Lysine acetylation regulates antibiotic resistance in Escherichia coli

Abstract

Antibiotic resistance is increasingly becoming a serious challenge to public health. The regulation of metabolism by post-translational modifications (PTMs) has been widely studied; however, the comprehensive mechanism underlying the regulation of acetylation in bacterial resistance against antibiotics is unknown. Herein, with Escherichia coli as the model, we performed quantitative analysis of the acetylated proteome of wild-type sensitive strain (WT) and ampicillin- (Re-Amp), kanamycin- (Re-Kan), and polymyxin B-resistant (Re-Pol) strains. Based on bioinformatics analysis combined with biochemical validations, we found that a common regulatory mechanism exists between the different resistant strains. Acetylation negatively regulates bacterial metabolism to maintain antibiotic resistance, but positively regulates bacterial motility. Further analyses revealed that key enzymes in various metabolic pathways were differentially acetylated. Particularly, pyruvate kinase (PykF), a key glycolytic enzyme regulating bacterial metabolism, and its acetylated form were highly expressed in the three resistant types and were identified as reversibly acetylated by the deacetylase CobB and the acetyl-transferase PatZ, and also could be acetylated by non-enzyme AcP in vitro. Further, the deacetylation of Lys413 of PykF increased the enzyme activity by changing the conformation of ATP binding site of PykF, resulting in an increase in energy production, which in turn increased the sensitivity of drug-resistant strains to antibiotics. This study provides novel insights for understanding bacterial resistance and lays the foundation for future research on regulation of acetylation in antibiotic-resistant strains.ImportanceThe misuse of antibiotics has resulted in an emergence of a large number of antibiotic-resistant strains, which seriously threaten human health. Bacterial metabolism is tightly controlled by protein post-translational modifications, especially acetylation. However, the comprehensive mechanism underlying regulation of acetylation in bacterial resistance remains unexplored. Here, acetylation was found to positively regulate bacterial motility and negatively regulate energy metabolism, which was common in all the different antibiotic-resistant strains. Moreover, the acetylation and deacetylation process of PykF was uncovered, and deacetylation of the Lys 413 of PykF was found to contribute to bacterial sensitivity to antibiotics. This study provides a new direction for research on development of bacterial resistance through post-translational modifications and provides a theoretical basis for the development of antibacterial drugs.

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

“…Furthermore, homologs for at least nine Kac or Ksu E. tarda proteins have been reported to be related to antibiotic resistance in other bacterial species ( Table 1 ). For example, there are at least three Kac sites at K76, K413, and K445 of pyruvate kinase PykF in E. coli , and the deacetylation of Lys413 in PykF was found to contribute to bacterial sensitivity to antibiotics such as ampicillin and polymyxin B [ 17 ]. These proteins were also found to be lysine acetylated or succinylated in our E. tarda data, though the modification sites might have differed, suggesting that lysine acylated proteins may have unique characteristics in E. tarda antibiotic resistance.…”

“…Moreover, common lysine acylations such as Kac and Ksu modifications were reported to be involved in bacterial antibiotic resistance, as well. For example, Fang et al proposed that the deacetylation of the K413 site of Escherichia coli PykF led to the bacterium becoming sensitive to ampicillin, polymyxin B, and kanamycin by increasing the enzyme activity [ 17 ]. In addition to this, the accumulation of succinyl-CoA in the sucC mutant was reported to increase the methicillin-resistant Staphylococcus aureus (MRSA) succinylome and thereby increase the susceptibility to beta-lactam antibiotics [ 18 ].…”