Histone deacetylases control lysine acetylation of ribosomal proteins in rice

Abstract

Lysine acetylation (Kac) is well known to occur in histones for chromatin function and epigenetic regulation. In addition to histones, Kac is also detected in a large number of proteins with diverse biological functions. However, Kac function and regulatory mechanism for most proteins are unclear. In this work, we studied mutation effects of rice genes encoding cytoplasm-localized histone deacetylases (HDAC) on protein acetylome and found that the HDAC protein HDA714 was a major deacetylase of the rice non-histone proteins including many ribosomal proteins (r-proteins) and translation factors that were extensively acetylated. HDA714 loss-of-function mutations increased Kac levels but reduced abundance of r-proteins. In vitro and in vivo experiments showed that HDA714 interacted with r-proteins and reduced their Kac. Substitutions of lysine by arginine (depleting Kac) in several r-proteins enhance, while mutations of lysine to glutamine (mimicking Kac) decrease their stability in transient expression system. Ribo-seq analysis revealed that the hda714 mutations resulted in increased ribosome stalling frequency. Collectively, the results uncover Kac as a functional posttranslational modification of r-proteins which is controlled by histone deacetylases, extending the role of Kac in gene expression to protein translational regulation.

Quantitative Proteomic Analysis Reveals Important Roles of the Acetylation of ER-Resident Molecular Chaperones for Conidiation in Fusarium oxysporum

“…However, it has been shown that post translational modifications such as the ubiquitylation and phosphorylation of ribosomal proteins may have functional effects on translational control (39). A more recent study demonstrated that Kac is an important post translational modification of R-proteins that reduces R-protein stability and may increase the combinatorial diversity of ribosome activities (40). The data obtained in this work showed that 30% of total ribosomal proteins were acetylated (Fig.…”

Amino Acids in Rice Grains and Their Regulation by Polyamines and Phytohormones

“…It should be emphasized that genetic improvement is the most important way to improve rice quality [104][105][106]. In recent years, a number of good-quality rice varieties or lines have been bred through molecular breeding technologies such as transgenic and gene-editing [106][107][108]. Further studies are needed to breed rice varieties or lines with a high content of amino acids, especially essential amino acids such as Lys, in the ripe grains though genetically optimizing the spatial and temporal distributions of the content and compositions of amino acids in the grain during the filling.…”

Advances in proteome-wide analysis of plant lysine acetylation

“…This suggests that LysAc is probably necessary for the regulation of protein synthesis and assembly. A KDAC (HDA714) has been shown to target RPs for LysDeAc, which is likely to affect the stability of the ribosome and its translational efficiency ( Xu et al., 2021 ). However, rare homologous Lys-acetylated HSPs or conserved Lys-acetylated sites have been found in the current study.…”