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. 2018 Nov 1;23(11):2843.
doi: 10.3390/molecules23112843.

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

Zhiyong Li  1 , Yifeng Wang  2 , Babatunde Kazeem Bello  3 , Abolore Adijat Ajadi  4 , Xiaohong Tong  5 , Yuxiao Chang  6 , Jian Zhang  7
Affiliations

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

Zhiyong Li et al. Molecules. .

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.

Keywords: Rice (Oryza sativa L.); post-translational modification; protein lysine acetylation; proteome; tissue atlas.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Tissue morphologies of different rice tissues tested in this study. (A) leaf and root; (B) callus; (C) mature panicle. Scale bar = 1 cm; (D) Total proteins of different tissues were resolved by SDS-PAGE and stained by Coomassie brilliant blue (CBB) and (E) Western blot analysis of the acetylation dynamics in different rice tissues by using anti-acetyl lysine antibodies. Equal amount of proteins (20 μg) were used. Anti-actin was used as an internal control for normalization [32].
Figure 2
Figure 2
(A) The counts of acetylsites, acetylpeptides and acetylproteins in the callus, leaf, panicle, and root, respectively; (B) Venn diagram showing the overlap of our identified acetylproteins in the callus, leaf, panicle, and root, respectively; (C) Numbers of each identified peptide length; (D) Numbers of each identified modified site in a protein.
Figure 3
Figure 3
(A) Acetylation sequence motifs and conservation of acetylation sites in identified callus, leaf, panicle acetylproteins; and (B) Heat map of the amino acid composition of the acetylation sites, showing the frequency of different amino acids surrounding the acetylated lysine (K).
Figure 4
Figure 4
GO analysis of differentially-acetylated proteins in terms of: biological process (A); molecular function (B); cellular component (C); subcellular location (D); and acetylation intensity, respectively. The abbreviations in (D) represent the following. E.R.: endoplasmic reticulum; extr: extracellular matrix; cyto: cytoplasm; mito: mitochondrial; chlo: chloroplast; vacu: vacuole; cysk: cytoplasmic skeleton; cyto nucl: cytoplasm nuclear.
Figure 5
Figure 5
Protein domain enrichment analysis (A) and KEGG pathway enrichment analysis (B) proteins identified acetylproteins in this study.
Figure 6
Figure 6
Hierarchical clustering analysis of the DA proteins in the callus, leaf, panicle, and root; Color bar at the bottom represents the log 2 acetylation site quantitation values. Green, black, and red indicate the low, medium, and high acetylation intensity, respectively.
Figure 7
Figure 7
Protein–protein interaction (PPI) network of DA proteins identified in this study. (A) callus; (B) leaf; (C) mature panicle, and (D) root.
See this image and copyright information in PMC

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