Global Lysine Acetylome Analysis of Desiccated Somatic Embryos of Picea asperata

Abstract

Partial desiccation treatment (PDT) promotes the germination capacity of conifer somatic embryos. Lysine acetylation (LysAc) is a dynamic and reversible post-translational modification that plays a key role in many biological processes including metabolic pathways and stress response. To investigate the functional impact of LysAc in the response of Picea asperata somatic embryos to PDT, we performed a global lysine acetylome analysis. Here, combining antibody-based affinity enrichment and high-resolution mass spectrometry, we identified and validated 1079 acetylation sites in 556 acetylated proteins from P. asperata somatic embryos during PDT. These data represent a novel large-scale dataset of lysine-acetylated proteins from the conifer family. Intensive bioinformatics analysis of the Gene Ontology of molecular functions demonstrated that lysine-acetylated proteins were mainly associated with binding, catalytic activities, and structural molecular activities. Functional characterization of the acetylated proteins revealed that in the desiccated somatic embryos, LysAc is mainly involved in the response to stress and central metabolism. Accordingly, the majority of these interacting proteins were also highly enriched in ribosome, proteasome, spliceosome, and carbon metabolism clusters. This work provides the most comprehensive profile of LysAc for a coniferous species obtained to date and facilitates the systematic study of the physiological role of LysAc in desiccated somatic embryos of P. asperata.

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

“…Nevertheless, only two reports are presently available on Arabidopsis, which profiled a total of 398 PKA sites on 251 proteins from suspension cells and young seedlings [ 13 , 14 ]. Similar works have also been done on grape fruits, pea seedlings, soybean developing seeds, wheat leaf, strawberry leaf, grass leaf, potato tuber, and spruce somatic embryo, but only yielded the identification of less than 7000 PKA sites in total [ 6 , 15 , 16 , 17 , 18 , 19 , 20 , 21 ].…”

Advanced Proteomic Approaches to Elucidate Somatic Embryogenesis

“…The implementation of protein fractionation or enrichment before or after trypsin digestion could help to overcome the limitation by reducing the complexity of the sample for the mass spectrometry protein identification. A sample with a reduced complexity via an antibody-based enrichment for acetylated peptides from Picea asperata somatic embryos had facilitated the generation of deep acetylome that contains nearly two acetylated sites per protein identified ( Xia et al, 2016 ).…”

“…Deciphering the interconnected proteome responsible for somatic cell switch to somatic embryo requires the determination of important protein features such as protein location, protein stability, posttranslational modifications (PTMs), and protein-protein interactions for the proteins present in the proteome of the SE process. Besides keeping most of the proteins in the sample in solution during the preparation of protein homogenate or in step-wise isolation of specific kinds of proteins ( Niu et al, 2018 ), the preservation of proteins and PTM is a key factor to get insights into SE proteome ( Peltier et al, 2004 ; Xia et al, 2016 ; Aguilar-Hernández et al, 2017 ).…”

“…The integration of fractionation and/or type-enrichment for proteins or peptides, including resolving protein homogenate by 1D-PAGE followed by in-gel digestion and LC-MS/MS antibody-based acetylated-lysine enrichment ( Zhao et al, 2015a , b ; dos Santos et al, 2016 ; Xia et al, 2016 ; Alves et al, 2017 ), may provide new insights and in-depth proteome coverage during the induction of SE. However, few of the exquisite variety of proteomic tools have been implemented so far.…”

“…A variety of explants have been used to study the proteome during the induction of SE, including hypocotyl and leaf sections, immature zygote embryos, unpollinated ovules, shoot meristems, ZE sections, and anther tissue. 2DE is the most exploited proteomic approach followed by 2DE-DIGE, and more recently by techniques such as label-free proteomics, iTRAQ, or antibody-based proteomics approaches ( Xia et al, 2016 ). PGR metabolism and signaling, the ROS scavengers, primary and secondary metabolism associated enzymes, transcription regulation, signal transduction, disease/defense-related proteins, molecular chaperones, proteolysis, and proteasomal component/factors have been identified in SE proteomes.…”