Phylogenetic analysis, subcellular localization, and expression patterns of RPD3/HDA1 family histone deacetylases in plants

Abstract

Background: Although histone deacetylases from model organisms have been previously identified, there is no clear basis for the classification of histone deacetylases under the RPD3/HDA1 superfamily, particularly on plants. Thus, this study aims to reconstruct a phylogenetic tree to determine evolutionary relationships between RPD3/HDA1 histone deacetylases from six different plants representing dicots with Arabidopsis thaliana, Populus trichocarpa, and Pinus taeda, monocots with Oryza sativa and Zea mays, and the lower plants with Physcomitrella patens.

Results: Sixty two histone deacetylases of RPD3/HDA1 family from the six plant species were phylogenetically analyzed to determine corresponding orthologues. Three clusters were formed separating Class I, Class II, and Class IV. We have confirmed lower and higher plant orthologues for AtHDA8 and AtHDA14, classifying both genes as Class II histone deacetylases in addition to AtHDA5, AtHDA15, and AtHDA18. Since Class II histone deacetylases in other eukaryotes have been known to undergo nucleocytoplasmic transport, it remains unknown whether such functional regulation also happens in plants. Thus, bioinformatics studies using different programs and databases were conducted to predict their corresponding localization sites, nuclear export signal, nuclear localization signal, as well as expression patterns. We also found new conserved domains in most of the RPD3/HDA1 histone deacetylases which were similarly conserved in its corresponding orthologues. Assessing gene expression patterns using Genevestigator, it appears that RPD3/HDA1 histone deacetylases are expressed all throughout the plant parts and developmental stages of the plant.

Conclusion: The RPD3/HDA1 histone deacetylase family in plants is divided into three distinct groups namely, Class I, Class II, and Class IV suggesting functional diversification. Class II comprises not only AtHDA5, AtHDA15, and AtHDA18 but also includes AtHDA8 and AtHDA14. New conserved domains have also been identified in most of the RPD3/HDA1 family indicating further versatile roles other than histone deacetylation.

Figure 1

Bootstrap consensus tree of RPD3/HDA1 family histone deacetylases in Arabidopsis, yeast and other metazoans. Neighbor Joining phylogenetic tree of RPD3/HDA1 type histone deacetylases in Arabidopsis (AtHDA2-18), yeast (ScHDA201-205), and other metazoans including Caenorhabditis elegans (CeHDA301-308), Drosophila melanogaster (DmHDA401-405), Candida albicans (CaHDA3201-3206), and Homo sapiens (HsHDA501-511) was reconstructed using MEGA4. Bootstrap support on the left of each node was inferred from 1000 replicates.

Figure 2

A phylogenetic tree of RPD3/HDA1 histone deacetylases from Arabidopsis thaliana, Populus trichocarpa, Pinus taeda, Oryza sativa, Zea mays, and Physcomitrella patens was generated using the Neighbor Joining method. The bootstrap consensus tree inferred from 1000 replicates is taken to represent the evolutionary history of the different RPD3/HDA1 proteins analyzed.

Figure 3

Radiation tree. Radiation tree of RPD3/HDA1 histone deacetylases in plants was inferred using the neighbor joining method.

Figure 4

Conserved domains of RPD3/HDA1 family histone deacetylases in Arabidopsis. Conserved domains of RPD3/HDA1 histone deacetylases in Arabidopsis thaliana are shown with their corresponding amino acid length on the right. Arrows indicate histidine active site in histone deacetylase (HD) domain. Abbreviations and amino acid residues in parenthesis: PB, Pfam B database; DUF, domain of unknown function; G, poly-glycine rich region (HDA6: 311–314, HDA7: 302–305, HDA9: 296–299, HDA17: 27–31); Asp, aspartate rich region (HDA6: 428–465, HDA9: 384–424, HDA10: 100–140, HDA17: 116–156, HDA15: 58–77); BAD, BH3-only pro-apoptotic domain; ad, aldehyde dehydrogenase (HDA15: 25–36); ZF, Zinc finger (86–115); 60s RP, ribosomal protein (193–203); CR6, cytokine-responsive protein 6 interacting protein (402–559); LZ, leucine zip motif (457–478); CC, coiled-coil domain (430–610); COG6, conserved oligomeric golgi complex 6 (629–641); RtcR, RNA terminal phosphate cyclase regulator (297–312); NLS, nuclear localization signal (HDA6:17–20 and 14–20, HDA19: 12–18 and 428–434, HDA5: 10–26, HDA14: 406–412, HDA15: 14–17, 521–537 and 522–538, HDA18: 43–59 and 121–137); NES, nuclear export signal (HDA2, 180–187 and 245–257, HDA8: 162–168, HDA15: 484–491, HDA18: 538–549).

Figure 5

Expression patterns of RPD3/HDA1 histone deacetylases based on Genevestigator. Expression patterns of Class I (A-D), Class II and Class IV (E-H) histone deacetylases are shown in different anatomical parts (A, E), developmental stages (B, F), and those induced by biotic and abiotic stress (C, G), and hormones (D, H). These data have been generated using Genevestigator produced from microarray data by Schmidt et al. (2005) and Kilian et al. (2007).

Figure 6

Multiple sequence alignment of Class II and Class IV histone deacetylases in Arabidopsis. Multiple sequence alignment of Class II and Class IV histone deacetylases was generated using ClustalW. Three putative conserved serine/threonine residues (red box) may be potential binding sites for 14-3-3 proteins for nucleocytoplasmic transport.