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Journal of Bacteriology, May 2006, p. 3494-3497, Vol. 188, No. 10
0021-9193/06/$08.00+0 doi:10.1128/JB.188.10.3494-3497.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Increased Persistence in Escherichia coli Caused by Controlled Expression of Toxins or Other Unrelated Proteins
Nora Vázquez-Laslop,*
Hyunwoo Lee, and
Alexander A. Neyfakh
Center for Pharmaceutical Biotechnology, University of Illinois, Chicago, Illinois 60607
Received 16 January 2006/
Accepted 7 March 2006

ABSTRACT
Bacterial populations contain persisters, cells which survive
exposure to bactericidal antibiotics and other lethal factors.
Persisters do not have a genetic resistance mechanism, and their
means to tolerate killing remain unknown. In exponentially growing
populations of
Escherichia coli the frequency of persister formation
usually is 10
7 to 10
5. It has been shown that
cells overexpressing either of the toxic proteins HipA and RelE,
both members of the bacterial toxin-antitoxin (TA) modules,
have the ability to form more persisters, suggesting a specific
role for these toxins in the mechanism of persistence. However,
here we show that cells expressing proteins that are unrelated
to TA modules but which become toxic when ectopically expressed,
chaperone DnaJ and protein PmrC of
Salmonella enterica, also
form 100- to 1,000-fold more persisters. Thus, persistence is
linked not only to toxicity caused by expression of HipA or
dedicated toxins but also to expression of other unrelated proteins.

INTRODUCTION
A small number of cells in a bacterial population can survive
treatment with lethal concentrations of bactericidal antibiotics.
These survivors, which appear with a frequency of

10
6,
are known as persisters (
3). The nature of their tolerance to
killing and the molecular mechanisms triggering the persister
state remain unknown.
Persisters do not have a genetic resistance mechanism, and their progeny are fully sensitive to antibiotics (3, 14, 18). The only gene that has been linked to persistence in Escherichia coli has been hipA (4, 5, 15, 16, 19, 20, 23). A mutation in this gene, the hipA7 mutation, was identified because cells carrying this mutant gene formed persisters at a higher frequency (101 to 103) compared to the wild-type strain (16, 19, 23). The high frequency of persister formation is not restricted to cells with the chromosomal hipA7 mutation; it has also been shown for cells overexpressing the toxic wild-type HipA (4, 7, 16, 20). Cells expressing this protein form 10- to 1,000-fold more persisters tolerant to bactericidal antibiotics with different mechanisms of actions, such as ampicillin and ciprofloxacin (7).
It has been suggested that the hipA gene, encoding the toxic factor, together with hipB, encoding a putative antidote, constitutes one of the several toxin-antitoxin (TA) modules present in bacteria (8, 9). Similar to typical TA operons, like relBE and mazEF, hipB and hipA are organized in an operon with the gene encoding the antitoxin, hipB, located upstream of hipA, the toxin gene (4, 5, 8, 9).
It has been shown recently that, similar to HipA, cells overproducing the toxin RelE, another member of a TA module, form 10- to 10,000-fold more persisters (15). Both proteins, HipA and RelE, have the effect of slowing down or even stopping cell division, raising the possibility that toxins from the TA modules have a role in increasing the fraction of dormant or nongrowing cells in a population, the fraction, it has been suggested, that constitute the persister cells (2, 3, 14, 15, 18). The various roles in cell physiology of toxins RelE and MazF are most likely related to their specific activity in inhibiting translation by cleaving mRNA at particular sites (6, 21). It is unclear, however, whether the increase in the number of persisters observed when HipA (7) or RelE (15) is overexpressed from plasmids is a result of a specific dedicated role of these toxins in the mechanism of forming persisters. It is known that expression of a wide variety of recombinant proteins, even those that are not dedicated toxins, often has a detrimental effect on the growth of bacteria (11). Evidently, most of these proteins share no homology in sequence, gene organization, or function with the toxins of the TA modules, and thus their effects on cell physiology are probably of a different nature.
In this work, we asked whether the increase in frequency of persister formation is specific to cells overexpressing toxins from the TA modules or if cells expressing proteins that become toxic when produced from plasmids would also show high persistence.

MATERIALS AND METHODS
Strains and plasmids.
Plasmids pBAD
18CM and pBAD
22CM were used as cloning vectors
for expression of
E. coli genes
thrB,
dnaJ,
mazF, and
hipA and
Salmonella enterica gene
pmrC. pBAD
CM plasmids were prepared
by replacing the ampicillin resistance gene with the chloramphenicol
resistance gene. Genes to be cloned were PCR amplified using
pairs of primers (Table
1) and high-fidelity AccuPrime
Taq DNA
polymerase (Invitrogen). DNA from
E. coli strain MG1655 was
prepared using a genomic DNA isolation kit (Sigma; catalog no.
NA2120) and used as a template for amplification of
hipA,
mazF,
dnaJ, and
thrB. p
pmrC plasmid (
17) carrying the
pmrC gene of
Salmonella enterica serovar Typhimurium 14028s was used as a
template for PCR amplification of
pmrC. The amplified PCR products
were cut with the appropriate restriction enzymes and cloned
in the corresponding sites of the vector plasmids (Table
1).
Escherichia coli strain LMG194 (F
lacX74 galE thi rpsL
phoA (PvuII)
ara714 leu::Tn
10) was used as the host strain for
the empty vector pBAD
22CM and all the constructs described in
Table
1.
Determination of the effect of protein overexpression on the different strains.
LMG194 cells carrying pBADCM plasmids were streaked on Luria-Bertani (LB) agar plates containing 0.2% glucose and 25 µg/ml chloramphenicol. Overnight cultures were grown from single colonies in RMG minimal medium (2% Casamino Acids, 1x M9 salts, 1 mM MgCl2, and 1% glycerol) supplemented with 25 µg/ml chloramphenicol (RMG-CM). Aliquots of 0.85 ml were mixed with 0.15 ml of sterile glycerol, snap-frozen in a dry ice-ethanol bath, and kept at 80°C.
For the protein expression experiments, cultures were started from these glycerol stocks. After an overnight growth in RMG-CM medium, cultures were diluted 100-fold into 30 ml of fresh medium in 125-ml Erlenmeyer flasks. Flasks were shaken at 160 rpm in a platform shaker (Innova 2300; New Brunswick Scientific) at 37°C. When cell densities of the cultures reached an optical density at 600 nm (OD600) of
0.15, 3- to 5-ml aliquots were transferred to 30- by 115-mm conical plastic tubes. Arabinose was added at different concentrations for an adequate time period (see below). Tubes were placed at an inclination of 45°, and shaking continued under the same conditions. Cell growth was determined by monitoring the OD600. The numbers of viable cells (CFU) in the cultures, before and after the addition of arabinose, were determined as follows. Ten-microliter aliquots were serially diluted in a 10-fold fashion. One hundred-microliter aliquots from these dilutions were plated on LB agar-chloramphenicol plates and kept overnight at 37°C. Due to the toxicity of the proteins expressed, a drop in the cell counts was expected. Therefore, it was important to carry out a wide range of dilutions in order to use the adequate ones to reliably determine CFU.
Determination of persistence frequency in cells overexpressing proteins.
To determine the number of persisters formed by cells expressing proteins from pBAD vectors, cells were grown and protein expression was induced as described above. We found that keeping these conditions was critical to obtain reproducible persistence frequencies between experiments. Similar observations about different factors influencing reproducibility of the persistence frequency have been reported previously (15). An antibiotic, ampicillin (Fisher Scientific BP1760) or ciprofloxacin (Bayer Co.), was added from stock solutions to a final concentration of 100 µg/ml or 0.4 µg/ml, respectively. Incubation continued for 4 h. Chloramphenicol (25 µg/ml) was kept throughout the experiments to ensure the stability of the plasmids. In order to determine viable-cell counts in the cultures after incubation with the antibiotics, 1-ml aliquots were removed and cells were spun and resuspended in fresh medium without antibiotics. Determination of viable cells was performed as described above. Persistence frequency was calculated by dividing the number of CFU/ml in the culture after incubation with the antibiotic by the number of CFU/ml in the culture before adding the antibiotic.

RESULTS AND DISCUSSION
Cells overexpressing toxins from TA modules show an increase
in persistence frequency (
4,
7,
15,
16,
20). Here we asked if
expression of proteins that become toxic when ectopically produced
also results in a higher frequency of persister formation. In
order to test this, we chose to express in
E. coli cells, in
parallel to the toxins from the TA modules HipA and MazF, two
unrelated proteins. One was protein DnaJ from the chaperone
system DnaJ/DnaK/GrpE (
12), which becomes toxic when overexpressed
from a high-copy-number plasmid (
http://ecoli.aist-nara.ac.jp/gb5/Resources/archive/archive.html).
The second protein, PmrC from
Salmonella enterica serovar Typhimurium
14028s, an enzyme that transfers phosphoethanolamine to lipid
A, is also toxic to
E. coli cells when expressed from a plasmid
(
17). In addition, ectopic expression of
thrB was used as a
control, since threonine B, a component of homoserine kinase,
can be produced to high levels with no detrimental consequences
for cell growth (
13).
Due to the expected differential toxicity of the proteins, it was important to express them in a tightly regulated system. The PCR-amplified genes hipA, mazF, and dnaJ (from E. coli K-12 strain MG1655) and pmrC (from the ppmrC plasmid described in reference 17) were cloned under the control of the ParaBAD promoter into the pBADCM vector, carrying a chloramphenicol resistance determinant (see above). E. coli LMG194 cells unable to metabolize L-arabinose (10) were transformed with the obtained expression plasmids and were grown in RM minimal medium supplemented with 1% glycerol and chloramphenicol (25 µg/ml). In this expression system, the activity of the PBAD promoter could be tightly controlled by the concentration of arabinose, and the basal levels of expression of the cloned genes are negligible (10).
To test how expression of the cloned genes affects cell growth, arabinose at a final concentration of 0.2% was added to logarithmically growing cultures at 37°C. Overexpression of the control protein ThrB slowed down the growth rate of the cells in a relatively mild fashion. In contrast, expression of toxins HipA and MazF, as well as proteins DnaJ and PmrC, caused a complete growth arrest after some time at this saturating concentration of inducer (Fig. 1A). The toxic effect of the toxins HipA and MazF or the proteins DnaJ and PmrC on dividing cells could be reached at different levels of induction and, generally, could be bacteriostatic or bactericidal. This fact makes difficult the analysis and interpretation of any experiments comparing cells producing these proteins. In the case of TA module proteins, it has been reported that ectopic overexpression of MazF may have a lethal effect depending on the conditions and duration of the toxin expression (1, 22). Similarly, overproduction of HipA has been shown to cause occasional lysis of the cells (16). No information in this regard was available for the effect of overexpressing DnaJ or PmrC. Therefore, it was important to adjust the expression of the different proteins so that they would produce comparably mild inhibitory effects on the growth rate of the cells. In order to achieve this, logarithmically growing cultures of each strain were induced with different concentrations of arabinose. The densities (OD600) and numbers of viable cells (CFU) of the cultures were determined over time (not shown). Based on these data, induction conditions were chosen under which expression of the cloned proteins caused a minimal but evident decrease in the culture densities compared to the uninduced controls. Under these conditions, protein expression barely affected (strain with empty vector and strains expressing ThrB, PmrC, and MazF) or decreased only moderately (strains expressing DnaJ and HipA) the number of viable cells in the cultures (Fig. 1B). The level of protein expression in these cultures was examined by gel electrophoresis (not shown). A 34-kDa band corresponding to ThrB could be clearly identified, in agreement with the fact that ThrB can reach high expression levels without having any important effect on the growth rate or the number of cells (Fig. 1). In contrast, no bands could be detected for either DnaJ, PmrC, MazF, or HipA on Coomassie-stained gels. This suggests that the toxic effect of all these proteins is attained at low levels of induction. It should be noted that at low level of induction protein expression may vary between individual cells (24).
The frequency of persister formation in cells expressing proteins
under the conditions described above was determined. In order
to do this, bactericidal antibiotics with unrelated mechanisms
of action, ampicillin and ciprofloxacin, were used. Logarithmically
growing cells were induced with adequate concentrations of arabinose
for 1 (strains expressing ThrB, HipA, MazF, or PmrC or carrying
an empty vector) or 2 h (DnaJ-producing strain). The induced
cultures were then challenged with either 0.4 µg/ml of
ciprofloxacin or 100 µg/ml of ampicillin for 4 h. In order
to determine persistence frequency in the induced cultures,
a fraction of the cells before and after the antibiotic treatment
were washed with fresh medium and plated on LB agar-chloramphenicol
plates containing 0.2% glucose to prevent any further production
of the toxins. The frequency of persister formation was also
determined for each strain grown in the absence of inducer.
Figure
2 shows the ratios of the frequency of appearance of
persisters in strains overproducing the cloned protein compared
to the frequency in the absence of the inducer. Overexpression
of the control protein ThrB, which showed only a mild negative
effect on the growth of the cells, did not significantly increase
the frequency of persisters. In contrast, strains expressing
at limited induction levels members of the TA pairs MazF and
HipA increased the frequency of formation of both ampicillin
and ciprofloxacin persisters 100- to 10,000-fold. Remarkably,
a similar increment of persistence was also detected for the
strains expressing the chaperone DnaJ or even the foreign protein
PmrC (100- to 1,000-fold), under comparably low levels of induction.
These results show that, at least in the mid-log-phase cells
used for these experiments, the increase in number of persisters
is not unique to strains expressing HipA or other dedicated
toxins. Instead, cells expressing proteins totally unrelated
to the TA modules, which become toxic when ectopically expressed,
also have the ability to form more persisters. It has been suggested
that the formation of persisters during stationary phase is
highly dependent on the
hipBA locus, since its deletion causes
a sharp drop in persister formation during this stage (
15).
However, to the best of our knowledge, no systematic effort
to study the effect of other gene deletions on persistence of
stationary-phase cells has been reported. Therefore, it is possible
that deletions of genes other than
hipA might also have the
effect of diminishing persistence frequency.
One of the main questions about the phenomenon of persistence
is whether bacterial cells have evolved a dedicated mechanism
that allows them to survive lethal stresses including exposure
to bactericidal antibiotics. Such a mechanism may potentially
be based on a deliberate or sporadic expression of toxin proteins
from the TA modules in a small fraction of cells to maintain
them in a dormant or nongrowing stress-tolerant state (
9,
15,
18). However, our findings suggest that limited levels of induction
of unrelated proteins also increase persistence. Deleterious
effects of such proteins will be attained at different intracellular
concentrations, and the mechanism of their toxicity will likely
have nonspecific targets. Given the low frequency of persisters
in a wild-type population (

10
6), it is conceivable that
stochastic variations or illicit gene expression would lead
to rare toxic levels of a broad variety of proteins in a small
fraction of cells, increasing their chances to become persisters.

ACKNOWLEDGMENTS
We are grateful to G. H. Araia for excellent technical assistance.
The critical reading of the manuscript by A. S. Mankin is greatly
appreciated.
This work was supported by Public Health Service grants AI-049214 and AI- 056575 from the National Institute of Allergy and Infectious Diseases to A.N.

FOOTNOTES
* Corresponding author. Mailing address: Center for Pharmaceutical Biotechnology, m/c 870, University of Illinois, 900 S. Ashland Ave., Chicago, IL 60607. Phone: (312) 996-3371. Fax: (312) 413-4034. E-mail:
nvazquez{at}uic.edu.


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Journal of Bacteriology, May 2006, p. 3494-3497, Vol. 188, No. 10
0021-9193/06/$08.00+0 doi:10.1128/JB.188.10.3494-3497.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
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