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

Wu N, He L, Cui P, Wang W, Yuan Y, Liu S, Xu T, Zhang S, Wu J, Zhang W, Zhang Y - Front Microbiol (2015)

Bottom Line: We found that oxyR, dnaK, sucB, relA, rpoS, clpB, mqsR, and recA were prominent persister genes involved in persistence to multiple antibiotics.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.These findings have implications for improved understanding of persistence phenomenon and developing new drugs targeting persisters for more effective cure of persistent infections.

View Article: PubMed Central - PubMed

Affiliation: Key Lab of Molecular Virology, Institute of Medical Microbiology, Department of Infectious Diseases, Huashan Hospital, Fudan University Shanghai, China.

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.

No MeSH data available.


Related in: MedlinePlus

Deletion mutant ranking depends on cell survival over time under conditions of gentamicin exposure. Stationary phase cultures of W3110 and single-gene mutants were diluted 100-fold and exposed to 20 μg/ml gentamicin for 0.5, 1, and 2 h. The data for each mutant was plotted and compared with that of W3110. Error bars indicate the standard deviation (n = 3). The asterisk indicates statistical significance as determined using Mann–Whitney U tests (∗P < 0.05).
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Figure 3: Deletion mutant ranking depends on cell survival over time under conditions of gentamicin exposure. Stationary phase cultures of W3110 and single-gene mutants were diluted 100-fold and exposed to 20 μg/ml gentamicin for 0.5, 1, and 2 h. The data for each mutant was plotted and compared with that of W3110. Error bars indicate the standard deviation (n = 3). The asterisk indicates statistical significance as determined using Mann–Whitney U tests (∗P < 0.05).

Mentions: When stationary phase cells were transferred to fresh medium, considerably fewer gentamicin-tolerant persisters were alive after 4 h. All of the mutant cells were completely killed by gentamicin in 8 h including the wild-type strain (data not shown). Given the rapid sterilization by gentamicin, we ranked these mutants 0.5 h onward. After 2 h treatment, gentamicin effectively sterilized rpoS, smpB, phoU, oxyR, and dnaK mutants and the number of CFU dropped below the detection limit, whereas the wild-type strain had about 2.3 × 102 (0.001%) viable bacteria left. Interestingly, unlike the high persistence during ampicillin and norfloxacin treatment, we found that deletion of rpoS caused a significant decrease in persister levels when the mutant was subjected to gentamicin compared with the parent strain (Figure 3).


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

Wu N, He L, Cui P, Wang W, Yuan Y, Liu S, Xu T, Zhang S, Wu J, Zhang W, Zhang Y - Front Microbiol (2015)

Deletion mutant ranking depends on cell survival over time under conditions of gentamicin exposure. Stationary phase cultures of W3110 and single-gene mutants were diluted 100-fold and exposed to 20 μg/ml gentamicin for 0.5, 1, and 2 h. The data for each mutant was plotted and compared with that of W3110. Error bars indicate the standard deviation (n = 3). The asterisk indicates statistical significance as determined using Mann–Whitney U tests (∗P < 0.05).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4588708&req=5

Figure 3: Deletion mutant ranking depends on cell survival over time under conditions of gentamicin exposure. Stationary phase cultures of W3110 and single-gene mutants were diluted 100-fold and exposed to 20 μg/ml gentamicin for 0.5, 1, and 2 h. The data for each mutant was plotted and compared with that of W3110. Error bars indicate the standard deviation (n = 3). The asterisk indicates statistical significance as determined using Mann–Whitney U tests (∗P < 0.05).
Mentions: When stationary phase cells were transferred to fresh medium, considerably fewer gentamicin-tolerant persisters were alive after 4 h. All of the mutant cells were completely killed by gentamicin in 8 h including the wild-type strain (data not shown). Given the rapid sterilization by gentamicin, we ranked these mutants 0.5 h onward. After 2 h treatment, gentamicin effectively sterilized rpoS, smpB, phoU, oxyR, and dnaK mutants and the number of CFU dropped below the detection limit, whereas the wild-type strain had about 2.3 × 102 (0.001%) viable bacteria left. Interestingly, unlike the high persistence during ampicillin and norfloxacin treatment, we found that deletion of rpoS caused a significant decrease in persister levels when the mutant was subjected to gentamicin compared with the parent strain (Figure 3).

Bottom Line: We found that oxyR, dnaK, sucB, relA, rpoS, clpB, mqsR, and recA were prominent persister genes involved in persistence to multiple antibiotics.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.These findings have implications for improved understanding of persistence phenomenon and developing new drugs targeting persisters for more effective cure of persistent infections.

View Article: PubMed Central - PubMed

Affiliation: Key Lab of Molecular Virology, Institute of Medical Microbiology, Department of Infectious Diseases, Huashan Hospital, Fudan University Shanghai, China.

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.

No MeSH data available.


Related in: MedlinePlus