Antibiotic tolerance is associated with a broad and complex transcriptional response inE. coli

Abstract

In a given bacterial population, antibiotic treatment will kill a large portion of the population, while a small, tolerant subpopulation will survive. Tolerant cells disrupt the efficacy of antibiotic treatment and increase the likelihood that a population gains antibiotic resistance. When a population becomes resistant, antibiotic treatment fails, which is a major health concern. Since antibiotic tolerance often leads to resistance, we have taken a systems biology approach to examine how transcriptional networks respond to antibiotic stress so that cells can survive and recover after antibiotic treatment. We have compared gene expression with and without ampicillin in E. coli. While many previous studies have identified aspects of the antibiotic stress response at either the protein or transcriptional level, our work leverages existing knowledge of transcriptional regulation to link the dynamics of the two allowing for a more holistic approach. Here, we are the first to develop a whole-cell, transcriptional regulatory network (TRN) of antibiotic tolerant subpopulations and examine how cells respond at the transcriptional level to bactericidal concentrations of an antibiotic. Using TRN analysis, we show how certain sigma and transcription factors are affecting transcriptional regulation under antibiotic stress, and that changes in gene expression specific to ampicillin treatment can be directly linked to cell survival and recovery. The resulting network demonstrates that cells are mounting an active and coordinated response to the antibiotic that spans multiple systems and pathways. The redundancy and interconnectivity of the networks suggest that accounting for whole-cell dynamics may be crucial when modeling and studying antibiotic tolerance in the future.

Bacterial degrons in synthetic circuits

“…This is due to the mismatch between the cell’s relatively low number of proteases and the high number of proteins (table 1). Proteolytic queueing has been observed in wild-type bacteria during stress conditions and linked to up-regulation of the sigma factors σ S and σ 32 [24,174–177]. It is also associated with antibiotic survival strategies [177,178].…”

The transcription factor network of E. coli steers global responses to shifts in RNAP concentration

“…It has been shown that global regulators (9)(10)(11)(12), DNA supercoiling (13) and small RNAs (14), among other, can select large cohorts of stress-specific, responsive genes. It was also reported that 60%-90% of E. coli genes respond to changing growth conditions following a constant global scaling factor (15).…”

Antibiotic tolerance, persistence, and resistance of the evolved minimal cell,Mycoplasma mycoidesJCVI-Syn3B

“…In our recent work, we demonstrate that antibiotic tolerance in Escherichia coli is a whole-cell response and can occur through multiple pathways or networks, which may work simultaneously and cooperatively to survive against antibiotics (Deter et al, 2020). Our strategy to study the underlying mechanisms of persistence was to use a bacterial species that contains mainly essential genes and networks with reduced complexity and fewer networks.…”

“…This result is also coherent with our recently published data, which established that interfering with protein degradation by forming a proteolytic queue at ClpXP will increase tolerance levels dramatically (Deter et al, 2019a). Transcriptomic analysis of queuing-tolerant population showed upregulation of genes related to metabolism and energy (Deter et al, 2020b). However, other studies reported that ppGpp and ATP reduction are not essential for persistence (Bhaskar et al, 2018; Chowdhury et al, 2016; Pontes and Groisman, 2019).…”

“…Since persistence and tolerance are present in phylogenetically diversified bacterial species (Meylan et al, 2018; Wilmaerts et al, 2019b), it is feasible that an underlying genetic mechanism is conserved in evolutionarily related microorganisms, and the most likely candidates are essential genes or the disruption of crucial networks. In our recent work, we demonstrate that antibiotic tolerance in Escherichia coli may result from a whole-cell response and can occur through multiple pathways or networks, which may work simultaneously and cooperatively to survive against antibiotics (Deter et al, 2020b).…”