Pharmacology & Pharmacy, 2013, 4, 6-12
doi:10.4236/pp.2013.45A002 Published Online August 2013 (http://www.scirp.org/journal/pp)
Comparative Proteomic Analysis of Helicobacter pylori
Strains Isolated from Chinese Patients
Boqing Li1,2*, Wanju Sun1*, Lihua He2, Hong Jiang3, Zhen Zhang1, Donglong Du1,
Jianzhong Zhang2#
1Department of Pathogen Biology, Binzhou Medical University, Yantai, China; 2State Key Laboratory for Infectious Disease Preven-
tion and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Pre-
vention, Beijing, China; 3Affiliated Hospital of Binzhou Medical University, Binzhou, China.
Received July 2nd, 2013; revised July 29th, 2013; accepted August 6th, 2013
Copyright © 2013 Boqing Li et al. This is an open access article distributed under the Creative Commons Attribution License, which
permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
ABSTRACT
Helicobacter pylori, the major cause of gastritis, peptic ulcer and gastric cancer, infects half of the world population,
but only a few infections lead to serious disease. In order to investigate specific proteins related to the pathogenic dif-
ference of this bacterium, comparative proteome analyses of Helicobacter pylori C1 (isolated from patients with gastric
cancer) and G1 (isolated from patients with gastritis) were performed using two-dimensional gel electrophoresis (2-DE)
and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). Four proteins (in-
organic pyrophosphatase, 3-oxoadipate CoA-transferase subunit B, translation elongation factor, and aldo-keto reduc-
tase) were found only in Helicobacter pylori C1, and one protein (alkyl hydroperoxide reductase) was found in G1. Ad-
ditionally, different isoelectric points (pI) of Hsp60 were observed from the two strains. Then we cloned and sequenced
Hsp60 genes from forty-nine Helicobacter pylori isolated from gastric cancer and gastritis. Gene sequencing showed
that one C→G single nucleotide polymorphism occurred in the 1399th nucleotide of Hsp60. These results indicate that
pathogenic differences exist in various Helicobacter pylori isolated from Chinese patients.
Keywords: Helicobacter pylori; Two-Dimensional Gel Electrophoresis; Proteome Map; Gastric Cancer; Gastritis; Heat
Shock Protein 60
1. Introduction
The gastric cancer is the fourth most common cancer and
the second leading cause of cancer-related deaths. It is a
multistep process caused by multiple factors including
human host genotype, physiological, immunological, and
environmental factors, as well as Helicobacter pylori (H.
pylori) infection. Epidemiological studies have deter-
mined that H. pylori confers an attributable risk for gas-
tric cancer of approximately 75% [1]. WHO has ranked
H. pylori as a class I carcinogen.
H. pylori is a gram-negative, spiral-shaped microaero-
philic bacterium that colonizes the human stomach and
causes type-B gastritis, gastric/duodenal ulcers, and gas-
tric cancer. According to epidemiological studies, half of
the world population is infected by H. pylori, but only a
fraction of these infections lead to overt disease, includ-
ing gastric cancer [2]. In addition to the human host
genotype and environmental factors, the H. pylori sub-
type also plays an important role in the outcome of infec-
tion.
Strain diversity among H. pylori isolates has been
studied at the gene level, and some reports have shown
that H. pylori isolates from different clinical outcomes
are genetically diverse with partial virulence factors,
which play an important role in pathogenesis [3-6]. With
more complete genomes of H. pylori strains sequenced
[7-10], the information accumulated from genomic stud-
ies allows the use of proteomics technologies in studies
of these bacteria. Proteomics analyses can be used to
study the production and function of proteins coded by
active genes and to investigate the pathogenic properties
of H. pylori strains. Jungblut et al. reported that there were
certain differences in the positions of protein spots in
2-DE maps of H. pylori strains 26695 and J99 [11]. Us-
ing comparative analyses of 2-DE maps from H. pylori
isolates derived from duodenal ulcers and gastritis, Perei-
*Contributed equally.
#Corresponding author.

Comparative Proteomic Analysis of Helicobacter pylori Strains Isolated from Chinese Patients 7
ra et al. reported that H. pylori isolates differentially ex-
pressed certain proteins [12]. However, whether gastroin-
testinal diseases are related to different patterns of H.
pylori protein expression is still debated and further stud-
ies must be performed.
In our study, we compare 2-DE proteome maps of H.
pylori clinical isolates obtained from patients with gastric
cancer and gastritis in order to investigate whether there
are specific proteins related to the pathogenic differ-
ences.
2. Experimental
2.1. H. pylori Strains and Culture Conditions
Forty-nine H. pylori strains were isolated from biopsies
of gastric antrum mucosa obtained from patients with
gastritis (n = 31; No. G1-31; mean age, 53.2 years; male/
female, 16/15) and gastric cancer (n = 18; No. C1-18;
mean age, 59.8 years; male/female, 10/8). Two of these
strains, No. G1 and C1, isolated from the female patients
(with age of 48 and 52 years, respectively) at the affili-
ated hospital of Binzhou Medical University (China),
were used to 2-DE. Isolates were grown for 72 h on Co-
lumbia agar base, including vancomycin (6 μg/mL),
trimethoprim (5 μg/mL), polymyxin B (4 μg/mL), am-
photericin B (2.5 μg/mL), and 10% sheep’s blood, at
37˚C in microaerophilic conditions containing 5% O2,
10% CO2, and 85% N2.
2.2. Sample Preparations
H. pylori strains G1 and C1 were harvested and washed
with phosphate-buffered saline (PBS). Total protein was
extracted using the trichloroacetic acid (TCA)/acetone
precipitation method. Precipitated proteins were lysed
overnight at 4˚C with lysis buffer, containing 2 M thio-
urea, 7 M urea, 1% (w/v) DDT, 2% (w/v) CHAPS, 4%
immobilized pH gradient (IPG) buffer, and 10 mM
PMSF. The suspension was sonicated for 90s on ice, fol-
lowed by centrifugation for 10 min at 12000 × g. The su-
pernatant was removed and protein concentrations were
determined using the Bradford method [13].
2.3. 2-DE and Image Analyses
The first-dimension IEF and second-dimension SDS-
PAGE were performed according to the manufacturer’s
instructions (Pharmacia Biotech, USA). The protein
samples (200 µg) were mixed with 450 µL rehydration
buffer (8 M urea, 2% CHAPS, 60 mM DTT, and 0.5%
IPG buffer) and applied to 24-cm IPG dry strips (pH 3 -
10). Isoelectric focusing was performed for 80,000 Vh
over a 25 h period by using the Ettan IPGphor II appara-
tus (Pharmacia Biotech, USA). The focused strips were
equilibrated with equilibration buffer I (50 mM Tris-HCl,
pH 8.8, 6 M urea, 30% glycerol, 2% SDS, and 1% DTT)
and equilibrated again with equilibration buffer II (50
mM Tris-HCl, pH 8.8, 6M urea, 30% glycerol, 2% SDS,
and 4.8% iodoacetamide). After equilibration, SDS-
PAGE was performed on 12.5% polyacrylamide gels at
2.5 W for 30 min, and at 18 W until the bromophenol
blue reached the bottom of the gel. After staining with
Coomassie Brilliant Blue, the individual gels were im-
aged using an Image Scanner (Pharmacia Biotech, USA)
and analyzed by 2-D Image Master V3.1.
2.4. In-Gel Digestion
Differentially expressed spots were excised from the
2-DE gels using a SpotPicker automated gel station
(Pharmacia Biotech, USA) and subjected to washing,
destaining, reduction, alkylation, trypsin digestion, and
peptide extraction. Briefly, each fragment was washed in
25 mM ammonium bicarbonate and destained in a solu-
tion of 25 mM ammonium bicarbonate and 30% acetoni-
trile. After equilibration with 25 mM ammonium bicar-
bonate, the gel pieces were reduced with 25 mM ammo-
nium bicarbonate (pH 8.0) containing 10 mM DTT for
60 min and alkylated with 25 mM ammonium bicarbon-
ate (pH 8.0) containing 55 mM IAA for 30 min. After
equilibration with 25 mM ammonium bicarbonate, each
gel fragment was treated with 20 μg/ml trypsin (Sigma),
and then incubated in 25 mM ammonium bicarbonate
(pH 8.0) at 37˚C for 16 h. After trypsinization, the re-
sulting peptides were extracted with 50% ACN and 0.1%
TFA, and dried in a vacuum centrifuge. Samples, con-
centrated to a final volume of 10 μl with 5% TFA in 60%
CH3CN, were used for mass spectrometry analyses.
2.5. Protein Identification by MALDI-TOF-MS
Analyses
Peptide analyses were performed using Matrix-Assisted
Laser Desorption Ionization-Time of Flight Mass Spec-
trometry (MALDI-TOF-MS). Briefly, protein samples
and matrix solution (α-cyano-4-hydroxycinamic acid pre-
pared in 70% acetonitrile/1.1% trifluoroacetic acid) were
mixed (1:1) and loaded into the target wells. The wells
were dried at room temperature and subjected to
MALDI-TOF-MS analyses using a Reflex (Bluker). MS
spectra were analyzed using the program Mascot (based
on the NCBInr and SWISSPROT databases).
2.6. Gene Sequencing
Total DNA was extracted from H. pylori strains (G1-31
and C1-18) according to the manufacturer’s protocol
(QIAGEN, Germany). The Hsp60 gene was cloned using
the following conditions: 95˚C for 5 min, followed by 30
cycles of 94˚C for 30s, 52˚C for 30s, and 72˚C for 90s.

Comparative Proteomic Analysis of Helicobacter pylori Strains Isolated from Chinese Patients 8
This was followed by a final extension at 72˚C for 5 min.
A forward primer (5’-CTTACATCATGCC-3’) and a
reverse primer (5’-CGTTCGAAGTAGAGAAATCG-3’)
were used in this amplification. The products were se-
quenced by Majorbio Shanghai Technologies Company.
Sequence comparisons and analyses were performed us-
ing DNAstar 5.0 software.
3. Results
3.1. Protein Expression of H. pylori Clinical
Isolates
To obtain the protein expression profiles of H. pylori G1
and C1, we performed 2-DE analysis. After staining with
Coomassie Brilliant Blue, we found that whereas several
main spots were in the same position, we observed four
spots (spots 1, 2, 3, and 4) of H. pylori C1 that were not
observed in H. pylori G1. There was one spot (spot 5) of
H. pylori G1 that was not visualized in H. pylori C1. In
addition, the isoelectric point (pI) of spot 6 is different in
the two strains despite its conserved expression. Proteome
maps of H. pylori G1 and C1 are shown in Figure 1.
3.2. Identification of Differentially Expressed
Proteins
The differentially expressed protein spots (spot No. 1 - 6)
in the different proteome maps were excised from the gel
and mass fingerprintings of the 6 proteins were obtained
using MALDI-TOF-MS. Corresponding amino acid resi-
due numbers are indicated on the peaks that match the
identified protein based on a NCBInr database query.
Spots numbered 1 - 6 were identified as shown in Table
1. In the six proteins, three are enzymes associated with
metabolism, including inorganic pyrophosphatase (Ppa),
3-oxoadipate CoA-transferase subunit B (OXCTB), and
translation elongation factor (EF-P). Two are related to
anti-oxidation effects, aldo-keto reductase and alkyl hy-
droperoxide reductase (AhpC/TsaA). The final spot, heat
shock protein 60, belongs to the chaperonin family.
3.3. Gene Sequencing
The Hsp60 gene was cloned and sequenced. Sequence
alignment and analyses were performed using DNAstar
5.0 software. Although the Hsp60 gene contains many
highly conserved nucleotide sequences, we found one
C→G single nucleotide polymorphism occurred in the
1399th, and 22.58% (7/31) of nucleotides changed from
C to G in H. pylori strains isolated from patients with
gastritis. In one gastric cancer patient, the ratio of nu-
cleotide mutation (C→G) is only 5.56% (1/18) (Figure
2(a)). When translated into protein sequences, the nu-
cleotide mutation results in an amino acid substitution at
codon 467 from Q (Gln) to E (Glu) (Figure 2(b )).
(a)
(b)
Figure 1. Proteome maps of H. pylori clinical isolates G1(a)
and C1(b). The protein spots were separated over the mo-
lecular weight (Mr) range of 10 - 200 kDa and the pI range
of 3 - 10.
4. Discussion
Recently, strain variations in H. pylori have been studied
at the gene level and compared among different patient
groups [3-6]. In this study, we focused on specific H.
pylori proteins derived from patients with gastric cancer
and non-gastric cancer. By comparing 2-DE proteome
maps, five proteins were differentially present or absent
between H. pylori G1 and C1. These proteins are classi-
fied into two groups: anti-oxidant proteins and enzymes
related to metabolism. The anti-oxidation system, which
eliminates damage due to oxygen free radicals released
by host macrophages and neutrophils, plays a vital role in
H. pylori colonization. The energy metabolism of H. py-
lori is essential for its growth and survival. The enzymes
related to metabolism are thought to assist virulence fac-
tors in modulating adaptation to hosts and to cause per-

Comparative Proteomic Analysis of Helicobacter pylori Strains Isolated from Chinese Patients 9
(a)
(b)
Figure 2. (a) Gene sequence alignment of Hsp60 protein in H. pylori clinical isolates; (b) Amino acid sequence alignment of
Hsp60 protein in H. pylori clinical isolates.

Comparative Proteomic Analysis of Helicobacter pylori Strains Isolated from Chinese Patients 10
Table 1. Identified proteins on the proteome maps of H. pylori isolates.
H. pylori (a)
Spot No.
C1 NC1
pI
Values MW (Da) Identification Gene (b)
1 + − 4.80 19271.9 inorganic pyrophosphatase (Ppa) Hp0620
2 + − 5.35 22262.9 3-oxoadipate CoA-transferase subunit B (YjxE) Hp0692
3 + − 5.35 20787.8 translation elongation factor (EF-P) Hp0177
4 + − 7.65 37073.8 aldo-keto reductase Hp1139
5 − + 6.25 22235.6 alkyl hydroperoxide reductase (AhpC/tsaA) Hp1563
6 + + 5.55 58227.5 chaperone and heat shock protein (GroEL) Hp0010
(a) Symbols “+” or “−” show the presence or absence of the protein spot on the proteome maps, respectively; (b) Homolog of the gene of H. pylori strain 26695.
sistent bacterial infection. Combining our results with
other pertinent studies [11,14-16], these strain-specific
proteins are thought to play a role in the pathogenicity of
H. pylori and can be used for H. pylori infection charac-
terization. However, this hypothesis is still debated and
requires more studies.
In addition, differences in pI values of Hsp60 were
found in our study. The Hsp60 spot from H. pylori C1
isolated from gastric cancer shifted into acidic regions
compared to the H. pylori G1 isolated from non-gastric
cancer, despite its conserved expression. Interestingly,
our results are similar to what has been previously re-
ported. Govorun et al. characterized some proteins of H.
pylori isolates, including Hsp60, by different pI values
[12,17]. Krah et al. also reported that the pattern expres-
sion of Hsp60 was different in gastrointestinal diseases
[18]. Many reports have shown that Hsp60 is an immu-
nogen and can lead to host inflammation [19-22]. Hsp60,
which has different pI values, may play a different role in
inflammation and result in different diseases induced by
H. pylori infection.
We speculated that these changes in pI values might
have been attributed to possible amino acid mutations.
Therefore, we cloned and sequenced the Hsp60 gene. At
the 1399th, we found the ratio of nucleotide mutation
(C→G) was different in H. pylori associated with gastric
cancer and non-gastric cancer (5.56% vs. 22.58%). With
the increasing availability of gene sequences, sequence
analyses of Hsp60 genes have been reported. It can dis-
tinguish species and/or subspecies in different taxa, such
as Enterococcus [23,24], Staphylococcus [25], and Bifid
bacterium [26]. Therefore, the utility of Hsp60 for bacte-
rial species identification is well established. The 1399th
site mutation of Hsp60 might be a biomarker for identi-
fication of H. pylori associated with gastric cancer.
In this study, we have investigated variations in dif-
ferent H. pylori isolates at the protein level and found
differently expressed protein spots that are useful for
characterizing H. pylori strains. A single nucleotide
polymorphism at the 1399th of Hsp60 might be a bio-
marker for distinguishing subspecies of H. pylori strains
but this hypothesis requires more research.
5. Acknowledgements
This work is supported in part by grants from the Na-
tional Key Program for Infectious Diseases of China (No.
2008ZX1004-002), the National Technology R&D Pro-
gram in the 12th Five-Year Plan of China (No. 2012
BAI06B02), the NSFC (81072429), the Program for New
Century Excellent Talents in University (NCET-111026),
Grants-in-Aid for Shandong Province Outstanding Young
Scientist Research Award Fund (2010BSB140), Colleges
and Universities in Shandong Province Science and
Technology projects (J10LF21), and the Yantai Muicipal
Science and Technology Development Program (2010172).
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