Genome-Wide Identification of Histone Modifiers and Their Expression Patterns during Fruit Abscission in Litchi.

Manjun Peng,Peiyuan Ying,Minglei Zhao,Rui Xia,Xuncheng Liu,Caiqin Li,Jianguo Li

doi:10.3389/fpls.2017.00639

Abstract

Modifications to histones, including acetylation and methylation processes, play crucial roles in the regulation of gene expression in plant development as well as in stress responses. However, limited information on the enzymes catalyzing histone acetylation and methylation in non-model plants is currently available. In this study, several histone modifier (HM) types, including six histone acetyltransferases (HATs), 11 histone deacetylases (HDACs), 48 histone methyltransferases (HMTs), and 22 histone demethylases (HDMs), are identified in litchi (Litchi chinensis Sonn. cv. Feizixiao) based on similarities in their sequences to homologs in Arabidopsis (A. thaliana), tomato (Solanum lycopersicum), and rice (Oryza sativa). Phylogenetic analyses reveal that HM enzymes can be grouped into four HAT, two HDAC, two HMT, and two HDM subfamilies, respectively, while further expression profile analyses demonstrate that 17 HMs were significantly altered during fruit abscission in two field treatments. Analyses reveal that these genes exhibit four distinct patterns of expression in response to fruit abscission, while an in vitro assay was used to confirm the HDAC activity of LcHDA2, LcHDA6, and LcSRT2. Our findings are the first in-depth analysis of HMs in the litchi genome, and imply that some are likely to play important roles in fruit abscission in this commercially important plant.

Highlights

Eukaryote genomic DNA is tightly compacted into a complex structure known as chromatin
Results show that the litchi genome encodes three proteins that belong in the HAG group; of these, we found LcHAG1 to be closely related to the GCN5 clade while LcHAG3 is closely related to the ELP3 clade
Our data show (Figure 1B) that LcHAC1 is characterized by TAZ (PF02135), PHD (PF00628), KAT11 (PF08214), ZZ, and TAZ domains (Pandey et al, 2002), while the litchi genome comprises just one HAM protein (LcHAM1) consisting of the same conserved domains, an N-terminal Chromo (PF00385), C2H2 (PF00096), and a C-terminal MOZ_SAS (PF01853), as previously reported in Arabidopsis, rice, and tomato HAMs (Latrasse et al, 2008)

Summary

Introduction

Eukaryote genomic DNA (gDNA) is tightly compacted into a complex structure known as chromatin. 23, as well as the H4 lysine (K) residues 5, 8, 12, 16, and 20 (Fuchs et al, 2006) Based on their domain composition, plant HATs can be classified into one of four groups: (i) HAGs with an acetyltransf_1 domain (PF00583) (AT1) which includes GCN5-, ELP3-, and HAT1-like acetyltransferases; (ii) HAMs that include a MOZ-YBF2/SAS3-SAS2-TIP60 domain (MYSTs); (iii) HACs that are similar to the p300/CREB-binding protein; and (iv) HAFs related to the TATA-binding protein-associated factor 1 (Pandey et al, 2002). On the basis of their sequence similarity and cofactor dependencies, HDACs in all eukaryotes can be divided into three families: reduced potassium dependence 3/histone deacetylase 1 (RPD3/HDA1); silent information regulator 2 (SIR2); and plant-specific histone deacetylase 2 (HD2) (Pandey et al, 2002). Nicotine adenine dinucleotide (NAD) is required as a cofactor by the SIR2 family (Haigis and Guarente, 2006), while members of the RPD3/HDA1 family need a Zn2+ cofactor for deacetylase activity (Yang and Seto, 2007)

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Conclusion