Systematic analysis of the lysine succinylome in the model medicinal mushroom Ganoderma lucidum

Abstract

Background: Ganoderma lucidum, one of the best-known medicinal mushrooms in the world, produces more than 400 different bioactive compounds. However, the regulation of these bioactive compounds biosynthesis is still unclear. Lysine succinylation is a critical post-translational modification and has many important functions in all aspects of eukaryotic and prokaryotic cells. Although it has been studied for a long time, its function is still unclear in G. lucidum. In this study, a global investigation was carried out on the succinylome in G. lucidum.

Results: In total, 382 modified proteins which contain 742 lysine succinylated sites were obtained. The proteomics data are available through ProteomeXchange with the dataset accession number PXD013954. Bioinformatics analysis revealed that the succinylated proteins were distributed in various cellular biological processes and participated in a great variety of metabolic pathways including carbon metabolism and biosynthesis of secondary metabolites. Notably, a total of 47 enzymes associated with biosynthesis of triterpenoids and polysaccharides were found to be succinylated. Furthermore, two succinylated sites K90 and K106 were found in the conserved Fve region of immunomodulatory protein LZ8. These observations show that lysine succinylation plays an indispensable role in metabolic regulation of bioactive compounds in G. lucidum.

Conclusions: These findings indicate that lysine succinylation is related to many metabolic pathways, especially pharmacologically bioactive compounds metabolism. This study provides the first global investigation of lysine succinylation in G. lucidum and the succinylome dataset provided in this study serves as a resource to further explore the physiological roles of these modifications in secondary metabolism.

Keywords: Ganoderma lucidum; Immunomodulatory protein; Polysaccharides; Post-translational modification; Succinylome; Triterpenoids.

Fig. 1

Systematic analysis of lysine succinylation sites in G. lucidum. a Work flow used in this study. b Distributions of mass errors for all the succinylpeptides. c Distributions of all the modified peptides length

Fig. 2

Analysis the conservation of identified succinylproteins in G. lucidum. a The number of homologous succinylproteins in 7 species. b A pie chart showing the conservative orthologs in A. flavus, C. albicans, F. ananassa, H. capsulatum, P. aeruginosa, T. aestivum and V. parahemolyticus. The group classification criteria were as follows: Well-conserved, five to seven orthologous succinylproteins; Conserved, three to four orthologous succinylproteins; Poorly conserved, one to two orthologs; Novel, zero orthologs

Fig. 3

Properties of the modified peptides in G. lucidum. a A pie chart showing the percentage and number of succinylated residues per protein. b A heat map of the amino acid compositional frequencies surrounding the succinylated residues. c The modified peptides motifs containing ±10 amino acids surrounding the identified residues. d Number of succinylation sequence motifs. e Analysis the secondary structure of succinylproteins. f Predicted surface accessibility of succinylated residues

Fig. 4

Functional classification for the identified succinylproteins in G. lucidum. a Classification of succinylproteins based on their biological processes. b Classification of succinylproteins according to their molecular functions. c Classification of succinylproteins based on their cellular components. d Analysis the intracellular locations of the identified succinylproteins

Fig. 5

Enrichment analysis of succinylproteins based on KEGG pathway in G. lucidum

Fig. 6

PPI network of the succinylproteins in G. lucidum

Fig. 7

Working scheme of triterpenoid and polysaccharide biosynthesis. The succinylated proteins were highlighted in red. Enzyme annotations are included in Additional file 2: Table S10

Fig. 8

The structure of immunomodulatory protein LZ8. a An overview of succinylation sites in LZ8. b Three-dimensional structure of LZ8-LZ8 homodimer with succinylated sites K90 and K106. The structure was modeled from PDB database