Ethylene response factor MdERF4 and histone deacetylase MdHDA19 suppress apple fruit ripening through histone deacetylation of ripening-related genes

Abstract

Histone deacetylase enzymes participate in the regulation of many aspects of plant development. However, the genome-level targets of histone deacetylation during apple (Malus domestica) fruit development have not been resolved in detail, and the mechanisms of regulation of such a process are unknown. We previously showed that the complex of ethylene response factor 4 (MdERF4) and the TOPLESS co-repressor (MdTPL4) (MdERF4-MdTPL4) is constitutively active during apple fruit development, but whether this transcriptional repression complex is coupled to chromatin modification is unknown. Here, we show that a histone deacetylase (MdHDA19) is recruited to the MdERF4-MdTPL4 complex, thereby impacting fruit ethylene biosynthesis. Transient suppression of MdHDA19 expression promoted fruit ripening and ethylene production. To identify potential downstream target genes regulated by MdHDA19, we conducted chromatin immunoprecipitation (ChIP) sequencing of H3K9 and ChIP-quantitative PCR assays. We found that MdHDA19 affects ethylene production by facilitating H3K9 deacetylation and forms a complex with MdERF4-MdTPL4 to directly repress MdACS3a expression by decreasing the degree of acetylation. We demonstrate that an early-maturing-specific acetylation H3K9ac peak in MdACS3a and expression of MdACS3a were specifically up-regulated in fruit of an early-maturing, but not a late-maturing, cultivar. We provide evidence that a C-to-G mutation in the EAR motif of MdERF4 reduces the repression of MdACS3a by the MdERF4-MdTPL4-MdHDA19 complex. Taken together, our results reveal that the MdERF4-MdTPL-MdHDA19 repressor complex participates in the epigenetic regulation of apple fruit ripening.

MdMADS6 Recruits Histone Deacetylase MdHDA19 to Repress the Expression of the Carotenoid Synthesis-Related Gene MdCCD1 during Fruit Ripening

“…Combined with the result of Figure 5 A, we concluded that MdMADS6 targeted MdCCD1 and positively regulated the expression of MdCCD1 . To detect the regulating effect of MdHDA19 on MdCCD1 , we measured the MdCCD1 relative expression level in the ‘Orin’ apple calli overexpressed or silenced for MdHDA19 [ 19 ]. The results showed that the expression level of MdCCD1 decreased compared with the overexpressed pRI101 empty vector but increased significantly compared with overexpressed pRI101-RNAi empty vector, indicating that MdHDA19 negatively regulated the expression of MdCCD1 ( Figure 5 C).…”

“…Malus domestica ‘Gala’ and MdHDA19 -transgenic ‘Orin’ apple calli were used in this study [ 19 ]. Fruits were harvested at 90–110 d after flower blossoming.…”

“…His- MdMADS6 was immobilized on the chromatographic column, the solution was passed through the chromatographic column, the flow-through was collected, and the flow-through was incubated with GST antibody. The pull-down assays were performed as previously described [ 19 ]. The primers used are listed in Supplementary Table S2 .…”

Transcriptional regulation of fleshy fruit texture

“…C/C and C/G alleles of MdERF4 at the EAR motif confer firm and soft texture respectively and other experiments indicate that MdERF4 affects firmness by reducing ethylene production by repressing MdERF3, a TF shown to be involved in the activation of ethylene biosynthesis by targeting MdACS1 (Hu et al, 2020). A recent study revealed a novel module, the MdERF4‐MdTPL‐MdHDA19 repressor complex that directly represses MdACS3a expression by decreasing the degree of histone acetylation, a critical epigenetic modification associated with transcriptional regulation (Hu et al, 2022). SlERF.F12, MaERF11, CpERF9 and MdERF4 have also been shown to recruit histone deacetylase and form a complex that targets CW genes, plus ethylene biosynthetic genes (Han et al, 2016; Fu et al, 2019; Deng et al, 2022; Hu et al, 2022) (Figure 4).…”

“…A recent study revealed a novel module, the MdERF4‐MdTPL‐MdHDA19 repressor complex that directly represses MdACS3a expression by decreasing the degree of histone acetylation, a critical epigenetic modification associated with transcriptional regulation (Hu et al, 2022). SlERF.F12, MaERF11, CpERF9 and MdERF4 have also been shown to recruit histone deacetylase and form a complex that targets CW genes, plus ethylene biosynthetic genes (Han et al, 2016; Fu et al, 2019; Deng et al, 2022; Hu et al, 2022) (Figure 4).…”