EmhR is an indole‐sensing transcriptional regulator responsible for the indole‐induced antibiotic tolerance in Pseudomonas fluorescens

Abstract

Indole is well known as an interspecies signalling molecule to modulate bacterial physiology; however, it is not clear how the indole signal is perceived and responded to by plant growth promoting rhizobacteria (PGPR) in the rhizosphere. Here, we demonstrated that indole enhanced the antibiotic tolerance of Pseudomonas fluorescens 2P24, a PGPR well known for its biocontrol capacity. Proteomic analysis revealed that indole influenced the expression of multiple genes including the emhABC operon encoding a major multidrug efflux pump. The expression of emhABC was regulated by a TetR-family transcription factor EmhR, which was demonstrated to be an indole-responsive regulator. Molecular dynamics simulation showed that indole allosterically affected the distance between the two DNArecognizing helices within the EmhR dimer, leading to diminished EmhR-DNA interaction. It was further revealed the EmhR ortholog in Pseudomonas syringae was also responsible for indole-induced antibiotic tolerance, suggesting this EmhR-dependent, indole-induced antibiotic tolerance is likely to be conserved among Pseudomonas species. Taken together, our results elucidated the molecular mechanism of indole-induced antibiotic tolerance in Pseudomonas species and had important implications on how rhizobacteria sense and respond to indole in the rhizosphere.

A response regulator controls Acinetobacter baumannii virulence by acting as an indole receptor

“…There are several verified or potential indole effectors, which could be clearly classified into two categories based on cell of origin. The first category consists of some sensors, regulators, and enzymes in bacteria, including the two-component systems BaeSR and CpxAR in Escherichia coli ( 19 ), Le-QseC in Lysobacter enzymogenes ( 20 ), EmhR in Pseudomonas fluorescens ( 21 ), pyruvate kinase in Stigmatella aurantiaca ( 47 ), the RNA polymerase regulator protein DksA in Vibrio cholerae ( 23 ), and IsrR in enterohemorrhagic E. coli ( 48 ). The second category is the aryl hydrocarbon receptor (AHR) of host cells.…”

The Two-Component System RstA/RstB Regulates Expression of Multiple Efflux Pumps and Influences Anaerobic Nitrate Respiration in Pseudomonas fluorescens

“…The in-frame deletion mutants were constructed via double-crossover homologous recombination with the suicide plasmid pK18Km as reported previously ( 26 ). For each gene, both flank regions (longer than 1Kb) including 100 bp in-frame were PCR-amplified, respectively, and linked together using overlap PCR.…”

“…As P. fluorescens can be resistant to a wide spectrum of antibiotics ( 24 ), it is therefore urgent to better understand the multidrug-resistance mechanism of P. fluorescens . In P. fluorescens 2P24, the RND (resistance-nodulation-cell division) superfamily efflux pump EmhABC is characterized to be a key determinant to the resistance toward multiple antibiotics including ampicillin, chloramphenicol, and tetracycline ( 25 , 26 ). However, it is still elusive if there are any other efflux pumps responsible for the multidrug resistance and how these efflux pumps are regulated in P. fluorescens .…”

Bacterial survivors: evaluating the mechanisms of antibiotic persistence

“…Indole pulse signalling has been shown to generate E. coli quinolone persisters by targeting DNA gyrase, and indole production was not increased in response to the antibiotic stress [137]. In Pseudomonas fluorescens, exogenous indole that could come from the plant rhizosphere enhances persister formation via modulating efflux systems and protect this rhizobacterium from multiple antibiotics [138]. As a proton ionophore, indole inhibits E. coli cell division at a high concentration (3-5 mM) and regulates E. coli pH via pulse signalling [139,140].…”