Adaptation and compensation in a bacterial gene regulatory network evolving under antibiotic selection

Abstract

Gene regulatory networks allow organisms to generate coordinated responses to environmental challenges. In bacteria, regulatory networks are re-wired and re-purposed during evolution, though the relationship between selection pressures and evolutionary change is poorly understood. In this study, we discover that the early evolutionary response of Escherichia coli to the antibiotic trimethoprim involves derepression of PhoPQ signaling, an Mg2+-sensitive two-component system, by inactivation of the MgrB feedback-regulatory protein. We report that derepression of PhoPQ confers trimethoprim-tolerance to E. coli by hitherto unrecognized transcriptional upregulation of dihydrofolate reductase (DHFR), target of trimethoprim. As a result, mutations in mgrB precede and facilitate the evolution of drug resistance. Using laboratory evolution, genome sequencing, and mutation re-construction, we show that populations of E. coli challenged with trimethoprim are faced with the evolutionary ‘choice’ of transitioning from tolerant to resistant by mutations in DHFR, or compensating for the fitness costs of PhoPQ derepression by inactivating the RpoS sigma factor, itself a PhoPQ-target. Outcomes at this evolutionary branch-point are determined by the strength of antibiotic selection, such that high pressures favor resistance, while low pressures favor cost compensation. Our results relate evolutionary changes in bacterial gene regulatory networks to strength of selection and provide mechanistic evidence to substantiate this link.

The Sub-Inhibitory Effect of Azithromycin and Ciprofloxacin on VirF Gene Expression in Enteroinvasive Escherichia Coli and Shigella Flexneri

“…In antibiotic stress conditions, alterations in gene expression in genes involved in surface structures, re ux systems, and enzymes linked to antibiotic inactivation, have been observed. The regulation of these genes are usually under control of bacterial sensory systems (10,24). A substantial increase in the expression of the virF of Shigella and EIEC was seen in response to cipro oxacin Sub-MICs in our study.…”

“…In some bacteria, similar responses to other environmental stresses such as antimicrobial pressure have been shown (10,11).…”

Evolutionary innovation through transcription factor promiscuity in microbes is constrained by pre-existing gene regulatory network architecture

“…These have a dual effect, both hyperactivating the NtrB kinase, and strongly upregulating ntrBC expression through their positive autoregulatory loop. Mutational loss of a negative repressor leading to overactivity and overexpression of a positively autoregulated transcription factor has also been observed to drive adaptation in several experimental and clinical settings 35,64,65 . In contrast, we have identified that to achieve the same effect of high activity and high expression in PFLU1131/2, multiple mutations were required.…”

Evaluation of Mycobacterium tuberculosis associated with treatment failure for intrinsic and efflux pump mediated resistance: a comparative retro perspective cohort study

“…Similarly, activation of two component regulatory systems linked to e ux pumps such as PhoPQ, PmrA, in response to therapeutics were proposed to mediate drug resistance in many bacteria [32,33]. Two component regulatory systems are activated in the response of environmental stimuli [34]. In vivo, environment is complex and can vary from patient to patient depending upon the disease status, co morbidity and use of other drugs.…”