Ranking of persister genes in the same Escherichia coli genetic background demonstrates varying importance of individual persister genes in tolerance to different antibiotics

Nan Wu,Jing Wu,Wenjie Wang,Tao Xu,Peng Cui,Youhua Yuan,Ying Zhang,Lei He,Shanshan Zhang,Shuang Liu,Wenhong Zhang

doi:10.3389/fmicb.2015.01003

Nan Wu, Jing Wu + Show 9 more

Open Access

https://doi.org/10.3389/fmicb.2015.01003

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Abstract

Despite the identification of many genes and pathways involved in the persistence phenomenon of bacteria, the relative importance of these genes in a single organism remains unclear. Here, using Escherichia coli as a model, we generated mutants of 21 known candidate persister genes and compared the relative importance of these mutants in persistence to various antibiotics (ampicillin, gentamicin, norfloxacin, and trimethoprim) at different times. We found that oxyR, dnaK, sucB, relA, rpoS, clpB, mqsR, and recA were prominent persister genes involved in persistence to multiple antibiotics. These genes map to the following pathways: antioxidative defense pathway (oxyR), global regulators (dnaK, clpB, and rpoS), energy production (sucB), stringent response (relA), toxin–antitoxin (TA) module (mqsR), and SOS response (recA). Among the TA modules, the ranking order was mqsR, lon, relE, tisAB, hipA, and dinJ. Intriguingly, rpoS deletion caused a defect in persistence to gentamicin but increased persistence to ampicillin and norfloxacin. Mutants demonstrated dramatic differences in persistence to different antibiotics at different time points: some mutants (oxyR, dnaK, phoU, lon, recA, mqsR, and tisAB) displayed defect in persistence from early time points, while other mutants (relE, smpB, glpD, umuD, and tnaA) showed defect only at later time points. These results indicate that varying hierarchy and importance of persister genes exist and that persister genes can be divided into those involved in shallow persistence and those involved in deep persistence. Our findings suggest that the persistence phenomenon is a dynamic process with different persister genes playing roles of variable significance at different times. These findings have implications for improved understanding of persistence phenomenon and developing new drugs targeting persisters for more effective cure of persistent infections.

Highlights

Materials and MethodsPersisters are a small subpopulation of generally quiescent bacterial cells that are tolerant to bactericidal antibiotics (Lewis, 2010)
The 11 genes could be divided into three groups according to the time points when a significant defect in persistence was observed, suggesting that different persister genes play roles of variable importance at different time points during the persistence phenomenon
These findings suggest that the persistence phenomenon is not a fixed feature but rather is hierarchical and dynamic in nature, which is consistent with our previous study on the persister gene phoU (Li and Zhang, 2007)

Summary

Introduction

Materials and MethodsPersisters are a small subpopulation of generally quiescent bacterial cells that are tolerant to bactericidal antibiotics (Lewis, 2010). Other genes involved in persistence are found in the pathways of stringent response (Korch et al, 2003), SOS response (Debbia et al, 2001; Dorr et al, 2009), energy metabolism (Ma et al, 2010; Girgis et al, 2012), global regulators such as PhoU (Li and Zhang, 2007), trans-translation (Shi et al, 2011; Li et al, 2013) and signaling pathways (Vega et al, 2012) These findings suggest that persistence is a very complex phenomenon with redundant mechanisms. We hypothesize that not all persister genes are created equal and that different persister genes may play a different role under different conditions

Results

Discussion

Conclusion