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. 2022 Jan 21;23(3):1173.
doi: 10.3390/ijms23031173.

Comprehensive Profiling of Paper Mulberry (Broussonetia papyrifera) Crotonylome Reveals the Significance of Lysine Crotonylation in Young Leaves

Yibo Dong  1   2 , Chao Chen  2
Affiliations

Comprehensive Profiling of Paper Mulberry (Broussonetia papyrifera) Crotonylome Reveals the Significance of Lysine Crotonylation in Young Leaves

Yibo Dong et al. Int J Mol Sci. .

Abstract

Lysine crotonylation is a newly discovered and reversible posttranslational modification involved in various biological processes, especially metabolism regulation. A total of 5159 lysine crotonylation sites in 2272 protein groups were identified. Twenty-seven motifs were found to be the preferred amino acid sequences for crotonylation sites. Functional annotation analyses revealed that most crotonylated proteins play important roles in metabolic processes and photosynthesis. Bioinformatics analysis suggested that lysine crotonylation preferentially targets a variety of important biological processes, including ribosome, glyoxylate and dicarboxylate metabolism, carbon fixation in photosynthetic organisms, proteasome and the TCA cycle, indicating lysine crotonylation is involved in the common mechanism of metabolic regulation. A protein interaction network analysis revealed that diverse interactions are modulated by protein crotonylation. These results suggest that lysine crotonylation is involved in a variety of biological processes. HSP70 is a crucial protein involved in protecting plant cells and tissues from thermal or abiotic stress responses, and HSP70 protein was found to be crotonylated in paper mulberry. This systematic analysis provides the first comprehensive analysis of lysine crotonylation in paper mulberry and provides important resources for further study on the regulatory mechanism and function of the lysine crotonylated proteome.

Keywords: PPI; lysine crotonylation; paper mulberry; plant metabolism; posttranslational modification.

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Conflict of interest statement

The authors declare that they have no conflict of interest with the contents of this article.

Figures

Figure 1
Figure 1
Identification of global crotonylation sites and proteins in paper mulberry leaves. (A) Experimental workflow for the identification of lysine crotonylome. (B) Basic statistical table of MS results. (C) Number of each identified peptide length. (D) Number of each identified modified site in a protein.
Figure 1
Figure 1
Identification of global crotonylation sites and proteins in paper mulberry leaves. (A) Experimental workflow for the identification of lysine crotonylome. (B) Basic statistical table of MS results. (C) Number of each identified peptide length. (D) Number of each identified modified site in a protein.
Figure 2
Figure 2
Properties of lysine-crotonylated peptides. (A) Crotonylation sequence motifs for ±10 amino acids around the lysine crotonylation sites. (B) Heat map of the amino acid compositions of the crotonylated sites.
Figure 3
Figure 3
Gene ontology functional characterization of the identified crotonylated proteins. (A) Distribution of the crotonylated proteins in terms of biological processes. (B). Distribution of the crotonylated proteins in terms of cellular components. (C) Distribution of the crotonylated proteins in terms of molecular functions. (D) Subcellular location prediction.
Figure 3
Figure 3
Gene ontology functional characterization of the identified crotonylated proteins. (A) Distribution of the crotonylated proteins in terms of biological processes. (B). Distribution of the crotonylated proteins in terms of cellular components. (C) Distribution of the crotonylated proteins in terms of molecular functions. (D) Subcellular location prediction.
Figure 4
Figure 4
Enrichment analysis of the lysine-acetylated proteins in paper mulberry. (A) GO-based enrichment analysis in terms of cell component (red bars), molecular function (blue bars) and biological process (green bars). (B) KEGG pathway enrichment analysis. (C) Proteins identified as crotonylproteins in this study.
Figure 4
Figure 4
Enrichment analysis of the lysine-acetylated proteins in paper mulberry. (A) GO-based enrichment analysis in terms of cell component (red bars), molecular function (blue bars) and biological process (green bars). (B) KEGG pathway enrichment analysis. (C) Proteins identified as crotonylproteins in this study.
Figure 5
Figure 5
(A) Crotonylated proteins involved in photosynthesis. The identified crotonylated proteins are highlighted in red. (B) Crotonylated proteins involved in carbon fixation in photosynthetic organisms. The identified crotonylated proteins are highlighted in red. (C) Crotonylated proteins involved in glyoxylate and dicarboxylate metabolism. The identified crotonylated proteins are highlighted in red.
Figure 5
Figure 5
(A) Crotonylated proteins involved in photosynthesis. The identified crotonylated proteins are highlighted in red. (B) Crotonylated proteins involved in carbon fixation in photosynthetic organisms. The identified crotonylated proteins are highlighted in red. (C) Crotonylated proteins involved in glyoxylate and dicarboxylate metabolism. The identified crotonylated proteins are highlighted in red.
Figure 6
Figure 6
Interaction networks of the crotonylated proteins in paper mulberry.
Figure 7
Figure 7
Analysis of proteins modified by crotonylation, succinylation, and ubiquitylation. (A) Overlap of crotonylated (Kcr) proteins in this study with reported paper mulberry succinylated (Ksu) and ubiquitylated (Kub) proteins. (B) Overlap of crotonylated lysine residues in this study with reported succinylated (Ksu) and ubiquitylated (Kub) lysine residues in paper mulberry. (C) Analysis of heat shock protein (HSP70) modified by crotonylation, succinylation and ubiquitination.
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