Proteomic analysis of lysine acetylation provides strong evidence for involvement of acetylated proteins in plant meiosis and tapetum function

Abstract

SUMMARYProtein lysine acetylation (KAC) is a dynamic and reversible post-translational modification that has important biological roles in many organisms. Although KAC has been shown to affect reproductive development and meiosis in yeast and animals, similar studies are largely lacking in flowering plants, especially proteome-scale investigations for particular reproductive stages. Here, we report results from a proteomic investigation to detect the KAC status of the developing rice anthers near the time of meiosis (RAM), providing strong biochemical evidence for roles of many KAC-affected proteins during anther development and meiosis in rice. We identified a total of 1354 KAC sites in 676 proteins. Among these, 421 acetylated proteins with 629 KAC sites are novel, greatly enriching our knowledge on KAC in flowering plants. Gene Ontology enrichment analysis showed chromatin silencing, protein folding, fatty acid biosynthetic process and response to stress to be over-represented. In addition, certain potentially specific KAC motifs in RAM were detected. Importantly, 357 rice meiocyte proteins were acetylated; and four proteins genetically identified to be important for rice tapetum and pollen development were acetylated on 14 KAC sites in total. Furthermore, 47 putative secretory proteins were detected to exhibit acetylated status in RAM. Moreover, by comparing our lysine acetylome with the RAM phosphoproteome we obtained previously, we proposed a correlation between KAC and phosphorylation as a potential modulatory mechanism in rice RAM. This study provides the first global survey of KAC in plant reproductive development, making a promising starting point for further functional analysis of KAC during rice anther development and meiosis.

Construction of a Quantitative Acetylomic Tissue Atlas in Rice (Oryza sativa L.)

“…In rice germinating embryo, 699 PKA sites on 389 proteins were found to be acetylated, including 144 sites that were simultaneously modified by succinylation [ 26 ]. In an effort to discover the PKA in rice anthers in the stage of meiosis, Li et al (2018) identified a total of 1354 PKA sites in 676 proteins, which are mostly related to chromatin silencing, protein folding, and fatty acid biosynthetic processes [ 27 ]. There were also 44 and 692 lysine acetylated proteins that were identified from suspension cells and grain-filling stage seeds [ 24 , 28 ].…”

“…This also intrigued researchers to explore PKAs in rice. So far, at least 8 independent cases have been reported regarding the profiling of PKA sites, peptides, and proteins in rice seedlings, reproductive organs, and leaves under oxidative stress, which yielded the identification of over 8599 PKA sites and 4990 proteins [ 7 , 24 , 25 , 26 , 27 , 28 , 29 , 30 ]. Despite efforts being made on rice, the previous studies only explored the tip of the iceberg of rice acetylome, given that rice genome contains over 56,000 protein coding genes [ 31 ].…”

Tackling Plant Meiosis: From Model Research to Crop Improvement

“…Meiotic proteome complexity was reduced based on: comparative proteomics combined with transcriptomics in A. thaliana ( Lu et al, 2016 ); ASY1 affinity proteomics in B. oleracea ( Osman et al, 2018 ); proteomic approaches focusing on the identification of posttranslational protein modifications (PTMs) in rice ( Ye et al, 2015 ; Li et al, 2018 ). Surprisingly, a comparison of available Arabidopsis flower bud proteomes suggests that protein detection was not saturated ( Lu et al, 2016 ).…”

“…Proteomics from rice anthers identified 357 acetylated proteins including eight rice homologs of known meiotic genes ( Li et al, 2018 ). A positive correlation of simultaneous acetylation and phosphorylation of candidates functionally enriched for ribosome assembly, protein translation, UPS, and RNA degradation was found, further linking these processes to plant meiosis (see section “Meiotic Transcriptome”).…”

“…Interestingly, in rice H3K9 hyperacetylation correlates with meiotic arrest in mel1 ( Liu and Nonomura, 2016 ), H3K9 acetylation affects yeast recombination hotspots ( Yamada et al, 2013 ) and H4K12/H4K16 acetylation impacts meiotic chromosome segregation in human and mouse ( van den Berg et al, 2011 ; Ma and Schultz, 2013 ). All of these sites were acetylated in rice ( Li et al, 2018 ).…”