Content uploaded by Christopher J Alteri
Author content
All content in this area was uploaded by Christopher J Alteri on May 20, 2015
Content may be subject to copyright.
Fitness of
Escherichia coli
during Urinary Tract Infection
Requires Gluconeogenesis and the TCA Cycle
Christopher J. Alteri, Sara N. Smith, Harry L. T. Mobley*
Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
Abstract
Microbial pathogenesis studies traditionally encompass dissection of virulence properties such as the bacterium’s ability to
elaborate toxins, adhere to and invade host cells, cause tissue damage, or otherwise disrupt normal host immune and
cellular functions. In contrast, bacterial metabolism during infection has only been recently appreciated to contribute to
persistence as much as their virulence properties. In this study, we used comparative proteomics to investigate the
expression of uropathogenic Escherichia coli (UPEC) cytoplasmic proteins during growth in the urinary tract environment
and systematic disruption of central metabolic pathways to better understand bacterial metabolism during infection. Using
two-dimensional fluorescence difference in gel electrophoresis (2D-DIGE) and tandem mass spectrometry, it was found that
UPEC differentially expresses 84 cytoplasmic proteins between growth in LB medium and growth in human urine (P,0.005).
Proteins induced during growth in urine included those involved in the import of short peptides and enzymes required for
the transport and catabolism of sialic acid, gluconate, and the pentose sugars xylose and arabinose. Proteins required for
the biosynthesis of arginine and serine along with the enzyme agmatinase that is used to produce the polyamine putrescine
were also up-regulated in urine. To complement these data, we constructed mutants in these genes and created mutants
defective in each central metabolic pathway and tested the relative fitness of these UPEC mutants in vivo in an infection
model. Import of peptides, gluconeogenesis, and the tricarboxylic acid cycle are required for E. coli fitness during urinary
tract infection while glycolysis, both the non-oxidative and oxidative branches of the pentose phosphate pathway, and the
Entner-Doudoroff pathway were dispensable in vivo. These findings suggest that peptides and amino acids are the primary
carbon source for E. coli during infection of the urinary tract. Because anaplerosis, or using central pathways to replenish
metabolic intermediates, is required for UPEC fitness in vivo, we propose that central metabolic pathways of bacteria could
be considered critical components of virulence for pathogenic microbes.
Citation: Alteri CJ, Smith SN, Mobley HLT (2009) Fitness of Escherichia coli during Urinary Tract Infection Requires Gluconeogenesis and the TCA Cycle. PLoS
Pathog 5(5): e1000448. doi:10.1371/journal.ppat.1000448
Editor: Jorge E. Gala
´n, Yale University School of Medicine, United States of America
Received October 6, 2008; Accepted April 27, 2009; Published May 29, 2009
Copyright: ß2009 Alteri et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: Funding was provided by Public Health Service grants AI43363 and AI059722 from the National Institutes of Health. The funders had no role in study
design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing Interests: The authors have declared that no competing interests exist.
* E-mail: hmobley@umich.edu
Introduction
Traditional studies of bacterial pathogenesis have focused on
pathogen-specific virulence properties including toxins, adhesins,
secretion, and iron acquisition systems, and mechanisms to avoid
the innate and adaptive immune response. Examining bacterial
metabolism during the course of an infection is also critical to
further our understanding of pathogenesis and identifying
potential targets for new antimicrobial agents. Infectious diseases
represent a serious threat to global health because many bacteria
that cause disease in humans such as Staphylococcus aureus,
Mycobacterium tuberculosis, and E. coli are steadily developing
resistance to many of the available treatments [1–3]. Since the
introduction of antibiotics in the last century, the emergence of
bacteria that resist these compounds has rapidly outpaced the
discovery and development of new antimicrobial agents [4]. The
need to understand bacterial physiology during infection of the
host is critical for the development of new antimicrobials or
antibiotics that will reduce their burden upon human health.
Among common infections, urinary tract infections (UTI) are
the most frequently diagnosed urologic disease. The majority of
UTIs are caused by E. coli and these uropathogenic E. coli (UPEC)
infections place a significant financial burden on the healthcare
system by generating annual costs in excess of two billion dollars
[5,6]. Because UTIs are a significant healthcare burden and E. coli
is one of the best studied model organisms for studying
metabolism, these traits can be exploited to understand and
identify metabolic pathways that are required for the growth of the
bacterium during infection of the host.
Despite being arguably the most studied organism, E. coli
metabolism during colonization of the intestine has only recently
been explored [7,8]. Commensal E. coli acquires nutrients from
intestinal mucus, a complex mixture of glycoconjugates, and
subsequently expresses genes involved in the catabolism of N-
acetylglucosamine, sialic acid, glucosamine, gluconate, arabinose
and fucose [8,9]. E. coli mutants in the Entner-Doudoroff
and glycolytic central metabolic pathways have diminished
colonization levels reflecting the importance of sugar acid
catabolism [8]. These findings suggest that commensal E. coli uses
multiple limiting sugars for growth in the intestine [8].
Together, this developing body of evidence supports the
assertion that E. coli grows in the intestine using simple sugars
released by the breakdown of complex polysaccharides by
anaerobes [9,10].
PLoS Pathogens | www.plospathogens.org 1 May 2009 | Volume 5 | Issue 5 | e1000448
Much less is known about the metabolism of enteric pathogens
during colonization of the gastrointestinal tract. Enterohemor-
rhagic E. coli (EHEC) O157:H7 requires similar carbon metabolic
pathways as do commensal strains, however, mutations in
pathways that utilize galactose, hexuronates, mannose, and ribose
resulted in colonization defects only for EHEC [9]. It was also
found that multiple mutations in a single EHEC strain had an
additive effect on colonization levels suggesting that this pathogen
depends on the simultaneous metabolism of up to six sugars to
support the colonization of the intestine [9]. When faced with
limiting sugars due to consumption by other colonizing bacteria,
EHEC may switch from glycolytic to gluconeogenic substrates to
sustain growth in the intestine [11]. Synthesis and degradation of
glycogen, an endogenous glucose polymer, plays an important role
for EHEC and pathogenic Salmonella during colonization of the
mouse intestine presumably by functioning as an internal carbon
source during nutrient limitation [12–14]. Although it is not
known which external carbon sources are used by S. enterica serovar
Typhimurium during colonization it has been demonstrated that
full virulence requires the conversion of succinate to fumarate in
the tricarboxylic acid (TCA) cycle [15,16]. These studies have
contributed much to the understanding of the in vivo metabolic
requirements of EHEC colonization; however, these studies were
done in an animal model that is not suitable for studying
pathogenesis because these animals do not exhibit signs of EHEC
infection [9,11,13].
In contrast to the nutritionally diverse intestine, the urinary tract
is a high-osmolarity, moderately oxygenated, iron-limited envi-
ronment that contains mostly amino acids and small peptides
[17,18]. The available studies on UPEC metabolism during UTI
has revealed that the ability to catabolize the amino acid D-serine
in urine, which not only supports UPEC growth, appears
important as a signaling mechanism to trigger virulence gene
expression [19,20]. Metabolism of nucleobases has been demon-
strated to play a role for UPEC colonization of the urinary tract;
signature-tagged mutagenesis screening identified a mutant in the
dihydroorotate dehydrogenase gene pyrD that was outcompeted by
wild-type UPEC in vivo [21] and in a separate transposon screen a
gene involved in guanine biosynthesis, guaA, was identified and
found to be attenuated during experimental UTI [22].
To better understand bacterial metabolism during infection, we
used a combination of comparative proteomics and systematic
disruption of central metabolism to identify pathways that are
required for UPEC fitness in vivo. By examining the expression of
UPEC cytoplasmic proteins during growth in human urine, we
confirmed that E. coli is scavenging amino acids and peptides and
found that disruption of peptide import in UPEC significantly
compromised fitness during infection. Consistent with the notion
that peptides are a key in vivo carbon source for UPEC, only
mutations ablating gluconeogenesis and the TCA cycle demon-
strated reduced fitness in vivo during experimental UTI. These
findings represent the first study of pathogenic E. coli central
metabolism in an infection model and further our understanding
of the role of metabolism in bacterial pathogenesis.
Results
Proteomic profile for uropathogenic E. coli growing in
urine
Culturing UPEC in human urine partially mimics the urinary
tract environment and has proven to be a useful tool to identify
bacterial genes and proteins involved in UTI [18,22–24]. Because
it is well established that urine is iron-limited and our previous
studies clearly demonstrated that the majority of differentially
expressed genes and proteins are involved in iron acquisition
[18,23], we determined the protein expression profile of E. coli
CFT073 during growth in human urine and compared that with
bacterial cells cultured in iron-limited LB medium to unmask
proteins involved in processes other than iron metabolism. Using
this strategy and 2D-DIGE it was possible to visualize 700
cytoplasmic protein spots, 84 of which were differentially
expressed (P,0.05) between urine and iron-limited LB medium
(Fig. 1). Of these, 56 were more highly expressed in human urine
(green) than in iron-limited LB medium, while 28 demonstrated
greater expression in iron-limited LB medium (red) than in urine
(Fig. 1).
Proteins induced in human urine with .2-fold differences from
expression levels in iron-limited LB medium were identified by
tandem mass spectroscopy (Table 1). The results indicate that E.
coli growing in urine are expressing proteins involved in the
catabolism of pentose sugars; XylA (xylose isomerase), AraF (high-
affinity arabinose-binding protein), and the non-oxidative pentose
Figure 1. Fluorescence difference in gel electrophoresis (2D-
DIGE) of UPEC cytoplasmic proteins during growth in urine.
Soluble proteins (50 mg) from E. coli CFT073 cultured in urine were
labeled with Cy3 (green), from CFT073 grown in LB with Cy5 (red), and
the pooled internal standard representing an equal amount of urine
and LB soluble proteins with Cy2 (blue). The labeled proteins (150 mg)
were pooled and applied to a pH 4–7 IPG strip and second dimension
10% SDS-PAGE. Green spots indicate protein features induced in urine;
red spots represent proteins induced in LB medium.
doi:10.1371/journal.ppat.1000448.g001
Author Summary
Bacteria that cause infections often have genes known as
virulence factors that are required for bacteria to cause
disease. Studying virulence factors such as toxins, adhe-
sins, and secretion and iron-acquisition systems is a
fundamental part of understanding infectious disease
mechanisms. In contrast, little is known about the
contribution of bacterial metabolism to infectious disease.
This study shows that E. coli, which cause most urinary
tract infections, utilize peptides as a preferred carbon
source in vivo and requires some, but not all, of the central
metabolic pathways to infect the urinary tract. Specifically,
pathways that can be used to replenish metabolites,
known as anaplerotic reactions, are important for uro-
pathogenic E. coli infections. These findings help explain
how metabolism can contribute to the ability of bacteria
to cause a common infection.
UPEC Metabolism during UTI
PLoS Pathogens | www.plospathogens.org 2 May 2009 | Volume 5 | Issue 5 | e1000448
phosphate pathway enzyme TalA (transaldolase) were induced
5.25-, 2.02-, and 5.66-fold, respectively (P,0.001) (Table 1). Other
proteins that were induced are the involved in metabolism of the
sugar acids gluconate (UxuA, mannonate dehydratase), glucono-
lactone (YbhE, 6-phosphogluconolactonase), sialic acid (NanA, N-
acetylneuraminate lyase), and fructose (FruB, fructose-specific
Table 1. UPEC cytoplasmic proteins differentially expressed in human urine.
Name ORF Function Fold-Change
P
-Value
OmpF c1071 outer membrane protein F precursor 7.84 2.50E-11
OmpF c1071 outer membrane protein F precursor 5.97 2.33E-05
TalA c2989 transaldolase 5.66 0.00021
XylA c4385 xylose isomerase 5.25 6.90E-07
TpiA c4871 triosephosphate isomerase 4.58 1.30E-07
SerA c3494 D-3-phosphoglycerate dehydrogenase 4.44 3.40E-09
SpeB c3522 agmantinase 4.06 3.90E-07
UxuA c5402 mannonate dehydratase 3.76 7.20E-03
NanA c3979 N-acetylneuraminate lyase subunit 3.64 4.50E-06
ArgG c3929 argininosuccinate dehydrogenase 3.41 5.80E-03
FklB c5306 peptidyl-prolyl cis trans isomerase 3.38 6.00E-04
NanA c3979 N-acetylneuraminate lyase subunit 3.37 4.50E-06
AtpA c4660 ATP synthase subunit A 3.34 6.30E-05
XylA c4385 xylose isomerase 3.32 5.60E-05
NmpC c1560 outer membrane protein NmpC precursor 3.3 6.10E-05
FruB c2704 PTS system, fructose-specific IIA/FPr component 2.93 3.40E-06
RpoA c4056 DNA-directed RNA polymerase 2.84 4.40E-04
GlyA c3073 serine hydroxymethyl transferase 2.72 1.50E-10
LivK c4248 leucine-specific binding protein 2.72 2.90E-08
FruB c2704 PTS system, fructose-specific IIA/FPr component 2.71 3.20E-04
DppA c4361 dipeptide substrate-binding protein 2.63 5.20E-04
SurA c0066 peptidyl-prolyl cis trans isomerase 2.61 3.10E-07
YliJ c0923 hypothetical GST protein 2.61 4.00E-04
HisJ c2851 histidine-binding protein precursor 2.55 1.90E-04
ArgG c3929 argininosuccinate dehydrogenase 2.41 2.60E-02
OppA c1707 oligopeptide substrate-binding protein 2.39 7.80E-03
OppA c1707 oligopeptide substrate-binding protein 2.34 2.10E-04
SerA c3494 D-3-phosphoglycerate dehydrogenase 2.28 1.90E-05
YghU c3726 hypothetical GST-like protein 2.27 1.10E-05
YbhE c0844 6-phosphogluconolactonase 2.2 9.90E-03
SucC c0805 succinyl-CoA synthetase beta chain 2.14 1.50E-04
GlpA c2782 anaerobic glycerol-3-phosphate dehydrogenase 2.13 3.50E-07
XylA c4385 xylose isomerase 2.11 1.30E-02
MalK c5005 maltose/maltodextran ATP-binding 2.1 6.90E-03
DppA c4361 dipeptide substrate-binding protein 2.09 8.40E-03
NmpC c1560 outer membrane protein NmpC precursor 2.03 1.80E-03
AraF c2314 L-arabinose-binding protein 2.02 2.80E-06
UxuA c5402 mannonate dehydratase 1.94 8.30E-04
AsnS c1072 asparaginyl-tRNA synthetase 1.9 1.20E-02
GlnH c0896 glutamine-binding protein 1.68 1.40E-03
GroEL c5227 chaperonin 22.07 8.90E-08
GroEL c5227 chaperonin 22.07 7.10E-05
NusA c3926 transcription elongation factor 22.1 3.30E-02
BasR c5118 transcription factor 22.91 5.50E-03
HdeB c4320 acid resistance protein precursor 23.71 2.50E-04
doi:10.1371/journal.ppat.1000448.t001
UPEC Metabolism during UTI
PLoS Pathogens | www.plospathogens.org 3 May 2009 | Volume 5 | Issue 5 | e1000448
IIA/FPr PTS system component). Multiple isoforms of the
periplasmic dipeptide and oligopeptide substrate-binding proteins
DppA and OppA were also induced (.2-fold, P,0.009) in urine
confirming the notion that amino acids and small peptides are
being acquired from this milieu (Table 1). Proteins involved in
amino acid metabolism were also identified and include SerA (D-
3-phosphoglycerate dehydrogenase) that is involved in serine
biosynthesis and two enzymes in the arginine biosynthesis
pathway, ArgG (argininosuccinate dehydrogenase) and SpeB
(agmatinase) (Table 1). As expected, none of the proteins identified
were involved in iron uptake or metabolism, although DppA has
been reported to bind heme albeit with less affinity than dipeptide
substrates [25].
Notably, there was an increase in abundance for two central
metabolism enzymes, TalA, as mentioned above, and TpiA that
was increased 4.58-fold (P,0.0001) in urine (Table 1). TalA, a
non-oxidative pentose phosphate pathway enzyme, converts
sedoheptulose-7-phosphate and glyceraldehyde-3-phosphate to
erythrose-4-phosphate and fructose-6-phosphate. Due to the
transfer of the glycolytic intermediate glyceraldehyde-3-phosphate
by TalA, this enzyme is an important link between the pentose
phosphate pathway and glycolysis [26]. TpiA is a glycolytic
enzyme that catalyzes the reversible isomerization of glyceralde-
hyde-3-phosphate and dihydroxyacetone phosphate [27]. The
induction of TalA and TpiA suggested that the coupling of the
pentose phosphate pathway and glycolysis or gluconeogenesis via
the transfer and isomerization of glyceraldehyde-3-phosphate may
be an important route of carbon flux through these central
pathways during the bacterium’s growth in human urine.
Contribution of genes induced in urine to UPEC fitness in
vivo
To determine whether some proteins identified by 2D-DIGE
are required for UPEC fitness during UTI, CFT073 mutants were
constructed in the genes: talA,xylA,tpiA,serA,speB,uxuA,nanA,
argG,araF,dppA, and oppA. For these studies, an experimental
competition between each mutant strain and wild-type parental
CFT073 was performed. Wild-type UPEC and the mutant strain
were prepared in a 1:1 ratio and transurethrally inoculated into
the bladders of mice. The number of mutant (kanamycin-resistant)
and wild-type (kanamycin-sensitive) bacteria recovered from the
bladder and kidneys was determined by plating the tissue
homogenates for CFU on both LB agar and LB agar containing
kanamycin. Mutants containing defects in genes that affect fitness
in vivo are out-competed by the wild-type strain when inoculated
into the same animal. This was determined by comparing the ratio
of colony forming units (CFU) of bacteria recovered from the
infection to the ratio of bacteria contained within the inoculum to
obtain a competitive index (CI). A CI.1 indicates the wild-type
out-competes the mutant strain and a CI,1 indicates the wild-
type is out-competed by the mutant. In these series of
experimental infections, only mutants defective in peptide
transport (DdppA and DoppA) were dramatically out-competed by
wild-type UPEC in vivo,CI.50, P,0.005 for the bladder (Table 2).
One additional mutant, DtpiA, that functions in both glycolysis and
gluconeogenesis, was out-competed by wild-type in the kidneys at
48 hpi, CI = 2.54, P= 0.0206 (Table 2).
Despite the lack of attenuation in vivo for the many of the mutants,
these results reveal a number of important findings. The agmatinase
mutant DspeB out-competed wild-type in the bladder at 48 hpi,
CI = 0.14, P= 0.0122 (Table 2). Agmatinase is part of arginine
metabolism and catalyzes the formation of the polyamine putrescine
and urea from agmatine and H
2
O. This suggests that accumulation
of agmatine or reduced production of urea and putrescine by the
mutant may provide a modest advantage over wild-type UPEC
during infection of the bladder. CFT073 DargG was unable to grow
in MOPS defined medium unless supplemented with 10 mM
arginine (Fig. 2A), validating the expected auxotrophic phenotype.
Similarly, the DserA serine auxotroph required supplementation
with either 10 mM serine or glycine in MOPS, D-serine was unable
to rescue the in vitro growth defect (Fig. 2B). Lack of arginine or
serine biosynthesis had little effect upon the ability of UPEC to grow
logarithmically in human urine, although the DargG mutant
consistently entered stationary phase at a lower cell density, with
an O.D.
600
of 0.4560.04 compared to 0.5960.03 for wild-type
(P= 0.051) (Fig. 2C). When tested for in vivo fitness, neither the
DargG nor DserA strain were significantly out-competed by wild-type
UPEC at 48 hpi (Fig. 2D, 2E, and Table 2). Additionally, there was
no preference for serine over arginine or vice versa for UPEC
colonization at 48 hpi. When the auxotrophic strains were co-
inoculated into the same mice both mutants were recovered at
similar levels (Fig. 2F). These data clearly demonstrate that there are
sufficient concentrations of arginine, serine and/or glycine in the
urinary tract to support growth of these auxotrophic strains.
As mentioned, deletion of the genes encoding periplasmic
peptide substrate-binding proteins, dppA and oppA, had the greatest
impact on UPEC fitness in vivo of the CFT073 mutants in genes
whose products were induced during growth in human urine
(Table 2). The dipeptide transport mutant, DdppA, failed to
maintain colonization in the bladder at 48 hpi, 11/11 bladders
had undetectable levels (,200 CFU/g) for this mutant, while wild-
type levels from the same bladders reached a median of 10
4
CFU/
g(P= 0.0020) (Fig. 3A). Because these mice had low levels of
recoverable UPEC from the kidneys it was not possible to
determine the contribution of dipeptide transport for kidney
colonization. Import of oligopeptides via the OppA substrate-
binding protein is also required for UPEC fitness in vivo. CFT073
DoppA was out-competed nearly 500:1 wild-type:mutant in the
bladder (Table 2) with a 3-log reduction in the median CFU/g
from bladder tissue at 48 hpi (P= 0.0047) (Fig. 3B). In these co-
challenge infections, wild-type UPEC colonized 10/16 (62%) of
kidneys, while DoppA was detectable in 4/16 (25%) of kidneys at
Table 2. In vivo fitness for select 2D-DIGE mutants.
Bladder Kidneys
CI
a
P
-Value
b
CI
a
P
-Value
b
talA 0.150 0.1282 0.660 0.3829
xylA 1.66E202 0.0625 0.233 0.0649
tpiA 0.841 0.4050 2.540 0.0206
serA 5.310 0.4206 1.58 0.5476
speB 0.140 0.0122 2.248 0.3652
uxuA 0.397 0.0667 0.608 0.1750
nanA 0.659 0.1875 1.240 0.4075
argG 0.160 0.0625 1.970 0.3750
araF 0.854 0.4401 0.297 0.4507
dppA 56.33 0.0020 1.408 0.5625
oppA 4.77E+02 0.0047 1.56E+02 0.0420
a
Competitive Index, determined by dividing the ratio of wild-type to mutant at
48 hpi by the ratio present in the inoculum. Significant CI.1 indicates mutant
has a fitness defect.
b
P-values determined by Wilcoxon matched pairs test. Significant P-values are
bolded.
doi:10.1371/journal.ppat.1000448.t002
UPEC Metabolism during UTI
PLoS Pathogens | www.plospathogens.org 4 May 2009 | Volume 5 | Issue 5 | e1000448
48 hpi. The ratio of wild-type:mutant recovered from the kidneys
at this time point was 156:1 (Table 2) where wild-type UPEC had
3-logs greater CFU/g than DoppA (P= 0.0420) (Fig. 3B). Together,
the in vivo fitness defect for CFT073 harboring a deletion of either
dppA or oppA suggests that peptides may be an important carbon
source for UPEC during urinary tract infection.
Previously, we have shown that the low copy pGEN plasmid is
maintained in CFT073 in the absence of antibiotic pressure for up
Figure 2.
In vivo
contribution of UPEC arginine and serine biosynthesis. Demonstration of auxotrophic phenotypes for (A) DargG and (B)
DserA in MOPS defined medium containing 0.2% glucose and 10 mM of the indicated amino acid. (C) Growth in human urine. Growth curves
represent the average measurement at each time point from triplicate experiments. Individual female mice were transurethrally inoculated with
2610
8
CFU of a 1:1 mixture of wild-type and mutant bacteria. In vivo fitness at 48 h post infection (hpi) for UPEC mutants defective in (D) arginine and
(E) serine biosynthesis. (F) In vivo competition between arginine and serine auxotrophy. At 48 hpi, bladders and kidneys were aseptically removed,
homogenized, and plated on LB or LB containing kanamycin to determine viable counts of wild-type and mutant strains, respectively. Each dot
represents the log CFU/g from an individual animal. Bars represent the median CFU/g, and the limit of detection is 200 CFU. Significant differences in
colonization levels (P,0.05) were determined using a two-tailed Wilcoxon matched pairs test.
doi:10.1371/journal.ppat.1000448.g002
UPEC Metabolism during UTI
PLoS Pathogens | www.plospathogens.org 5 May 2009 | Volume 5 | Issue 5 | e1000448
to 48 h [28]. Using this ampicillin resistant plasmid system, we
cloned the entire dppA gene including 200 bp upstream from the
predicted start site of translation and introduced the resulting
construct, pGEN-dppA, into the CFT073 DdppA strain. To
determine if it was possible to complement the DdppA defect in
vivo, co-challenge infections were performed as described and
modified to enumerate bacteria in tissue homogenates by plating
on agar containing ampicillin (wild-type CFT073 harboring
pGEN) or ampicillin and kanamycin (CFT073 DdppA containing
pGEN or pGEN-dppA). The DdppA mutant containing empty
vector (pGEN-) demonstrated the expected fitness defect in
bladder colonization when co-inoculated with wild-type CFT073
(pGEN-) (P= 0.0002) while DdppA containing a wild-type copy of
dppA (pGEN-dppA) restored colonization to wild-type levels in the
bladder at 48 hpi (Fig. 3C). Although both mutant (pGEN-) and
wild-type (pGEN-) demonstrated poor colonization in the kidneys
of these animals, complementation of DdppA (pGEN-dppA) resulted
in a 2-log increase in median kidney CFU/g at 48 hpi (Fig. 3D).
Fitness of UPEC central carbon metabolism mutants
during UTI
The requirement for peptide transport for UPEC fitness during
infection implicates peptides as an important carbon source in vivo.
This predicts that certain central metabolism pathways that
operate during catabolism of amino acids or peptides may be more
important for in vivo growth of UPEC than pathways that function
primarily to catabolize sugars. To test the role of central metabolic
pathways during an actual infection mutants were constructed in
UPEC strain CFT073 to produce defects in glycolysis (pgi,
phosphoglucose isomerase and tpiA, triosephosphate isomerase)
[29], the Entner-Doudoroff pathway (edd, 6-phosphogluconate
dehydratase) [10], the oxidative branch (gnd, 6-phosphogluconate
Figure 3.
In vivo
contribution of UPEC peptide substrate-binding proteins. Individual female mice were transurethrally inoculated with
2610
8
CFU of a 1:1 mixture of wild-type and mutant bacteria. In vivo fitness at 48 hpi for UPEC mutants defective in import of dipeptides (A) DdppA
or oligopeptides (B) DoppA. At 48 hpi, bladders and kidneys were aseptically removed, homogenized, and plated on LB or LB containing kanamycin
to determine viable counts of wild-type and mutant strains, respectively. In vivo complementation of DdppA was performed by inoculating mice with
a mixture of wild-type CFT073 containing pGEN empty vector and DdppA containing pGEN empty vector or pGEN-dppA. At 48 hpi, (C) bladders and
(D) kidneys were aseptically removed, homogenized, and plated on LB with ampicillin or LB containing ampicillin and kanamycin to determine viable
counts of wild-type (closed symbols) and mutant strains (open symbols), respectively. Each dot represents the log CFU/g from an individual animal.
Bars represent the median CFU/g, and the limit of detection is 200 CFU. Significant differences in colonization levels (P,0.05) are indicated and were
determined using a two-tailed Wilcoxon matched pairs test.
doi:10.1371/journal.ppat.1000448.g003
UPEC Metabolism during UTI
PLoS Pathogens | www.plospathogens.org 6 May 2009 | Volume 5 | Issue 5 | e1000448
dehydrogenase) and the non-oxidative branch (talA, transaldolase)
of the pentose phosphate pathway [26], gluconeogenesis (pckA,
phosphoenolpyruvate carboxykinase) [30], and the TCA cycle
(sdhB, succinate dehydrogenase) [31]. The in vitro growth of these
central metabolism mutants were examined and compared to
wild-type UPEC during culture in human urine, LB medium, and
MOPS defined medium containing 0.02% glucose. All of the
central metabolism mutants produced similar logarithmic growth
as wild-type when cultured in human urine (Fig. 4A) and LB
medium (data not shown) under defined inoculation conditions. As
expected, only mutants with defects in glycolysis demonstrated
diminished growth in MOPS medium containing glucose as the
sole carbon source (Fig. 4B). The Dpgi strain produced an extended
lag phase of 5.561.1 h compared with wild-type (P= 0.001) and
DtpiA failed to reach exponential phase after 18 h (Fig. 4B). These
data and the indistinguishable growth of the glycolysis mutants
from wild-type in urine supported the proteomics data and
indicated that UPEC growing in urine utilizes carbon sources
other than glucose.
To determine the role for central metabolism during E. coli
infection of the urinary tract, the ascending model of murine UTI
was used as described above to measure the impact that a lesion in
central metabolism has upon the relative fitness of the strain in vivo.
Mutants with defects in glycolysis had levels of colonization in the
bladder at 48 hpi similar to wild-type (P.0.400) (Fig. 5A and 5B).
In the kidneys, Dpgi CFU/g were comparable to wild-type
(Fig. 5A), while DtpiA demonstrated a 10-fold reduction in the
median CFU/g (P= 0.0206) (Fig. 5B). The pentose phosphate
pathway mutants, Dgnd (Fig. 5C) and DtalA (Table 2), were not
significantly out-competed by wild-type in vivo. The mutant with a
defect in the Entner-Doudoroff pathway (Dedd) also was not
impaired in the ability to infect both the bladder and kidneys as
indicated by its similar colonization to wild-type at 48 hpi
(Fig. 5D). UPEC in vivo fitness was significantly reduced in the
TCA cycle mutant DsdhB, this mutation resulted in a 50-fold
reduction in median CFU/g in the bladder (P= 0.0134) and a 1.5-
log decrease in kidney CFU at 48 hpi (P= 0.0400) (Fig. 5E). This
defect in the TCA cycle impacted fitness to a greater extent in the
bladder, where 11/15 (73%) of mice had undetectable levels of
mutant bacteria, than in the kidneys where 6/15 (40%) mice had
undetectable counts (Fig. 5E). The gluconeogenesis mutant, DpckA
had a 2-log reduction in median CFU/g in both the bladder
(P= 0.0005) and kidneys (P= 0.0322) and half of the mice (7/14)
displayed undetectable levels of DpckA at 48 hpi (Fig. 5F).
To verify that this mutation is non-polar as expected and the
defect in colonization is not due to a secondary mutation, in vivo
complementation experiments were conducted. The DpckA mutant
with the pGEN empty vector demonstrated a 2-log reduction in
CFU/g at 48 hpi (P= 0.0039) in the bladder when co-inoculated
into mice with wild-type UPEC containing pGEN (Fig. 6). When
CFT073 DpckA (pGEN-pckA) were co-inoculated with CFT073
(pGEN-) there was no significant difference in bladder CFU/g at
48 hpi between the strains (Fig. 6). Thus, by re-introducing the
pckA gene into the mutant it was possible to complement the DpckA
defect in bladder colonization at 48 hpi.
The in vitro growth and in vivo fitness for the UPEC central
metabolism mutants is summarized in Table 3. As expected, only
mutations in glycolysis had a negative effect on growth in defined
medium with glucose. Only gluconeogenesis or TCA cycle
mutants demonstrated reduced persistence at 48 hpi in both the
bladder and kidneys (Table 3). Non-oxidative and oxidative
pentose phosphate pathway and Entner-Doudoroff pathway
mutants did not demonstrate any colonization defect and of the
glycolytic mutants only the triosephosphate isomerase deletion had
a measurable defect in the kidneys but not in the bladder (Table 3).
Together, the fitness defect for the peptide transport mutants and
these data indicate UPEC could be using amino acids as the
primary carbon source during infection. Surprisingly, there was no
correlation between the ability of the central metabolism mutants
to grow in human urine ex vivo and grow in the urinary tract in vivo.
Discussion
Bacterial pathogenesis traditionally involves studying virulence
traits involved in the production of toxins and effectors, iron
acquisition, adherence, invasion, and immune system avoidance.
Although many paradigms exist that describe mechanisms of
pathogenesis, the contribution of microbial metabolism to
bacterial virulence during an infection is less understood. Much
work has been done studying E. coli as model organism for
characterizing individual central metabolism pathways and
enzymes [10,27,32–38]. We have shown here that central
metabolism studies in E. coli can be extended to investigate the
contribution of central pathways to bacterial pathogenesis using a
virulent uropathogenic E. coli strain and a well-established animal
model of UTI. It is known that commensal E. coli require the
Entner-Doudoroff pathway and glycolysis for colonization in vivo;
while the TCA cycle, pentose phosphate pathway, and gluconeo-
Figure 4.
In vitro
growth of UPEC central metabolism mutants.
Optical density of wild-type UPEC and central metabolism mutants
during growth in (A) pooled and sterilized human urine from 8–10
donors and in (B) MOPS defined medium containing 0.2% glucose as
the sole carbon source. Growth curves represent the average
measurement at each time point from triplicate experiments.
doi:10.1371/journal.ppat.1000448.g004
UPEC Metabolism during UTI
PLoS Pathogens | www.plospathogens.org 7 May 2009 | Volume 5 | Issue 5 | e1000448
Figure 5.
In vivo
fitness of UPEC central metabolism mutants. Individual female mice were transurethrally inoculated with 2610
8
CFU of a 1:1
mixture of wild-type and mutant bacteria. In vivo fitness at 48 hpi for UPEC mutants defective in: (A,B) glycolysis, (C) pentose phosphate pathway, (D)
Entner-Doudoroff pathway, (E) TCA cycle, and (F) gluconeogenesis. At 48 hpi, bladders and kidneys were aseptically removed, homogenized, and
plated on LB or LB containing kanamycin to determine viable counts of wild-type and mutant strains, respectively. Each dot represents the log CFU/g
from an individual animal. Bars represent the median CFU/g, and the limit of detection is 200 CFU. Significant differences in colonization levels
(P,0.05) are indicated and were determined using a two-tailed Wilcoxon matched pairs test.
doi:10.1371/journal.ppat.1000448.g005
UPEC Metabolism during UTI
PLoS Pathogens | www.plospathogens.org 8 May 2009 | Volume 5 | Issue 5 | e1000448
genesis are dispensable in the intestine [8]. In contrast, we have
shown that during E. coli infection of the urinary tract, the
pathways required for commensal colonization are dispensable
while the TCA cycle and gluconeogenesis are necessary for UPEC
fitness in vivo. Adaptation to distinct host environments has been
previously shown to involve shared traits between commensal and
pathogenic strains [39,40]. Because commensal E. coli are an
important natural component of the intestine one concern faced
when developing antimicrobials that target pathogenic strains is
how to avoid eradicating commensal bacteria. Thus, these findings
highlight important differences between commensal and patho-
genic E. coli that could be exploited for the development of
antimicrobials that target these pathways in this pathogen during
infections that may not affect commensal strains. Interestingly, in
addition to UPEC, gluconeogenesis is required for virulence in
microbes that represent an array of pathogenic lifestyles, from
intracellular bacteria and parasites [41,42], plant-pathogenic [43],
and intestinal pathogens [16]; suggesting that anaplerosis may be a
common mechanism of microbial pathogenesis.
This study comprehensively examines the role of pathogenic E.
coli central metabolism in a disease model and provides insight not
only into UPEC metabolism in vivo but also information regarding
the nutrients available to support the growth of E. coli within the
urinary tract. The proteomics experiments did reveal that UPEC
growing in human urine induces expression of multiple isoforms of
both dipeptide- and oligopeptide-binding proteins, both of which
were found to be required for UPEC to effectively colonize the
urinary tract. This indicates that these bacteria actively import
short peptides in urine and this function may indicate that peptides
are an important carbon source in vivo. Consistent with this, only
bacteria with defects in peptide transport, gluconeogenesis, or the
TCA cycle demonstrated a significant reduction in fitness in vivo in
both the bladder and kidneys. These findings suggest a model that
describes the biochemistry of E. coli during UTI. For optimal
growth during infection, short peptides are taken up by UPEC and
degraded into amino acids that are catabolized and used in a series
of anaplerotic reactions that replenish TCA cycle intermediates
and generate gluconeogenesis substrates (Fig. 7).
Certain glycolytic steps are irreversible and the reverse
gluconeogenic reaction is performed by an enzyme specific for
gluconeogenesis. Carbon flux through glycolysis and gluconeo-
genesis must be carefully controlled by the cell to avoid a futile
cycle of carbon metabolism [44]. Allosteric regulation of enzymes
that catalyze irreversible reactions in these pathways and
catabolite repression are mechanisms used to avoid the futile
cycle [45,46]. A gluconeogenic-specific enzyme subject to
allosteric regulation is phophoenolpyruvate carboxykinase that
converts oxaloacetate to phosphoenolpyruvate [47]. Deletion of
the gene pckA that encodes this enzyme resulted in a significant
reduction in UPEC fitness in vivo. Because bacteria prevent
glycolysis and gluconeogenesis from occurring simultaneously and
deletion of pckA reduced fitness in vivo, we reason that carbon flux
through gluconeogenesis during UPEC infection may be an
important indication of amino acid catabolism in vivo.
It is not surprising that, in addition to gluconeogenesis, the TCA
cycle is also required for UPEC fitness in vivo. These two pathways
are connected and collectively described as ‘‘filling in’’ or
anaplerotic reactions. The TCA cycle is necessary to provide
substrates for gluconeogenesis when cells use amino acids as a
carbon source. Gluconeogenic amino acids can be degraded to
oxaloacetate or to pyruvate that can be converted to acetyl-CoA
and enter the TCA cycle [47]. Oxaloacetate, a TCA cycle
intermediate, is converted to phophoenolpyruvate during gluco-
neogenesis by PckA as described above. A mutation in the TCA
cycle enzyme succinate dehydrogenase, sdhB, results in a UPEC
strain that has reduced fitness in vivo. This finding suggests that
UPEC are growing aerobically in the urinary tract because
succinate dehydrogenase is replaced by fumarate reductase during
anaerobic growth and therefore, future work could confirm if the
reductive TCA cycle is not operating during UPEC infection. The
requirement for peptide import and the TCA cycle for UPEC
fitness during infection is consistent with the hypothesis that acetyl-
CoA production from the degradation of amino acids could be
occurring in vivo as has been shown by another group [48].
Interestingly, with the exception of peptide-transport proteins,
up-regulation of protein expression in urine ex vivo did not correlate
with functional importance in vivo. This could be due to the fact
that many central metabolism genes are constitutively expressed
and that human urine only partially mimics the complex lifestyle
of UPEC during UTI [49]. The absence of host cells and the
Figure 6.
In vivo
complementation of UPEC D
pckA
.Individual
female mice were transurethrally inoculated with 2610
8
CFU of a 1:1
mixture of wild-type CFT073 containing pGEN empty vector and DpckA
containing pGEN empty vector or pGEN-pckA. At 48 hpi, bladders were
aseptically removed, homogenized, and plated on LB with ampicillin or
LB containing ampicillin and kanamycin to determine viable counts of
wild-type (closed symbols) and mutant strains (open symbols),
respectively. Bars represent the median CFU/g, and the limit of
detection is 200 CFU. Significant differences in colonization levels
(P,0.05) are indicated and were determined using a two-tailed
Wilcoxon matched pairs test.
doi:10.1371/journal.ppat.1000448.g006
Table 3. Growth of central metabolism mutants in vitro and
in vivo.
Mutant Pathway
In Vitro
Growth
In Vivo
LB Urine Glucose
Colonization
Defect
edd Entner-Doudoroff ++ + None
gnd Pentose phosphate ++ + None
pckA Gluconeogenesis ++ + Bladder, Kidneys
pgi Glycolysis ++ 2None
sdhB TCA cycle ++ + Bladder, Kidneys
talA Pentose phosphate ++ + None
tpiA Glycolysis ++ 2Kidneys
doi:10.1371/journal.ppat.1000448.t003
UPEC Metabolism during UTI
PLoS Pathogens | www.plospathogens.org 9 May 2009 | Volume 5 | Issue 5 | e1000448
immune response during growth in urine ex vivo could in part
account for this discrepancy. It also remains possible that mutants
that lack growth defects in urine but demonstrate reduced fitness in
vivo could represent genes or metabolic pathways that are required
for intracellular phases of growth during cystitis [50].
Despite these disadvantages, up-regulation of both DppA and
OppA expression was seen in urine and loss of either dppA or oppA
was found to negatively impact UPEC colonization in vivo.
Induction of dppA has been reported in a hypervirulent UPEC
strain that has a lacks a functional D-serine deaminase gene (dsdA)
[51]. Deletion of dppA in this mutant strain resulted in a loss of the
hypervirulent phenotype in vivo and significantly reduced its ability
to colonize the urinary tract in competition with wild-type [51].
Surprisingly, in contrast to our findings, this group found that
mutation of dppA alone had no effect on UPEC fitness in vivo [51].
Due to lack of complementation, it is unclear from that work why
loss of dppA dramatically attenuated a hypervirulent strain but had
no effect on wild-type. Despite this inconsistency in that work, the
importance of peptide transport for UPEC fitness in vivo is
supported by the findings that loss of either dppA or oppA
significantly reduced colonization of the urinary tract and that
the reduced bacterial colonization in the DdppA strain can be
restored to wild-type levels by complementing the mutant with a
wild-type dppA gene.
In summary, defects in the both branches of the pentose
phosphate pathway, the Entner-Doudoroff pathway, and glycolysis
had limited or no impact on UPEC fitness in vivo. On the other
hand, the TCA cycle- and gluconeogenesis-defective strains
demonstrate significant fitness reductions during UTI. The
utilization of short peptides and amino acids as a carbon source
during bacterial infection of the urinary tract is supported by the
observation that UPEC mutants defective in peptide import have
reduced fitness in vivo while auxotrophic strains do not. Together,
these findings provide compelling evidence to support the notion
that catabolism of amino acids to form TCA cycle intermediates
and gluconeogenic substrates is important for the ability of UPEC
to infect the urinary tract efficiently. This shows that anaplerotic
and central metabolism pathways are required for UPEC fitness in
vivo and suggest microbial metabolism should be considered
important for bacterial pathogenesis.
Materials and Methods
Bacteria and growth conditions
Strains were derived from E. coli strain CFT073, a prototypic
UPEC strain isolated from the blood and urine of a patient with
acute pyelonephritis [52]; its genome has been sequenced and fully
annotated [53]. Isolated colonies were used to inoculate overnight
Luria-Bertani (LB) cultures. Bacteria from overnight cultures were
collected by centrifugation, washed with sterile PBS, and 10
6
CFU
were used to inoculate pre-warmed LB or human urine. To mimic
iron-limitation in urine, LB containing 10 mM deferoxamine
mesylate (Sigma) was used as a growth medium for comparative
proteomics. For human urine cultures, mid-stream urine was
collected into sterile sample containers from 8–10 male and female
donors, pooled, and sterilized by vacuum filtration through a
0.22 mm pore filter. MOPS defined medium containing 0.2%
glucose [54] with and without 10 mM L-arginine, L-serine,
Figure 7. UPEC acquires amino acids and requires gluconeogenesis and the TCA cycle for fitness
in vivo
.Peptide substrate-binding
protein genes dppA and oppA are required to import di- and oligopeptides into the cytoplasm from the periplasm. Short peptides are degraded into
amino acids in the cytoplasm and converted into pyruvate and oxaloacetate. Pyruvate is converted into acetyl-CoA and enters the TCA cycle to
replenish intermediates and generate oxaloacetate. Oxaloacetate is converted to phosphoenolpyruvate by the pckA gene product during
gluconeogenesis. Mutations in the indicated genes dppA,oppA,pckA,sdhB, and tpiA demonstrated fitness defects in vivo.
doi:10.1371/journal.ppat.1000448.g007
UPEC Metabolism during UTI
PLoS Pathogens | www.plospathogens.org 10 May 2009 | Volume 5 | Issue 5 | e1000448
glycine, aspartatic acid, or D-serine (Sigma) was also used to test
growth of mutant strains. Growth curves were established in
triplicate using a Bioscreen bioanalyzer in 0.4 ml volumes; OD
600
was recorded every 15 min. All cultures were incubated at 37uC;
LB overnight and MOPS cultures were incubated with aeration;
urine cultures were incubated statically. For preparation of
proteins, UPEC isolate CFT073 was grown statically to exponen-
tial phase (OD
600
= 0.25) in pre-warmed LB or human urine at
37uCin56100 ml cultures for each growth medium.
Preparation of cytoplasmic proteins
Bacteria were harvested from 500 ml of culture by centrifuga-
tion (10,0006g, 30 min, 4uC) and lysed in a French pressure cell
at 20,000 psi. Harvested cells were washed and resuspended in
10 ml of 10 mM HEPES, pH 7.0 containing 100 U of Benzonase
(Sigma). Following two passes through the chilled pressure cell,
lysates were centrifuged (75006g, 10 min, 4uC) to remove
unbroken cells and supernatants were ultracentrifuged (120,0006
g, 1 h, 4uC) to remove membranes and insoluble material. Soluble
proteins were quantified using the 2D Quant Kit (GE Healthcare)
following the manufacturer’s protocol and either used immediately
in DIGE-labeling procedures or stored at 280uC.
2D-DIGE and MS/MS
For fluorescence difference in gel electrophoresis (2D-DIGE)
[55], bacterial proteins were minimally labeled with cyanine-
derived fluors (CyDyes) containing an NHS ester-reactive group as
recommended by the manufacturer (GE Healthcare). To deter-
mine quantitative differences within the UPEC soluble proteome
during growth in human urine, cytoplasmic proteins prepared
from human urine cultures were labeled with Cy3, from LB broth
with Cy5, and a pooled internal standard representing equal
amounts of both urine and LB preparations with Cy2 as described
previously [23]. Briefly, 50 mg of protein was incubated with
400 pmol CyDye for 30 min and the reaction was stopped by
added 10 mM lysine. Following labeling, samples labeled with
each CyDye were pooled (150 mg total protein), mixed with an
equal volume of 26DIGE sample buffer; 7 M urea, 2 M thiourea,
10 mM tributylphosphine (TBP) (Sigma), 26biolytes 3–10 (Bio-
Rad), 2% ASB-14 and incubated on ice for 10 min. For
rehydration, samples were brought to 0.35 ml with 16DIGE
rehydration buffer (7 M urea, 2 M thiourea, 5 mM TBP, 16
biolytes 3–10, 1% ASB-14) and used to passively rehydrate pH 4–
7 IPG strips (Bio-Rad) overnight at room temperature. Rehydrat-
ed IPG strips were equilibrated and subjected to isoelectric
focusing for 50,000 V?h and second dimension SDS-PAGE on
10% gels within low fluorescence glass plates (Jule Biotechnologies,
Inc.) and were run at a constant current of 55 mA at 4uC for 4 hr.
Following SDS-PAGE, image acquisition and pixel intensity was
obtained using a Typhoon scanner (GE Healthcare) and
differential in-gel analysis and biological analysis of variance were
performed using the DeCyder 6.5 software suite (GE Healthcare).
Using this software, the normalized spot volume ratios from Cy3
or Cy5 labeled spots were quantified relative to the Cy2-labeled
internal standard from the same gel. The Cy2-labeled standard
was then used to standardize and compare normalized volume
ratios between the Cy3 and Cy5 labeled proteins between gels
representing three independent experiments to generate statistical
confidence for abundance changes using student’s t-test and
ANOVA. To identify the proteins, 500 mg of cytoplasmic proteins
were focused as described above and spots of interest were excised
from a colloidal Coomassie-stained 2D SDS-PAGE gel and
subjected to enzymatic digestion with trypsin. Mass spectra were
acquired on an Applied Biosystems 4700 Proteomics Analyzer
(TOF/TOF). MS spectra were acquired from 800–3500 Da and
the eight most intense peaks in each MS spectrum were selected
for MS/MS analysis. Peptide identifications were obtained using
GPS Explorer (v3.0, Applied Biosystems), which utilizes the
MASCOT search engine. Each MS/MS spectrum was searched
against NCBInr. Tryptic digestion and tandem mass spectrometry
were performed at the University of Michigan Proteome
Consortium.
Construction of UPEC metabolism mutants
Deletion mutants were generated using the lambda red
recombinase system [56]. Primers homologous to sequences
within the 59and 39ends of the target genes were designed and
used to replace target genes with a nonpolar kanamycin resistance
cassette derived from the template plasmid pKD4 [56]. Kanamy-
cin (25 mg/ml) was used for selection of all mutant strains. Gene
deletions begin with the start codon and end with the stop codon
for each gene. To determine whether the kanamycin resistance
cassette recombined within the target gene site, primers that flank
the target gene sequence were designed and used for PCR. After
amplification, each PCR product was compared to wild-type PCR
product and in cases where size-differences are negligible; PCR
products were digested with the restriction enzyme EagI (New
England Biolabs). Both the PCR products and restriction digests
were visualized on a 0.8% agarose gel stained with ethidium
bromide. For in vivo complementation, the dppA and pckA genes
were amplified from CFT073 genomic DNA using Easy-A high-
fidelity polymerase (Stratagene) and independently cloned into
pGEN-MCS [28,57] using appropriate restriction enzymes. The
sequences of pGEN-dppA and pGEN-pckA were verified by DNA
sequence analysis prior to electroporation into CFT073 DdppA or
DpckA mutant strains.
Experimental UTI
Six-to eight-week-old female CBA/J mice (20 to 22 g; Jackson
Laboratories) were anesthetized with ketamine/xylazine and
inoculated transurethrally over a 30 sec period with a 50 ml
bacterial suspension per mouse using a sterile polyethylene
catheter (I.D. 0.28 mm6O.D. 0.61 mm) connected to an infusion
pump (Harvard Apparatus). To measure relative fitness, overnight
LB cultures for CFT073 and the mutant strain were collected by
centrifugation and resuspended in sterile PBS, mixed 1:1 and
adjusted to deliver 2610
8
CFU per mouse. Dilutions of each
inoculum were spiral plated onto LB with and without kanamycin
using an Autoplate 4000 (Spiral Biotech) to determine the input
CFU/mL. After 48 hpi, mice were sacrificed by overdose with
isoflurane and the bladder and kidneys were aseptically removed,
weighed, and homogenized in sterile culture tubes containing 3 ml
of PBS using an OMNI mechanical homogenizer (OMNI
International). Appropriate dilutions of the homogenized tissue
were then spiral plated onto duplicate LB plates with and without
kanamycin to determine the output CFU/g of tissue. Plate counts
obtained on kanamycin were subtracted from those on plates
lacking antibiotic to determine the number of wild-type bacteria.
Competitive indices were calculated by dividing the ratio of wild-
type to mutant at 48 hpi by the ratio of wild-type to mutant input
CFU/mL. Groups of 5 mice per co-challenge were used to
determine defects in fitness, when a defect was apparent the co-
challenge was repeated two more times with groups of 5 mice.
Statistically significant differences in colonization (P-value,0.05)
were determined using a two-tailed Wilcoxon matched pairs test.
All animal protocols were approved by the University Committee
on Use and Care of Animals at the University of Michigan
Medical School.
UPEC Metabolism during UTI
PLoS Pathogens | www.plospathogens.org 11 May 2009 | Volume 5 | Issue 5 | e1000448
Acknowledgments
The authors would like to thank Daniel Reiss for assisting with the
proteomics experiments.
Author Contributions
Conceived and designed the experiments: CJA. Performed the experi-
ments: CJA SNS. Analyzed the data: CJA HLTM. Wrote the paper: CJA
HLTM.
References
1. Goering RV, Shawar RM, Scangarella NE, O’Hara FP, Amrine-Madsen H, et
al. (2008) Molecular epidemiology of methicillin-resistant and methicillin-
susceptible Staphylococcus aureus isolates from global clinical trials. J Clin Microbiol
46: 2842–2847.
2. Dorman SE, Chaisson RE (2007) From magic bullets back to the magic
mountain: the rise of extensively drug-resistant tuberculosis. Nat Med 13:
295–298.
3. Pitout JD, Laupland KB (2008) Extended-spectrum beta-lactamase-producing
Enterobacteriaceae: an emerging public-health concern. Lancet Infect Dis 8:
159–166.
4. Levy SB, Marshall B (2004) An tibacterial resistance worldwide: causes,
challenges and responses. Nat Med 10: S122–S129.
5. Foxman B, Barlow R, D’Arcy H, Gillespie B, Sobel JD (2000) Urinary tract
infection: self-reported incidence and associated costs. Ann Epidemiol 10:
509–515.
6. Litwin MS, Saigal CS, Yano EM, Avila C, Geschwind SA, et al. (2005) Urologic
diseases in America Project: analytical methods and principal findings. J Urol
173: 933–937.
7. Autieri SM, Lins JJ, Leatham MP, Laux DC, Conway T, et al. (2007) L-fucose
stimulates utilization of D-ribose by Escherichia coli MG1655 DfucAO and E. coli
Nissle 1917 DfucAO mutants in the mouse intestine and in M9 minimal medium.
Infect Immun 75: 5465–5475.
8. Chang DE, Smalley DJ, Tucker DL, Leatham MP, Norris WE, et al. (2004)
Carbon nutrition of Escherichia coli in the mouse intestine. Proc Natl Acad
Sci U S A 101: 7427–7432.
9. Fabich AJ, Jones SA, Chowdhury FZ, Cernosek A, Anderson A, et al. (2008)
Comparison of carbon nutrition for pathogenic and commensal Escherichia coli
strains in the mouse intestine. Infect Immun 76: 1143–1152.
10. Peekhaus N, Conway T (1998) What’s for dinner? Entner-Doudoroff
metabolism in Escherichia coli. J Bacteriol 180: 3495–3502.
11. Miranda RL, Conway T, Leatham MP, Chang DE, Norris WE, et al. (2004)
Glycolytic and gluconeogenic growth of Escherichia coli O157:H7 (EDL933) and
E. coli K-12 (MG1655) in the mouse intestine. Infect Immun 72: 1666–1676.
12. Bonafonte MA, Solano C, Sesma B, Alvarez M, Montuenga L, et al. (2000) The
relationship between glycogen synthesis, biofilm formation and virulence in
Salmonella enteritidis. FEMS Microbiol Lett 191: 31–36.
13. Jones SA, Jorgensen M, Chowdhury FZ, Rodgers R, Hartline J, et al. (2008)
Glycogen and maltose utilization by Escherichia coli O157:H7 in the mouse
intestine. Infect Immun 76: 2531–2540.
14. McMeechan A, Lovell MA, Cogan TA, Marston KL, Humphrey TJ, et al.
(2005) Glycogen production by different Salmonella enterica serotypes: contribution
of functional glgC to virulence, intestinal colonization and environmental
survival. Microbiology 151: 3969–3977.
15. Mercado-Lubo R, Gauger EJ, Leatham MP, Conway T, Cohen PS (2008) A
Salmonella enterica serovar typhimurium succinate dehydrogenase/fumarate reduc-
tase double mutant is avirulent and immunogenic in BALB/c mice. Infect
Immun 76: 1128–1134.
16. Tchawa Yimga M, Leatham MP, Allen JH, Laux DC, Conway T, et al. (2006)
Role of gluconeogenesis and the tricarboxylic acid cycle in the virulence of
Salmonella enterica serovar Typhimurium in BALB/c mice. Infect Immun 74:
1130–1140.
17. Brooks T, Keevil CW (1997) A simple artificial urine for the growth of urinary
pathogens. Lett Appl Microbiol 24: 203–206.
18. Snyder JA, Haugen BJ, Buckles EL, Lockatell CV, Johnson DE, et al. (2004)
Transcriptome of uropathogenic Escherichia coli during urinary tract infection.
Infect Immun 72: 6373–6381.
19. Anfora AT, Haugen BJ, Roesch P, Redford P, Welch RA (2007) Roles of serine
accumulation and catabolism in the colonization of the murine urinary tract by
Escherichia coli CFT073. Infect Immun 75: 5298–5304.
20. Roesch PL, Redford P, Batchelet S, Moritz RL, Pellett S, et al. (2003)
Uropathogenic Escherichia coli use d-serine deaminase to modulate infection of
the murine urinary tract. Mol Microbiol 49: 55–67.
21. Bahrani-Mougeot FK, Buckles EL, Lockatell CV, Hebel JR, Johnson DE, et al.
(2002) Type 1 fimbriae and extracellular polysaccharides are preeminent
uropathogenic Escherichia coli virulence determinants in the murine urinary tract.
Mol Microbiol 45: 1079–1093.
22. Russo TA, Jodush ST, Brown JJ, Johnson JR (1996) Identification of two
previously unrecognized genes (guaA and argC) important for uropathogenesis.
Mol Microbiol 22: 217–229.
23. Alteri CJ, Mobley HL (2007) Quantitative profile of the uropat hogenic
Escherichia coli outer membrane proteome during growth in human urine. Infect
Immun 75: 2679–2688.
24. Russo TA, Carlino UB, Mong A, Jodush ST (1999) Identification of genes in an
extraintestinal isolate of Escherichia coli with increased expression after exposure
to human urine. Infect Immun 67: 5306–5314.
25. Letoffe S, Delepelaire P, Wandersman C (2006) The housekeeping dipeptide
permease is the Escherichia coli heme transporter and functions with two optional
peptide binding proteins. Proc Natl Acad Sci U S A 103: 12891–12896.
26. Sprenger GA (1995) Genetics of pentose-phosphate pathway enzymes of
Escherichia coli K-12. Arch Microbiol 164: 324–330.
27. Fraenkel DG, Vinopal RT (1973) Carbohydrate Metabolism in Bacteria. Annu
Rev Microbiol 27: 69–100.
28. Lane MC, Alteri CJ, Smith SN, Mobley HL (2007) Expression of flagella is
coincident with uropathogenic Escherichia coli ascension to the upper urinary
tract. Proc Natl Acad Sci U S A 104: 16669–16674.
29. Irani M, Maitra PK (1974) Isolation and characterization of Escherichia coli
mutants defective in enzymes of glycolysis. Biochem Biophys Res Commun 56:
127–133.
30. Chao YP, Patnaik R, Roof WD, Young RF, Liao JC (1993) Control of
gluconeogenic growth by pps and pck in Escherichia coli. J Bacteriol 175:
6939–6944.
31. Hanson RS, Cox DP (1967) Effect of different nutritional conditions on the
synthesis of tricarboxylic acid cycle enzymes. J Bacteriol 93: 1777–1787.
32. Babul J, Clifton D, Kretschmer M, Fraenkel DG (1993) Glucose metabolism in
Escherichia coli and the effect of increased amount of aldolase. Biochemistry 32:
4685–4692.
33. Fraenkel DG (1986) Mutants in glucose metabolism. Annu Rev Biochem 55:
317–337.
34. Fraenkel DG, Levisohn SR (1967) Glucose and gluconate metabolism in an
Escherichia coli mutant lacking phosphoglucose isomerase. J Bacteriol 93:
1571–1578.
35. Josephson BL, Fraenkel DG (1974) Sugar metabolism in transketolase mutants
of Escherichia coli. J Bacteriol 118: 1082–1089.
36. Kim J, Copley SD (2007) Why metabolic enzymes are essential or nonessential
for growth of Escherichia coli K12 on glucose. Biochemistry 46: 12501–12511.
37. Vinopal RT, Hillman JD, Schulman H, Reznikoff WS, Fraenkel DG (1975)
New phosphoglucose isomerase mutants of Escherichia coli. J Bacteriol 122:
1172–1174.
38. Zablotny R, Fraenkel DG (1967) Glucose and gluconate metabolism in a mutant
of Escherichia coli lacking gluconate-6-phosphate dehydrase. J Bacteriol 93:
1579–1581.
39. Sokurenko EV, Chesnokova V, Dykhuizen DE, Ofek I, Wu XR, et al. (1998)
Pathogenic adaptation of Escherichia coli by natural variation of the FimH
adhesin. Proc Natl Acad Sci U S A 95: 8922–8926.
40. Sokurenko EV, Feldgarden M, Trintchina E, Weissman SJ, Avagyan S, et al.
(2004) Selection footprint in the FimH adhesin shows pathoadaptive niche
differentiation in Escherichia coli. Mol Biol Evol 21: 1373–1383.
41. Liu K, Yu J, Russell DG (2003) pckA-deficient Mycobacterium bovis BCG shows
attenuated virulence in mice and in macrophages. Microbiology 149:
1829–1835.
42. Naderer T, Ellis MA, Sernee MF, De Souza DP, Curtis J, et al. (2006) Virulence
of Leishmania major in macrophages and mice requires the gluconeogenic enzyme
fructose-1,6-bisphosphatase. Proc Natl Acad Sci U S A 103: 5502–5507.
43. Liu P, Wood D, Nester EW (2005) Phosphoenolpyruvate carboxykinase is an
acid-induced, chromosomally encoded virulence factor in Agrobacterium tumefa-
ciens. J Bacteriol 187: 6039–6045.
44. Chambost JP, Fraenkel DG (1980) The use of 6-labeled glucose to assess futile
cycling in Escherichia coli. J Biol Chem 255: 2867–2869.
45. Garfinkel L, Kohn MC, Garfinkel D (1979) Computer simulation of the fructose
bisphosphatase/phosphofructokinase couple in rat liver. Eur J Biochem 96:
183–192.
46. Koerner TA Jr, Voll RJ, Younathan ES (1977) A proposed model for the
regulation of phosphofructokinase and fructose 1,6-bisphosphatase based on
their reciprocal anomeric specificities. FEBS Lett 84: 207–213.
47. Gottschalk G (1986) Bacterial Metabolism. New York: Springer-Verlag.
48. Anfora AT, Halla din DK, Haugen BJ, Welch RA (2008) Uropathogenic
Escherichia coli CFT073 is adapted to acetatogenic growth but does not require
acetate during murine urinary tract infection. Infect Immun 76: 5760–5767.
49. Kau AL, Hunstad DA, Hultgren SJ (2005) Interaction of uropathogenic
Escherichia coli with host uroepithelium. Curr Opin Microbiol 8: 54–59.
50. Reigstad CS, Hultgren SJ, Gordon JI (2007) Functional genomic studies of
uropathogenic Escherichia coli and host urothelial cells when intracellular bacterial
communities are assembled. J Biol Chem 282: 21259–21267.
51. Haugen BJ, Pellett S, Redford P, Hamilton HL, Roesch PL, et al. (2007) In vivo
gene expression analysis identifies genes required for enhanced colonization of
the mouse urinary tract by uropathogenic Escherichia coli strain CFT073 dsdA.
Infect Immun 75: 278–289.
52. Mobley HL, Green DM, Trifillis AL, Johnson DE, Chippendale GR, et al.
(1990) Pyelonephritogenic Escherichia coli and killing of cultured human renal
UPEC Metabolism during UTI
PLoS Pathogens | www.plospathogens.org 12 May 2009 | Volume 5 | Issue 5 | e1000448
proximal tubular epithelial cells: role of hemolysin in some strains. Infect Immun
58: 1281–1289.
53. Welch RA, Burland V, Plunkett G 3rd, Redford P, Roesch P, et al. (2002)
Extensive mosaic structure revealed by the complete genome sequence of
uropathogenic Escherichia coli. Proc Natl Acad Sci U S A 99: 17020–17024.
54. Neidhardt FC, Bloch PL, Smith DF (1974) Culture medium for enterobacteria.
J Bacteriol 119: 736–747.
55. Unlu M, Morgan ME, Minden JS (1997) Difference gel electrophoresis: a single
gel method for detecting changes in protein extracts. Electrophoresis 18:
2071–2077.
56. Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes
in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 97:
6640–6645.
57. Galen JE, Nair J, Wang JY, Wasserman SS, Tanner MK, et al. (1999)
Optimization of plasmid maintenance in the attenuated live vector vaccine strain
Salmonella typhi CVD 908-htrA. Infect Immun 67: 6424–6433.
UPEC Metabolism during UTI
PLoS Pathogens | www.plospathogens.org 13 May 2009 | Volume 5 | Issue 5 | e1000448
