J O U RN A L OF P ROT EO M IC S 1 1 5 ( 2 01 5 ) 1 0 7 –11 6

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Proteomic analysis on the antibacterial activity of a

Ru(II) complex against Streptococcus pneumoniae

Xiao-Yan Yanga,b , Liang Zhanga , Jie Liuc , Nan Lia , Guangchuang Yua , Kun Caoa ,
Junlong Hana , Guandi Zenga , Yunlong Panb , Xuesong Suna,⁎⁎, Qing-Yu Hea,⁎
a
Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of
Life Science and Technology, Jinan University, Guangzhou 510632, China
b
The First Affiliated Hospital of Jinan University,Guangzhou 510632, China
c
Department of Chemistry, Jinan University, Guangzhou 510632, China

AR TIC LE I N FO ABS TR ACT

Article history: Streptococcus pneumoniae is a Gram-positive pathogen that causes a variety of infection
Received 2 June 2014 diseases in human. In this project, we determined the antibacterial activity of a Ru(II)
Accepted 27 November 2014 complex X-03 against S. pneumoniae in vitro, by comparing its toxicity to host cells A549 and
Available online 10 December 2014 HBE. We performed two-dimensional gel electrophoresis (2-DE)-based proteomic analysis
to characterize the protein alterations in S. pneumoniae after treatment with X-03. In total, 50
Keywords: proteins exhibiting significant differential expressions were identified. RT-PCR was used to
Ru(II) complex confirm the expression differences for selected proteins. Bioinformatics analysis on the
Antibacterial activity proteomic alterations suggested that Ru(II) complex X-03 may obstruct bacterial fatty acid
S. pneumoniae synthesis and oxidation–reduction process to suppress the growth of S. pneumoniae.
Proteomic profiling Metal-uptake experiments revealed that iron-acquisition pathway in the bacterium may
be interfered by X-03. These results provide useful clues for further investigations on the
mechanism of the antibacterial action of metal compounds.

Biological significance
The appearance of bacterial strains with broad antibiotic resistance is becoming an
alarming global health concern. The development of novel efficient antibacterial compound
is urgently needed. In the present study, we found that Ru(II) complex X-03 has a significant
antibacterial activity and applied proteomic technology combined with bioinformatics
analysis to investigate its antimicrobial mechanism in S. pneumoniae. Many proteins were
found to be dysregulated, implicating that X-03 may affect various molecular pathways
leading to the inhibition of bacterial growth. Metal-uptake experiments demonstrated that
X-03 treatment reduced the iron content in the bacterium, suggesting the interference with
iron acquisition systems by the complex. This disturbance in iron acquisition may directly
or indirectly induce the proteomic response that involved many pathways. In addition, X-03
could selectively suppress Gram-positive bacteria but execute less cytotoxicity to
Gram-negative bacteria, with almost no effect on human cells, implicating its potential to
be developed as a specific antimicrobial agent. These results provide useful information for

⁎ Corresponding author. Tel./fax: +86 20 85227039.

⁎⁎ Corresponding authors. Tel./fax: +86 20 85226165.
E-mail addresses: tsunxs@jnu.edu.cn (X. Sun), tqyhe@jnu.edu.cn (Q.-Y. He).

http://dx.doi.org/10.1016/j.jprot.2014.11.018
1874-3919/© 2014 Elsevier B.V. All rights reserved.
108 J O U RN A L OF P ROT EO M IC S 1 1 5 ( 2 01 5 ) 1 0 7 –11 6
further investigations on the mechanism of the antibacterial action of metal drugs and
development of efficient antibacterial drugs.
1. Introduction
Streptococcus pneumoniae (S. pneumoniae) is a leading health
hazard in young children and elderly peoples by causing several
diseases including pneumonia, otitis media, bacteraemia and
meningitis [1,2]. The emergence of S. pneumoniae resistance to
conventional antibiotics has stimulated an urgent search for
new types of antimicrobial compounds different from the
current range of antibiotics. Metal complexes that exhibit
anti-bacterial activities may represent a promising type of the
new compounds. In 1952, Dwyer et al. [3] observed that metal
compounds including polypyridylruthenium(II) complexes pos-
sess antibacterial activity; however, there have been few
subsequent studies on their antibacterial mechanism. Ru(II)
polypyridyl complexes have been extensively studied as anti-
cancer agents; in particular, two representatives of ruthenium
complexes KP1019 and NAMI-A have successfully entered
clinical trials [4–7]. In contrast, the antibacterial activity of the
Ru(II) polypyridyl complexes is poorly known; more detailed
studies are needed.
In this work, we determined the antibacterial activity of a
Ru(II) complex X-03 and investigated the proteomic alter-
ations in S. pneumoniae in response to the X-03 treatment by
using two-dimensional electrophoresis (2-DE) coupled with
MALDI-MS/MS technology. The obtained data suggest that
Ru(II) complex X-03 may regulate fatty acid biosynthesis and
oxidation–reduction process to inhibit bacterial growth.
2. Materials and methods
Ru(II) complex X-03 was synthesized according to the proce-
dure previously described in our earlier publication [8]. The
structure of X-03 is shown in Fig. 1.
2.1. Bacterial strains and growth conditions
S. pneumoniae D39, Streptococcus suis 05ZYH33, Streptococcus
pyogenes MGAS5005, Listeria monocytogenes 19117, Staphylococcus
aureus 29213, Escherichia coli K12, Vibrio alginolyticus V12G01,
Vibrio parahaemolyticus RIMD 2210633 and Acinetobacter
Fig. 1 – The chemical structure of Ru(II) complex X-03.
© 2014 Elsevier B.V. All rights reserved.
baumannii 19606 were used in the present study. S. pneumoniae
D39 and S. uberis 05ZYH33 were grown in THY broth
(Todd-Hewitt broth supplemented with 5% yeast extract) at
37 °C and 5% CO2. S. pyogenes MGAS5005 was grown in THY
broth (Todd-Hewitt broth supplemented with 5% yeast
extract) at 37 °C with shaking at 200 rpm. S. aureus 29213
was grown in tryptic soy broth at 37 °C with shaking at
200 rpm. L. monocytogene 19117, E. coli K12, V. alginolyticus
V12G01, V. parahaemolyticus RIMD 2210633 and A. baumannii
19606 were grown in LB medium (1% tryptone, 0.5% yeast
extract, 1% NaCl) at 37 °C with shaking at 200 rpm.
2.2. Determination of minimum inhibitory concentration (MIC)
X-03 was dissolved in ddH2O as a stock solution at 10 mg/mL.
The susceptibilities of Gram-positive species including S.
pneumoniae D39, S. uberis 05ZYH33, S. pyogenes MGAS5005, L.
monocytogene 19117, S. aureus 29213 and Gram-negative
species including E. coli K12, V. alginolyticus V12G01, V.
parahaemolyticus RIMD 2210633 and A. baumannii 19606 to
X-03 were tested by standard micro-dilution methodology:
X-03 was diluted in the media by two-fold serial dilutions
ranging from 200 μg/mL to 3.125 μg/mL. The bacteria were
grown in media with a series concentration of X-03 after 24 h
incubation at 37 °C; the bacterial concentration in each well
was determined at 600 nm using spectrophotometry (Ther-
mo) and MIC values were calculated [9].
2.3. Bacterial culture and preparation of cellular protein extracts
X-03-free and sub-MIC treated S. pneumoniae D39 were cultured
in Todd-Hewitt broth supplemented with 0.5% yeast extract
(THY) at 37 °C with 5% CO2. The cells were harvested by
centrifugation at 6000 g for 10 min at 4 °C when the absorbance
reading of 0.6 at 600 nm was reached. Then, cell pellet was
washed three times with 10 mM ice-cold PBS (pH 7.4) and finally
resuspended in lysis buffer (15 mM Tris–HCl, 7 M urea, 2 M
thio-urea, 1% DTT and 4% CHAPS, 1% protease inhibitor). The S.
pneumoniae cells were disrupted by three freeze-thawed cycles
and sonication (10 min, 5 s pulse with 5 s cooling time), then cell
debris was removed by centrifugation at 12,000 g for 10 min at
4 °C. The supernatant was transferred to clear microcentrifuge
tubes and stored at −80 °C until further use. Bradford assay was
applied to measure the protein concentrations.
2.4. Cytotoxicity assay
The alveolar epithelial cell line A549 and bronchial epithelial
cell line HBE were cultivated in DMEM medium supplemented
with 10% fetal bovine serum (FBS). Cells were seeded at a
density of 5 × 103 per well in 96-well plate and incubated at
37 °C with 5% CO2 for 24 h. Then X-03 was added to yield final
concentrations of 0, 25, 50, 100 and 200 μg/mL and the cells
were further incubated at 37 °C for 48 h in the dark. After
 J O U RN A L OF P ROT EO M IC S 1 1 5 ( 2 01 5 ) 1 0 7 –11 6 109

adding 10 μL/well WST-1 solution and incubating the cells for secondary effects of X-03 on the bacterium in long-time drug
another hour, the culture was vortexed at 300 rpm for 10 min; treatment, S. pneumonia D39 at OD600 = 0.3 treated with sub-MIC
the concentration of cells in each well was detected at 450 nm X-03 for 1 h and 2 h was also collected. Total RNA was extracted
using a microplate reader (Bio-Tek, USA). from S. pneumoniae D39 strain cultured in different conditions
using TRIzol (Invitrogen) according to the manufacturer's
2.5. ICP-MS analysis protocol. Any genomic DNA in the RNA samples was removed
by treatment with RNase-free DNase I (Omega). The cDNA
Determination of intracellular iron, ruthenium and manga- synthesis and real-time quantitative PCR were performed as
nese contents was carried out by inductively coupled plasma described previously [14]. Briefly, 1 μg of total RNA was used as
mass spectrometry (ICP-MS) (Thermo Scientific) analysis as the template for reverse transcription using iScript Reverse
previously described [10]. 5 × 108 CFU of mid-log phase Transcriptase (Bio-Rad) according to the kit's instructions.
bacteria were harvested by centrifugation and washed three Real-time quantitative PCR was carried out using EvaGreen Dye
times with chelex-100-treated PBS. The dry cell mass was (Bio-Rad) in a Miniopticon Real-Time PCR System (Bio-Rad). The
resuspended with 1.5 mL of 14% HNO3, and boiled at 95 °C for cycle threshold (Ct) value was measured, and relative quantifi-
20 min. The samples were then centrifuged at 13,200 g for cation of specific gene expression was calculated using the 2−ΔΔCt
30 min, and the supernatant was collected for metal content method [15], with the 16S rRNA as an internal control, and
analysis by ICP-MS. Results were expressed as ng of Fe2+, Ru2+ normalized against the normal control (without X-03 treatment),
and Mn2+ per mg dry weight of cells. Three independent respectively. The primer sequences are shown in Table 1.
biological experiments were repeated.
2.10. Determination of free fatty acid (FFA)
2.6. Two-dimensional gel electrophoresis (2-DE)
The commercial EnzyChrom™ Free Fatty Acid Assay Kit
The 2-DE was done as follows: briefly, 13 cm IPG strips in the (BioAssay Systems, USA) was used to determine the free
pH ranges of 4–7 were loaded with 100 μg total proteins, and fatty acid (FFA) content in S. pneumoniae D39 with or without
isoelectric focusing and SDS-PAGE electrophoresis were car- X-03 treatment. Briefly, bacteria were homogenized in 5%
ried out with the parameters in accordance with a previously isopropanol and 5% Triton X-100 in water and sonicated for
described protocol [11]. The gels were stained with silver 3 min (5 s pulse with 5 s cooling time), then cell debris was
nitrate and scanned with ImageScanner (Amersham Biosci- filtrated through a 0.45 μm PTFE syringe filter. The superna-
ences). After scanning, the 2-DE gels were subjected to tant was transferred to clear microcentrifuge tubes and then
differential spot-abundance analyses by ImageMaster 2D 10 μL of each sample was transferred into separate wells of a
Platinum 6.0 according to a previously described method clear flat bottom 96-well plate; 90 μL working reagent was
[11]. Only those protein spots with at least 2-fold spot volume added to each well, and then was mixed. After 30 min
ratio change (p < 0.05) in three independent experiments were incubation at room temperature, the concentration of FFA
selected for protein identification by MS. was determined at 570 nm using an Autoplate reader
(Bio-Tek, USA). Results were expressed as ng of FFA per mg
2.7. In-gel digestion and protein identification
Table 1 – Primers used in the study.
The differential proteins were digested with trypsin and analyzed Primer Sequence (5′-3′)
by ABI-4800 plus MALDI TOF/TOF mass spectrometer in accor-
16S RNA-F 5′-CTGCGTTGTATTAGCTAGTTGGTG-3′
dance with our previously described protocol [11]. Proteins were
16S RNA-R 5′-TCCGTCCATTGCCGAAGATTC-3′
identified by the MASCOT search engine (V2.1) against NCBI S. accA-F 5′-GAAGGCTACCGAAAGGCACT-3′
pneumoniae D39 protein database based on the MS and MS/MS accA-R 5′-TTCTTCCGCTCCGACACC-3′
spectra. The error tolerance values of the MS and MS/MS ion fabG-F 5′-CGATGATGAAAGCCAGAGAA-3′
masses were 100 ppm and 0.1 Da, respectively. Protein identifi- fabG-R 5′-CGTGCCACAGACTTGGTAAA-3′
cations with Mascot scores C. I. % > 95 were considered. fabK-F 5′-CGAATGCCCATCCAAACT-3′
fabK-R 5′-CACCCTCCACATCACCGT-3′
grpE-F 5′-ATCCAACGCCGTGCCA-3′
2.8. Bioinformatics analysis
grpE-R 5′-CATCGCCAAGCCCTTC-3′
eno-F 5′-TGGAAACTGCCGTAGGTG- 3′
With Gene Ontology (GO) database, the differentially expressed eno-R 5′-GCACAGTCAAATCCGAGA-3′
proteins (DEPs) were categorized according to their functions [12]. 1402-F 5′-CATTGGCAAAAACAAAGGA-3′
And the interaction network of DEPs was built by the STRING as 1402-R 5′-ACCGAGTGTAATCAAGCGT-3′
described previously (http://string-db.org/); the search parame- ghdA-F 5′-CCTCTTGGATTTGGTGGTA-3′
ghdA-R 5′-AAGTTCGGTTGCTTTTTGA-3′
ters were as follows: organism (S. pneumoniae D39), confidence
1590-F 5′-TGAAGCAGACTCAGTAAGCC-3′
(score = 0.40) and interactors (no more than 10 interactors) [13].
1590-R 5′-GAAACCAGATCCAAGACCAG-3′
piaA-F 5′-TAGTCAGACAGAGACCAGT-3′
2.9. Real-time quantitative PCR piaA-R 5′-CTTTCATAGAACCAACATT-3′
piuA-F 5′-ATTTGACGATTTGGATGGACTT-3′
The overnight cultured S. pneumoniae D39 were diluted 1:100 in piuA-R 5′-GATTTGTATGCTGCTACAGGAG-3′
THY broth medium and then grown in the presence or absence pitA-F 5′-ATGACTGTTGGTCTCTCTT-3′
pitA-R 5′-TTGTTTTAGCATTTTTACG-3′
of sub-MIC X-03 until the mid-log phase (about 5 h). To avoid the
110 J O U RN A L OF P ROT EO M IC S 1 1 5 ( 2 01 5 ) 1 0 7 –11 6

dry weight of cells. All data were calculated from at least three Table 2 – Minimal inhibitory concentrations (MICs) of
independent biological experiments. Ru(II) complex X-03 against S. pneumoniae D39, S. uberis,
S. pyogenes MGAS5005, L. monocytogenes 19117, S. aureus
2.11. Statistical analysis 29213, E. coli K12, V. alginolyticus V12G01, V.
parahaemolyticus RIMD 2210633 and A. baumannii 19606.

Statistical significance was performed using two-tailed Student's Bacteria MIC (μg/mL)
t-test and was assigned p < 0.05. All data are expressed as S. pneumoniae 25
mean ± SEM of triplicate samples, and reproducibility was S. suis 100
confirmed in three separate experiments. S. pyogenes 25
L. monocytogenes 25
S. aureus 50
E. coli >200
3. Results and discussion
Vibrio alginolyticus >200
Vibrio parahaemolyticus >200
3.1. Ru(II) complex X-03 has antibacterial activity with low A. baumannii >200
cytotoxic effect on human cells

Ru(II) complex X-03 can suppress the growth of S. pneumoniae.
The growth kinetics of S. pneumoniae D39 in the presence of 0,
3.125, 6.25, 12.5, 25, 50 and 100 μg/mL X-03 are shown in
Fig. 2A. Based on these growth curves, the MIC of X-03 against
S. pneumoniae D39 was determined to be 25 μg/mL. The MIC
values of X-03 against other bacteria were also determined.
Interestingly, as shown in Table 2, X-03 showed little activity
against the Gram-negative bacterium, suggesting that X-03 is
specifically active on Gram-positive bacteria. This difference
is intriguing and warrants further study. The sub-MIC of
12.5 μg/mL for S. pneumoniae D39 was used in the following
X-03 treatments and proteomic experiments.
The cytotoxicity of X-03 in alveolar epithelial cell line A549
and bronchial epithelial cell line HBE was measured to test its
side effects on host cells. As shown in Fig. 2B, WST-1 assay
revealed that only high doses (> 8 MIC against S. pneumoniae) of
X-03 slightly decreased the viability of A549 and HBE cells,
whereas low doses were almost non-toxic to these cells. This
result suggested that X-03 has selective toxicity for S.
pneumoniae D39 but not host cells, implicating its potential to
be developed as an antibacterial agent.
3.2. Bacterium S. pneumoniae uptakes X-03 into cells
To measure the effect of X-03 treatment on the metal acquisition
of the bacterium, the uptake of X-03 into S. pneumoniae was
determined by comparing the intracellular iron, ruthenium and
manganese levels with ICP-MS analysis. The results shown in
Fig. 3 revealed that, after treatment with 12.5 μg/mL X-03, the
ruthenium concentration in S. pneumoniae increased while the
iron concentration decreased and the manganese concentration
remained unchanged. This means that the uptake of Ru from
X-03 reduced the Fe acquisition in the bacterium with no effect
on Mn absorption. In view of the fact that Ru and Fe belong to
the same family in the periodic table, they have many
similarities in nature. Ru in X-03 may thus compete with Fe for
iron transportation pathways to enter the cells. Since iron is a
cofactor required for many proteins and enzymes in cell
metabolism, essential for bacterial growth and infection [16,17],
we can therefore reasonably speculate that ruthenium complex
X-03 interferes with iron acquisition systems in the bacterium to
inhibit bacterial growth.
3.3. X-03 regulated protein alterations in major pathways
To view the global impact of the antibacterial activity of X-03 on
proteome of S. pneumoniae, the profiling on whole-cell proteins
extracted from the bacterium with and without X-03 treatment
was performed by comparative proteomics. In total 50 DEPs
including 24 up-regulations and 26 down-regulations were
identified, showing at least 2-fold spot volume ratio changes
(p < 0.05) in three independent experiments (Fig. 4). The detailed

Fig. 2 – Effects of Ru(II) complex X-03 on S. pneumoniae and human A549 cells. (A) X-03 inhibited S. pneumoniae growth in a
concentration-dependent manner. (B) X-03 exhibited low cytotoxicity to alveolar epithelial cell line A549 and bronchial
epithelial cell line HBE. Cells were treated with the different concentrations of X-03, and the cell viability was measured by
WST-1 assay. The data shown represent the mean of three experiments; error bars indicate SEM.
 J O U RN A L OF P ROT EO M IC S 1 1 5 ( 2 01 5 ) 1 0 7 –11 6
Fig. 3 – ICP-MS determination of the intracellular Fe, Ru and
Mn accumulation in S. pneumoniae with/without X-03
treatment, expressed as ng metal/mg cells. Results are
representative of the mean ± SEM from three independent
experiments (**p < 0.01).
information of these DEPs is listed in Table 3. To validate the
proteomic data, real-time quantitative PCR of selected genes was
performed. The results manifested that all the selected genes had
similar changes with their proteins in expression levels (Fig. 6A).
To exclude the secondary effects of X-03 on the bacterium in
long-time drug treatment, we also examined the expression
levels of another six genes in S. pneumoniae upon X-03 treatment
for 1 h or 2 h. As shown in Fig. 6A, the alterations of most genes in
the bacterium during the long-time treatment of X-03 are
basically consistent with those in short-time treatment.
Gene Ontology (GO) database analysis on these DEPs
demonstrated that, these altered proteins are associated with
several important functions including translation, tRNA amino
acylation, protein folding, cell cycle or regulation, DNA replica-
tion or transcription, carbohydrate metabolism, fatty acid
metabolism, nucleotide metabolism and oxidation (Fig. 5A).
Nevertheless, as shown in Fig. 6A, gene eno did not change until
the long-term drug treatment, suggesting that eno-related
carbohydrate metabolism may be the secondary response to
X-03 stimulation.
Fig. 4 – Two dimensional electrophoresis of the whole-cell proteins of S. pneumoniae, in the pH range of 4–7. Protein extracts
were prepared from untreated control cells (A) and sub-MIC X-03-treated cells (B).
111
3.4. X-03 reduces the resistance ability to oxidative damage
We noted a surprisingly broad impact of X-03 on oxidation in the
bacterium, with six oxidation-related proteins down-regulated
following the exposure to X-03. One of them is ferritin
(SPD_1402), the primary iron storage protein in bacteria,
supplying the necessary iron for cells [18]. The SPD_1402
homologues in S. pyogenes are peroxide resistance protein
(Dpr); the deletion of this gene leads to the increased suscep-
tibility to oxidative stress [19]. In addition, based on the GO
analysis, 3-ketoacyl-(acyl-carrier-protein) reductase (FabG)
and glutamate dehydrogenase (GhdA) possess the oxidore-
ductase activity to produce reduced nicotinamide-adenine
dinucleotide phosphate (NADPH). Studies on Clostridium
difficile have suggested that GhdA contributes to oxidative
stress resistance [20]. Moreover, the down-regulated oxido-
reductase, aldo/keto reductase family protein (SPD_0693) and
oxidoreductase, Gfo/Idh/MocA family protein (SPD_1311) also
were predicted to have NADP binding domain. NADPH is
necessary for fatty acid and DNA synthesis, providing
protection for organism against reactive oxygen species
(ROS) damage [21]. In this regard, X-03 may down-regulate
the oxidation-related proteins to suppress the production of
NADPH and thus reduce the resistance ability of the
bacterium to oxidative damage.
3.5. X-03 suppresses fatty acid biosynthesis
Among these DEPs, three proteins including acetyl-CoA carbox-
ylase subunit alpha (AccA), FabG, and trans-2-enoyl-ACP reduc-
tase II (FabK) involved in fatty acid metabolism were
down-regulated by X-03. This down-regulation was also con-
firmed in their mRNA levels (Fig. 6A). Crucial for several essential
cellular functions, bacterial fatty acid biosynthesis is catalyzed
by a series of independent monofunctional enzymes (type II
FAS), differing from the catalysis by a single large multifunction-
al protein (type I FAS) in mammals. AccA is a subunit of bacterial
112 J O U RN A L OF P ROT EO M IC S 1 1 5 ( 2 01 5 ) 1 0 7 –11 6

Table 3 – The information of proteins with expression alteration in response to the X-03 treatment.
Spot Accession Protein name Gene Protein Protein pI F. D. ± S.D. Score
no. no. NAME M.W. (a) C. I. %

Translation
28 gi|116515784 Asparagine synthetase AsnA asnA 37,584.2 5.05 −3.7 ± 0.16 100
89 gi|116516740 30S ribosomal protein S6 rpsF 11,145.8 5.15 5.5 ± 0.23 99.95
86 gi|116516047 30S ribosomal protein S13 rpsM 13,413.5 10.63 7.3 ± 0.15 100

tRNA aminoacylation
53 gi|116516757 tRNA(5-methylaminomethyl-2-thiouridylate)- mnmA 41,600.3 5.23 2.9 ± 0.12 100
methyltransferase
44, 60, gi|116515696 Transcription antitermination protein NusG nusG 20,334.2 4.68 14.8 ± 1.01 100
79
28 gi|116515784 Asparagine synthetase AsnA asnA 37,584.2 5.05 −3.7 ± 0.16 100
41 gi|116516249 16S rRNA-processing protein rimM 19,804.2 4.78 2.2 ± 0.16 99.44
47 gi|116517090 Lysyl-tRNA synthetase lysS 56,645.8 5.32 3.7 ± 0.22 100

Protein folding
2, 74 gi|116515578 Cof family protein/peptidyl-prolyl cis-trans isomerase, SPD_1367 52,160.3 4.82 16.1 ± 0.85 99.6
cyclophilin type
10 gi|116517069 Heat shock protein GrpE grpE 19,956.9 4.55 −13.0 ± 0.25 100

Cell cycle or regulation

44, 60, gi|116515696 Transcription antitermination protein NusG nusG 20,334.2 4.68 14.8 ± 1.01 100
79
6 gi|116516172 UDP-N-acetylglucosamine pyrophosphorylase glmU 49,397.3 5.3 3.5 ± 0.13 100
68 gi|116517109 Catabolite control protein A ccpA 37,020.2 5.47 17.7 ± 2.25 95.08

DNA replication or transcription

13 gi|116515579 DNA-directed RNA polymerase subunit omega rpoZ 11,916.4 6.19 −12.5 ± 0.11 100
58 gi|116516073 Ribonucleotide-diphosphate reductase subunit alpha nrdE 81,540.8 5.32 8.9 ± 0.25 100
44, 60, gi|116515696 Transcription antitermination protein NusG nusG 20,334.2 4.68 14.8 ± 1.01 100
79
68 gi|116517109 Catabolite control protein A ccpA 37,020.2 5.47 17.7 ± 2.25 95.08

Amino acid metabolism

28 gi|116515784 Asparagine synthetase AsnA asnA 37,584.2 5.05 −3.7 ± 0.16 100

Carbohydrate metabolism
23 gi|116515997 6-Phosphofructokinase pfkA 35,191.1 5.33 −13.8 ± 1.21 100
56, 59 gi|116515886 Bifunctional acetaldehyde-CoA/alcohol dehydrogenase SPD_1834 97,224.4 6.11 18.5 ± 0.75 100
34 gi|116516780 Thioredoxin trx 11,469.9 4.75 −2.6 ± 0.18 100
46 gi|116516768 Phosphopyruvate hydratase eno 47,073.8 4.7 11.2 ± 2.21 99.5
76 gi|116517185 dTDP-4-dehydrorhamnose 3,5-epimerase, putative cps2M 22,307.3 5.17 11.5 ± 1.04 97.9
5 gi|116516194 D-fructose-6-phosphate amidotransferase glmS 65,437.5 5.04 6.6 ± 0.63 99. 7
6 gi|116516172 UDP-N-acetylglucosamine pyrophosphorylase glmU 49,397.3 5.3 3.5 ± 0.13 100
69 gi|116516192 UTP-glucose-1-phosphate uridylyltransferase galU 33,157.3 5.24 8.1 ± 0.85 100

Fatty acid metabolism

30 gi|116515382 3-Ketoacyl-(acyl-carrier-protein) reductase fabG 25,753.4 5.49 −3.4 ± 0.52 100
36 gi|116515640 Acetyl-CoA carboxylase subunit alpha accA 28,215.8 6.05 −6.3 ± 0.05 100
19 gi|116516513 Trans-2-enoyl-ACP reductase II fabK 34,155.9 5.33 −15.8 ± 1.63 100

Nucleotide metabolism
38 gi|116516609 Ribose-phosphate pyrophosphokinase prsA 35,428.7 5.68 −5.2 ± 0.11 100
27 gi|116515581 CTP synthetase pyrG 59,219.4 5.45 −10 ± 1.44 99.6
72 gi|116515358 Uracil phosphoribosyltransferase upp 23,640.7 5.6 8.4 ± 0.63 99.9

Oxidation
30 gi|116515382 3-Ketoacyl-(acyl-carrier-protein) reductase fabG 25,753.4 5.49 −3.4 ± 0.52 100
56, 59 gi|116515886 Bifunctional acetaldehyde-CoA/ SPD_1834 97,224.4 6.11 18.5 ± 0.75 100
alcohol dehydrogenase
58 gi|116516073 Ribonucleotide-diphosphate reductase subunit alpha nrdE 81,540.8 5.32 8.9 ± 0.25 100
67 gi|116516965 Glutamate dehydrogenase gdhA 48,765.7 5.43 −4.7 ± 0.25 100
32 gi|116515815 Non-heme iron-containing ferritin SPD_1402 19,273.8 4.59 −6.7 ± 0.55 100
31 gi|116515786 Oxidoreductase, aldo/keto reductase family protein SPD_0693 35,114.1 5.83 −10.6 ± 1.25 98.4
19 gi|116516513 Trans-2-enoyl-ACP reductase II fabK 34,155.9 5.33 −15.8 ± 1.63 100
24 gi|116516322 Oxidoreductase, Gfo/Idh/MocA family protein SPD_1311 36,351.3 5.77 −6.3 ± 0.28 100
 J O U RN A L OF P ROT EO M IC S 1 1 5 ( 2 01 5 ) 1 0 7 –11 6 113

Table 3 (continued)
Spot Accession Protein name Gene Protein Protein pI F. D. ± S.D. Score
no. no. NAME M.W. (a) C. I. %

Unknown
96 gi|116516184 Hypothetical protein SPD_0310 SPD_0310 55,030.5 5.51 −7.3 ± 0.73 100
64 gi|116516160 Metallo-beta-lactamase domain-containing protein SPD_0130 61,023.9 5.67 18.2 ± 3.04 100
63 gi|116516084 Metallo-beta-lactamase superfamily protein SPD_0533 61,128 5.38 19.0 ± 1.93 99.2
91 gi|116515795 Hypothetical protein SPD_0680 SPD_0680 12,928.8 6.97 7.5 ± 0.18 100
9 gi|116515908 General stress protein 24, putative SPD_1590 21,803.1 4.62 −4.4 ± 0.42 100
18 gi|116515506 Sugar ABC transporter, ATP-binding protein SPD_1409 41,807.6 5.83 −16.1 ± 0.84 100
20 gi|116515410 Preprotein translocase subunit SecA secA 94,981.2 5.39 −4.8 ± 0.25 100
21 gi|116516180 ABC transporter, ATP-binding protein SPD_1528 33,756 6.28 −6.4 ± 0.47 98.0
22 gi|116516594 cmp-binding-factor 1 cbf1 36,278.4 6.07 −11.2 ± 0.35 100
39 gi|116516843 UDP-N-acetylglucosamine 1-carboxyvinyltransferase murA-2 45,865.9 5.38 −8.4 ± 0.44 100
61 gi|116517204 Transcriptional regulator PlcR, putative SPD_1745 34,108.6 5.57 5.2 ± 0.34 97.5
66 gi|116515854 Sugar ABC transporter, ATP-binding protein SPD_0740 55,029.2 5.47 15.7 ± 2.11 100
70 gi|116516439 Branched-chain amino acid ABC transporter, livF 25,638.6 6.78 7.3 ± 1.12 100
ATP-binding protein
84 gi|116516713 Phosphocarrier protein HPr ptsH 8933.5 4.74 5.4 ± 0.83 100
85 gi|116515930 Deoxyuridine 5′-triphosphate nucleotidohydrolase dut 15,833.2 5.32 9.2 ± 0.92 100
98 gi|116515729 Transketolase tkt 71,067.6 5.05 −15.2 ± 0.11 100

(a) F. D. ± S.D. represents proteins fold changes in X-03 treatment vs untreated control in three experiment.

acetyl-CoA carboxylase (ACC), the first enzyme in fatty acid
biosynthesis catalyzing the carboxylation of acetyl-CoA to
malonyl-CoA [22]. FabG is the only enzyme known to catalyze
β-ketoacyl-ACP reduction to β-hydroxyacyl-ACP in NADPH-
dependent style. Moreover, FabG proteins are highly conserved
and widely distributed in bacteria, essential for bacteria growth
[23]. The enoyl-(ACP) reductase catalyzes the final step in
each cycle of fatty acid elongation in bacteria. At the same
time, FabK is a unique enzyme in S. pneumoniae, displaying
the low similarity to FabI in E. coli [24]. In view of their key
functions, these bacterial enzymes can be the targeted
molecules for developing novel antibacterial agents [25–27].
To validate whether the systematic down-regulation of the
fatty acid enzymes by X-03 really affects free fatty acid
metabolism in bacteria, we determined the intracellular FFA
contents in S. pneumoniae D39 with or without X-03 treatment
by measuring optical density with Free Fatty Acid Assay Kit.
The results in Fig. 6B showed that X-03 decreased the FFA
concentration in S. pneumoniae cells, confirming that X-03
may exert its antibacterial activity by disrupting the fatty acid
metabolism in bacteria.
3.6. X-03 affects protein folding
Heat shock protein GrpE, identified as a co-chaperone of the
DnaK chaperone system (GrpE, DnaJ, and DnaK) in the present
study, plays an essential role in protein folding and helps to
protect cells from stress [28]. Ang et al. [29] found that GrpE is
important for bacterial growth at all temperatures. Murakami et
al. [30] reported that GrpE-deficient mutants of Group A S.
pyogenes (GAS) possess low adherence/invasion rate to epithelial
cells as compared to the wild type, and that the expression of
GrpE on the surface of GAS and S. pneumoniae is helpful to
maintain cell morphology. In addition, a previous study reported
that a new antibacterial mechanism of apidaecins is to reduce the
expression of GroEL/GroES chaperone team in E. coli [31]. In line
with these results, we detected the down-regulated expressions
of GrpE at both protein and mRNA levels (Fig. 6A), implicating that
the compound X-03 may affect on the protein folding and thus
inhibited bacterial growth.
3.7. Interaction networks of DEPs suggest potential drug targets
In order to better understand the inhibitory mechanisms of
complex X-03 in S. pneumoniae, the interaction networks of DEPs
were constructed by using STRING (http://string-db.org/). As
shown in Fig. 5B, most of the DEPs in the map have direct or
indirect links. In particular, proteins AccA, FabG and FabK
functioning in fatty acid metabolism form a small close
network, suggesting that Ru(II) complex X-03 may regulate
this pathway. As discussed above, the fatty acid biosynthesis
pathway is a promising target for the development of novel
anti-bacterial agents [32].
Although it may be the secondary reaction to the drug
stimulation, the phosphopyruvate hydratase Eno was found to
be the core node associated with many other proteins in
the network, implicating its critical role in course of the bacterial
response to X-03 treatment. Eno is a key enzyme in glycolysis
metabolic pathway in bacteria, catalyzing the reversible conver-
sion of 2-phosphoglycerate into phosphoenolpyruvate, and thus
playing an important role in the virulence of S. pneumoniae [33].
The bacterium may increase the expression of Eno to produce
more ATP energy through the glycolytic pathway, to deal with the
X-03 challenge in the long term.
It is also interesting to note that proteins involved in
carbohydrate metabolism were comprised in the network.
These proteins include 6-phosphofructokinase (pfkA), bifunc-
tional acetaldehyde-CoA/alcohol dehydrogenase (SPD_1834),
dTDP-4-dehydrorhamnose 3,5-epimerase, putative (cps2M),
D-fructose-6-phosphate amidotransferase (glmS), UDP-N-
114 J O U RN A L OF P ROT EO M IC S 1 1 5 ( 2 01 5 ) 1 0 7 –11 6

Fig. 5 – Bioinformatics analysis of DEPs. (A) The biological function distribution of the identified DEPs in S. pneumoniae
according to Gene Ontology (GO) database. (B) The interaction networks of X-03-regulated DEPs in S. pneumoniae D39 as
analyzed by the STRING system.

acetylglucosamine pyrophosphorylase (glmU), and UTP-

glucose-1-phosphate uridylyltransferase (galU). Under the
stimulation of X-03, carbohydrate metabolism in the bacterium
may become active as secondary effects; the related proteins
were thus promoted, helping bacterial response to the stress
from the drug exposure.
4. Conclusions
In the present study, we applied proteomic technology combined
with bioinformatics analysis to investigate the antimicrobial
activity of Ru(II) complex X-03 in S. pneumoniae. Many proteins
 J O U RN A L OF P ROT EO M IC S 1 1 5 ( 2 01 5 ) 1 0 7 –11 6 115

Fig. 6 – Effects of X-03 on the gene expression and FFA content of the S. pneumoniae.(A) qRT-PCR expression analysis of selected
genes, piaA, piuA, piaA, SPD_1402, eno, accA, fabG, fabK, ghdA, SDP_1590 and grpE in S. pneumoniae D39 with/without X-03
treatment. The relative gene expression was calculated with the 16S rRNA as the reference gene. All results represent the
relative expression level between X-03-treated and -untreated bacteria, shown as the means value (± SEM) from three
independent cultures in triplicates. (B) The cellular FFA content of the wild-type S. pneumoniae with and without X-03
treatment. Results are representative of the mean ± SEM from three independent experiments (**p < 0.01).

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thesis and the resistance ability of the bacterium to oxidative
damage thus carries out the antibacterial activity. In addition,
X-03 could selectively suppress Gram-positive bacteria but
execute less cytotoxicity to Gram-negative bacteria, with almost
no effect on human cells, implicating its potential to be developed
as a specific antimicrobial agent. These results provide useful
information for further investigations on the mechanism of the
antibacterial action of metal drugs.
Conflict of interest
We clarify that we do not have any financial or commercial
conflicts of interested to be disclosed.
Acknowledgments
We thank Professor Xiyang Wu for providing L. monocytogenes
19117 strain and Professor Hui Li for providing V. alginolyticus
V12G01 and V. parahaemolyticus RIMD 2210633) strains. This
work was supported by the National Natural Science Founda-
tion of China (21271086, to Q.-Y. H.; 31000373, to X. S.), the
Guangdong Natural Science Research (Grant (32213027, to Q.-Y.
H.; S2012010008685 to X. S.), the Pearl River Rising Star of Science
and Technology of Guangzhou City (2011J2200003, to X. S.), and
Open Fund of The First Affiliated Hospital, Jinan University,
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