notably with respect to bromodomain occurrence and their number. Bromodomain-containing proteins in Arabidopsis differ strikingly from animal bromodomain proteins with respect to the numbers of bromodomains and the other types of domains that are present. The substantial diversification of HATs and HDACs that has occurred since the divergence of plants, animals and fungi suggests a surprising degree of evolutionary plasticity and functional diversification in these core chromatin components.
authors.affiliation: Department of Plant Sciences, University of Arizona, Tucson, AZ 85721-0036, USA.
authors.forename: Ritu
authors.initials: R
authors.lastname: Pandey
authors.forename: Andreas
authors.initials: A
authors.lastname: Müller
authors.forename: Carolyn A
authors.initials: CA
authors.lastname: Napoli
authors.forename: David A
authors.initials: DA
authors.lastname: Selinger
authors.forename: Craig S
authors.initials: CS
authors.lastname: Pikaard
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Richards
authors.forename: Judith
authors.initials: J
authors.lastname: Bender
authors.forename: David W
authors.initials: DW
authors.lastname: Mount
authors.forename: Richard A
authors.initials: RA
authors.lastname: Jorgensen
mesh_terms: D000123:Acetyltransferases / Q000145:classification / Q000235:genetics* / Q000502:physiology; D017398:Alternative Splicing; D000595:Amino Acid Sequence; D000818:Animals; D017360:Arabidopsis / Q000201:enzymology* / Q000235:genetics*; D050882:CREB-Binding Protein; D017173:Caenorhabditis elegans / Q000201:enzymology / Q000235:genetics; D002843:Chromatin / Q000378:metabolism; D029721:Drosophila Proteins; D004331:Drosophila melanogaster / Q000201:enzymology / Q000235:genetics; D005656:Fungal Proteins / Q000235:genetics; D018745:Genome, Plant; D051548:Histone Acetyltransferases; D056284:Histone Deacetylase 1; D006655:Histone Deacetylases / Q000145:classification / Q000235:genetics* / Q000502:physiology; D008969:Molecular Sequence Data; D009687:Nuclear Proteins / Q000235:genetics; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D012097:Repressor Proteins; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000145:classification / Q000235:genetics* / Q000502:physiology; D012568:Schizosaccharomyces / Q000201:enzymology / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D037761:Sirtuins / Q000235:genetics; D015534:Trans-Activators / Q000235:genetics; D014157:Transcription Factors; D019473:Transcription Factors, TFII / Q000235:genetics
chemical_list: D002843:Chromatin; D029721:Drosophila Proteins; D005656:Fungal Proteins; D009687:Nuclear Proteins; D012097:Repressor Proteins; D029701:Saccharomyces cerevisiae Proteins; D015534:Trans-Activators; D014157:Transcription Factors; D019473:Transcription Factors, TFII; D000123:Acetyltransferases; D050882:CREB-Binding Protein; D051548:Histone Acetyltransferases; C499673:HDA1 protein, S cerevisiae; C071665:RPD3 protein, S cerevisiae; D037761:Sirtuins; C512966:HDAC1 protein, Drosophila; D056284:Histone Deacetylase 1; D006655:Histone Deacetylases