In silico analysis of sirtuin-type histone deacetylase genes in sugar beet (Beta vulgaris L.)

Abstract

Histone deacetylase (HDAC) enzymes catalyze the removal of an acetyl group from the lysine residues of histone N-terminal tails, and they repress gene transcription through condensation of chromatin. In plants, the sirtuins/silent information regulator 2 (SIR2) proteins which are NAD+-dependent deacetylases, have been identified in distinct plant species such as Arabidopsis, rice, tomato, soybean, maize, etc., but little is known about their functions in plants. They are mainly investigated in Arabidopsis and rice and found to be involved in H3K9 acetylation, metabolic pathways, repression of genes associated with stress response, and energy metabolism. A total of eight RPD3/HDA1 family HDAC genes have been recently identified in the sugar beet (Beta vulgaris L.) genome. However, B. vulgaris SIR2-type HDACs have not yet been identified and characterized. In this work, an in silico analysis of SIR2 family members was performed in sugar beet. Three SIR2 family HDACs were identified from the sugar beet genome, named BvSRT1, BvSRT2, and BvSRT3. The beet SIR2 gene family is found to be located on chromosomes 4, and 9. The phylogenetic tree building with B. vulgaris, Arabidopsis, tomato, soybean, Vitis vinifera, pepper, rice, maize, and Sorghum bicolor showed that 3 sugar beet SRTs were divided into two classes: Class II (BvSRT2) and IV (BvSRT1 and BvSRT3). SIR2 family proteins consisted of SIR2 domain (PF02146). The conserved motifs ranged from 6 to 50 amino acids, while the intron-exon numbers of genes ranged from 10 to 14. BvSRT1 and BvSRT3 exhibited similar motif distributions and exon/intron structures. Moreover, nuclear, and cytoplasmic localization of BvSRT1 and BvSRT3 has been predicted. BvSRT2 protein was located on the mitochondrion. Analysis of cis-elements revealed the involvement of BvSRT genes in hormone regulation, light response, abiotic stress response, and meristem expression. This study may shed light on the potential role of SIR2-type HDACs in beets.