Acetylome and Succinylome Profiling of Edwardsiella tarda Reveals Key Roles of Both Lysine Acylations in Bacterial Antibiotic Resistance

Abstract

The antibiotic resistance of Edwardsiella tarda is becoming increasingly prevalent, and thus novel antimicrobial strategies are being sought. Lysine acylation has been demonstrated to play an important role in bacterial physiological functions, while its role in bacterial antibiotic resistance remains largely unclear. In this study, we investigated the lysine acetylation and succinylation profiles of E. tarda strain EIB202 using affinity antibody purification combined with LC-MS/MS. A total of 1511 lysine-acetylation sites were identified on 589 proteins, and 2346 lysine-succinylation sites were further identified on 692 proteins of this pathogen. Further bioinformatic analysis showed that both post-translational modifications (PTMs) were enriched in the tricarboxylic acid (TCA) cycle, pyruvate metabolism, biosynthesis, and carbon metabolism. In addition, 948 peptides of 437 proteins had overlapping associations with multiple metabolic pathways. Moreover, both acetylation and succinylation were found in many antimicrobial resistance (AMR) proteins, suggesting their potentially vital roles in antibiotic resistance. In general, our work provides insights into the acetylome and succinylome features responsible for the antibiotic resistance mechanism of E. tarda, and the results may facilitate future investigations into the pathogenesis of this bacterium.

Keywords: Edwardsiella tarda; acetylome; antibiotic resistance; succinylome.

Figure 1

Profile of E. tarda lysine acetylation and succinylation proteome. (A) Distributions of mass errors for Kac and Ksu peptides. (B) Distributions of Kac and Ksu peptides based on their lengths. (C) Distributions of modified sites in Kac and Ksu proteins.

Figure 2

Motif analysis of acetylated and succinylated peptides in E. tarda. Venn diagram shows the overlapping peptides between the PTMs.

Figure 3

Subcellular localization prediction and GO annotation analysis of acetylated/succinylated-lysine proteins in E. tarda strain EIB 202. (A) Subcellular localization of the identified Kac and Ksu proteins. (B–D) GO annotation analysis of the identified Kac and Ksu proteins in terms of biological process, cell components, and molecular function.

Figure 4

KEGG pathway overlap between lysine acetylation and succinylation in E. tarda. Venn diagram displaying the overlapping peptides and proteins between the two PTMs. The orange, purple, and blue regions represent the KEGG pathways related to unique acetylated, overlapping, and unique succinylated proteins, respectively.

Figure 5

Prediction of protein-protein interaction networks of lysine acetylation and succinylation proteins in E. tarda. There were five highly metabolic pathways of PTM proteins were enriched in the global PPI network, such as, (A) ribosome, (B) aminoacyl-tRNA biosynthesis, (C) oxidative phosphorylation, (D) RNA degradation, (E) pentose phosphate pathway. Different colors display different modifications; the pink and red cycles represent the proportions of Kac and Ksu modifications in single proteins, respectively.

Figure 6

Analysis of protein-protein interaction networks of 66 AMR proteins in E. tarda. The pink and red cycles represent the proportions of Kac and Ksu modifications in single AMR proteins, respectively.