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

Abstract

PKA (protein lysine acetylation) is a key post-translational modification involved in the regulation of various biological processes in rice. So far, rice acetylome data is very limited due to the highly-dynamic pattern of protein expression and PKA modification. In this study, we performed a comprehensive quantitative acetylome profile on four typical rice tissues, i.e., the callus, root, leaf, and panicle, by using a mass spectrometry (MS)-based, label-free approach. The identification of 1536 acetylsites on 1454 acetylpeptides from 890 acetylproteins represented one of the largest acetylome datasets on rice. A total of 1445 peptides on 887 proteins were differentially acetylated, and are extensively involved in protein translation, chloroplast development, and photosynthesis, flowering and pollen fertility, and root meristem activity, indicating the important roles of PKA in rice tissue development and functions. The current study provides an overall view of the acetylation events in rice tissues, as well as clues to reveal the function of PKA proteins in physiologically-relevant tissues.

Advances in proteome-wide analysis of plant lysine acetylation

“…(2018) O . sativa KacH, KacY, KacT, KacS, F∗Kac, Kac∗∗∗∗∗∗K, Kac∗R, YKac, D∗KacK Li et al. (2018b) O .…”

“…In O . sativa , LysAc levels were higher in callus, leaves, and panicles than in roots ( Li et al., 2018b ), and post-anthesis seeds exhibited higher LysAc levels than flowers and pollen ( Meng et al., 2018 ). In dormant buds of P .…”

“…(2011) localized Lys-acetylated proteins to the nucleus, plasma membrane, and chloroplast, whereas the chromocenter was hypo-Lys-acetylated. Subcellular localization predictions reveal that the number of Lys-acetylated proteins varies across subcellular compartments among plant species, tissues, and developmental stages ( Fang et al., 2015 ; He et al., 2016 ; Xia et al., 2016 ; Xiong et al., 2016 ; Zhang et al., 2016 ; Zhen et al., 2016 ; Chen et al., 2018 ; Jiang et al., 2018 ; Li et al., 2018b , 2021b ; Meng et al., 2018 ; Xue et al., 2018 ; Zhou et al., 2018 ; Zhu et al., 2018 ; Cao et al., 2019 ; Yan et al., 2020 ; Liao et al., 2021 ) ( Figure 2 B). Almost 90% of Lys-acetylated proteins are located in the chloroplast, cytoplasm, nucleus, and mitochondria of plant cells.…”

“…To date, plant Lys-acetylproteome analyses have focused mainly on higher plants, including A . thaliana ( Finkemeier et al., 2011 ; Wu et al., 2011 ; Koenig et al., 2014 ; Hartl et al., 2017 ; Uhrig et al., 2017 ; Liu et al., 2018 ; Koskela et al., 2018 ; Bienvenut et al., 2020 ), Vitis vinifera ( Melo-Braga et al., 2012 ; Liu et al., 2019 ), Pisum sativum ( Smith-Hammond et al., 2014a ), Glycine max ( Smith-Hammond et al., 2014b ; Li et al., 2021a ), Oryza sativa ( Nallamilli et al., 2014 ; He et al., 2016 ; Xiong et al., 2016 ; Wang et al., 2017 ; Li et al., 2018a , 2018b ; Meng et al., 2018 ; Xue et al., 2018 ; Zhou et al., 2018 ), Fragaria ananassa ( Fang et al., 2015 ), Medicago truncatula ( Marx et al., 2016 ), Triticum aestivum ( Zhang et al., 2016 ; Zhu et al., 2018 ; Guo et al., 2020 ), Brachypodium distachyon ( Zhen et al., 2016 ), Picea asperata ( Xia et al., 2016 ), Camellia sinensis ( Xu et al., 2017 ; Jiang et al., 2018 ), Zea mays ( Walley et al., 2018 ; Yan et al., 2020 ), Kandelia candel ( Pan et al., 2018 ), Gossypium hirsutum ( Singh et al., 2020 ), Hibiscus cannabinus ( Chen et al., 2019 ), Paulownia tomentosa ( Cao et al., 2019 ), Petunia hybrida ( Zhao et al., 2020 ), Nicotiana benthamiana ( Yuan et al., 2021 ), Populus tremula × Populus alba ( Liao et al., 2021 ), Broussonetia papyrifera ( Li et al., 2021b ), and Phoebe zhennan ( Zhao et al., 2021 ) ( Table 1 ). By contrast, the Lys-acetylproteomes of lower plants are poorly studied and have been documented only in Phaeodactylum tricornutum ( Chen et al., 2018 ) and ...…”

Special Issue: Mass Spectrometric Proteomics

“…The interest of Li and co-authors [6] was focused on the study of protein lysine acetylation (PKA), a key post-translational modification involved in the regulation of various biological processes in rice. They applied an MS-based label-free approach to perform a quantitative analysis of PKA proteins in rice callus, root, leaf and panicle.…”