The QseB response regulator imparts tolerance to positively charged antibiotics by controlling metabolism and minor changes to LPS

Abstract

The modification of lipopolysaccharide (LPS) in Escherichia coli and Salmonella spp. is primarily controlled by the two-component system PmrAB. LPS modification allows bacteria to avoid killing by positively charged antibiotics like polymyxin B. We previously demonstrated that in uropathogenic E. coli (UPEC), the sensor histidine kinase PmrB also activates a non-cognate transcription factor, QseB, and this activation somehow augments polymyxin B tolerance in UPEC. Here, we demonstrate – for the first time – that in the absence of the canonical LPS transcriptional regulator, PmrA, QseB can direct some modifications on the LPS. In agreement with this observation, transcriptional profiling analyses demonstrate regulatory overlaps between PmrA and QseB in terms of regulating LPS modification genes. However, both PmrA and QseB must be present for UPEC to mount robust tolerance to polymyxin B. Transcriptional and metabolomic analyses also reveal that QseB transcriptionally regulates the metabolism of glutamate and 2-oxoglutarate, which are consumed and produced during the modification of lipid A. We show that deletion of qseB alters glutamate levels in the bacterial cells. The qseB deletion mutant, which is susceptible to positively charged antibiotics, is rescued by exogenous addition of 2-oxoglutarate. These findings uncover a previously unknown mechanism of metabolic control of antibiotic tolerance that may be contributing to antibiotic treatment failure in the clinic.

Point mutations in the ygiV promoter region lead to cystobactamid resistance and reduced virulence in E. coli

“…20,21,22 This upregulation of proteins, potentially causing cationic peptide resistance due to positively charged membrane modifications, can be explained as a downstream effect of detected QseB overexpression, which is known to influence the expression of ArnA, ArnC and EptC. 20 This overexpression of QseB in CYS R mutant bacteria was very likely caused by the identified mutations (Table 2), suggesting a shared transcriptional regulatory region between ygiVW and qseBC. 17 However, no cross-resistance to colistin and polymyxin B was identified, which led us to conclude that, although being significantly upregulated, these membrane modifying proteins only play a minor role contributing to the CYS resistance phenotype of E. coli, further highlighting a very specific mode of resistance that occurs also independent of qseC mutation (Supplementary Table 2).…”

“…3b). 20,21,22 This upregulation of proteins, potentially causing cationic peptide resistance due to positively charged membrane modifications, can be explained as a downstream effect of detected QseB overexpression, which is known to influence the expression of ArnA, ArnC and EptC. 20 This overexpression of QseB in CYS R mutant bacteria was very likely caused by the identified mutations (Table 2), suggesting a shared transcriptional regulatory region between ygiVW and qseBC.…”

Multiple regulatory inputs including cell envelope stress orchestrate expression of the Escherichia coli rpoN operon

“…Therefore, we focused on transcription factors that respond to LPS deficiency or other stimuli found to activate lptA expression and/or mediate resistance to these stressors. This list included the response regulators BasR, PhoB, PhoP, QseB, QseF, RcsB and ZraR, which have known or proposed roles in ESR pathways (Bader et al, 2005;Choudhary et al, 2020;Hurst et al, 2023;Kato et al, 1999;Klein et al, 2016;Lee et al, 2005;Leonhartsberger et al, 2001;Reichenbach et al, 2009;Ren et al, 2016;Rome et al, 2018;Winfield & Groisman, 2004).…”