Table S4 Unique differentially expressed proteins in VPE compared with VPW
Accessiona
Protein name
Increased
proteins
L0I1Q9
ATP
synthase
subunit beta
F3RS00
L0HRV5
Trigger factor
DNA
gyrase
Transcription-repai
r coupling factor
L0HTD3
GMP
atpD
tig
subunit B
A6B133
Gene
gyrB
mfd
synthase
[glutamine-hydroly
guaA
zing]
L0HX50
GMP
synthase
[glutamine-hydroly
VPBB_0973
zing]
L0HSW7
30S
ribosomal
protein S9
L0HW03
rpsI
Translation
initiation
factor
infB
IF-2
Q87JZ6
A6BBF2
Putative isomerase
Ribosomal protein
S7 (Fragment)
F3RSW8
VPA0102
rpsG
Phenylalanine--tRN
A
ligase
beta
pheT
subunit
Q87M01
N
utilization
substance protein A
L0HYJ6
Ribosomal
small
VP2457
RNA
subunit
rlmI
methyltransferase I
L0HV54
30S
ribosomal
protein S10
A6B817
rpsJ
Cysteinyl-tRNA
synthetase
cysS
(Fragment)
L0HSH4
50S
ribosomal
protein L6
rplF
MW
iTRAQ
P
(kDa)
ratiob
Valuec
50.69
6
48.25
5
89.44
2
130.4
74
57.67
2
97.99
6
14.61
4
99.39
6
100.5
77
17.40
9
87.08
8
54.94
5
44.45
4
11.721
52.41
8
18.77
9
2.5823
3.3729
2.3121
2.2080
2.4889
2.5586
2.5119
3.73259
3.34199
2.2491
2.3335
2.0701
2.7290
3.5975
2.1878
3.3113
GO
0.003
ATP hydrolysis coupled
7
proton transport
0.000
2
cell cycle, cell division
0.014
DNA-dependent DNA
7
replication
0.004
6
0.001
4
0.001
7
0.001
5
0.000
1
0.006
7
0.000
5
DNA repair
GMP biosynthetic process
chromosome
translation
GTP catabolic process
metabolic process
translation
0.004
phenylalanyl-tRNA
0
aminoacylation
0.017
4
regulation of
DNA-dependent
transcription, termination
2.43E-
rRNA (cytosine)
05
methyltransferase activity
0.005
2
0.0119
0.001
0
translation
cysteinyl-tRNA
aminoacylation
translation
L0HV66
30S
ribosomal
protein S8
L0HVZ0
Peptide
chain
release factor 3
Q87P08
Glucose-6-phospha
te 1-dehydrogenase
Q87R87
rpsH
prfC
VP1710
C4-dicarboxylate-b
inding periplasmic
VP0910
protein
L0HW62
Thermostable
carboxypeptidase 1
L0HUI1
30S
ribosomal
protein S11
L0HZB1
30S
Uroporphyrinogen
decarboxylase
E1DBS5
L0HQN2
30S
ribosomal
50S
ribosomal
Aminomethyltransf
Electron
transport
complex
protein
Phenylalanine--tRNA
rpsM
rplI
VPA0805
L0HZJ5
Q87N59
F3RPW0
55.07
9
13.89
0
39.17
7
30S
ribosomal
Shikimate kinase
50S
ribosomal
protein L13
30S
ribosomal
protein S18
Uncharacterized
protein
Orotidine
5'-phosphate
13.29
1
15.70
9
40.32
2
97.73
10
0
pheS
Putative
protein S6
L0HVL1
2
VP10329_177
VP0351
CoA ligase
F3RU57
37.13
9
long-chain-fatty-acid-
L0I0X0
0
7_2547
ligase alpha subunit
Q87SS1
57.64
chaperone
RnfC
E1EMD9
5
70.87
erase
F3RPN2
hemE
59.24
VIPARAQ403
protein L9
Q87I01
rpsK
8
Molecular
protein S13
L0HYY1
VPBB_1603
14.00
rpsF
aroK
rplM
rpsR
VP2016
pyrF
36.87
3
67.92
0
14.98
3
19.47
2
15.96
1
8.843
38.89
4
25.29
3
4.6132
2.2699
2.6792
3.7670
4.7863
2.4660
3.2509
4.4055
2.1878
2.9648
2.2699
2.5586
2.6303
2.8840
2.0893
2.8576
2.1878
2.9648
3.5645
2.3335
0.008
6
translation
0.002
regulation of translational
4
termination
0.014
2
0.006
0
0.001
3
0.047
2
pentose-phosphate shunt
transport
proteolysis
translation
0.028
protoporphyrinogen IX
8
biosynthetic process
0.001
2
0.042
4
ATP binding
translation
0.002
structural constituent of
8
ribosome
0.029
1
0.033
6
glycine catabolic process
electron carrier activity
0.016
phenylalanyl-tRNA
2
aminoacylation
0.026
0
0.005
0
F:ligase activity
translation
0.003
chorismate biosynthetic
5
process
0.0118
translation
0.010
7
0.000
4
translation
iron ion binding
0.003
‘de novo’ UMP
4
biosynthetic process
decarboxylase
Q87JA9
L0HWB3
L0HTN3
Putative
multidrug
resistance protein
Ribonuclease 3
VPA0344
rnc
Peptide chain release
factor 1
prfA
117.25
2
25.06
8
40.29
4
2.0893
2.4210
2.7040
0.010
5
0.037
7
transporter activity
RNA processing
0.020
translation release factor
1
activity, codon specific
UDP-N-acetylglucos
L0HYK1
amine
1-carboxyvinyltransf
murA
44.110
2.3550
0.018
0
cell division
erase
tRNA
F3RRN2
(mo5U34)-methyltra
cmoB
nsferase
37.10
4
3.8726
0.002
5
Ubiquinone/menaqui
L0HSP1
none
biosynthesis
methyltransferase
cmoB
28.96
5
2.4889
0.023
5
tRNA wobble uridine
modification
ubiquinone biosynthetic
process
ubiE
Q87FS4
Putative
tyrosine
kinase
VPA1604
Dual-specificity RNA
L0HW25
methyltransferase
rlmN
RlmN
"Peptide
9
42.17
0
4.6989
2.7290
0.019
regulation of catalytic
9
activity
0.029
rRNA base methylation
2
ABC
transporter,
Q87QH8
78.99
periplasmic
VP1171
peptide-binding
60.93
4
2.3121
0.037
transporter activity
5
protein
Oligopeptide
L0HX06
transport
ATP-binding protein
VPBB_1924
36.03
5
3.7670
0.024
ATP catabolic process
8
OppD
L0HUF9
L0HYV4
50S
protein L31
50S
ribosomal
protein L19
"Nitrite
Q87HH8
ribosomal
rpmE
rplS
reductase
(NAD(P)H),
large
VPA0987
subunit
Q87PU8
Q87T55
Uncharacterized
VP1403
protein
Putative
protein
OtnG
VP0215
8.055
13.21
9
93.57
2
55.57
7
83.08
5
3.6983
3.4041
4.5290
9.6383
2.1281
0.027
translation
6
0.033
structural constituent of
3
ribosome
0.026
nitrate assimilation
9
1.7E-1
1
0.007
1
no GO
no GO
L0HWA8
Q87PU9
L0I1Z3
Q87LF1
Q87PV3
Decarboxylase
VPBB_0669
family protein
Uncharacterized
VP1402
protein
UPF0319
protein
VPBB_A1448
Uncharacterized
VP2661
protein
Uncharacterized
VP1398
protein
Putative
F3RSG6
uncharacterized
protein (Fragment)
"Type VI secretion
E1EMQ2
protein,
VC_A0110
family
Q87PW1
Q87JW0
Q87PW2
Q87PU8
Q87T55
L0HWA8
Decreased
Uncharacterized
Putative TldD protein
Uncharacterized
OtnG
protein
Decarboxylase
family protein
Uncharacterized
protein
L0I2S8
F3RTF5
24.07
6
37.53
2
65.70
1375
5
VPA0138
VP1403
VP0215
VPBB_0669
43.37
2
49.47
9
65.96
4
55.57
7
83.08
5
50.59
6
2.0701
14.7231
2.2699
2.2699
2.7040
2.8314
2.8840
2.2909
2.0512
3.9811
9.6383
2.1281
2.0701
0.040
3
8.23E05
0.041
3
0.028
0
0.003
2
0.001
3
0.017
3
0.046
2
0.028
0
0.016
0
1.7E-1
1
0.007
1
0.040
3
no GO
no GO
no GO
no GO
no GO
no GO
no GO
no GO
no GO
no GO
no GO
no GO
no GO
proteins
decarboxylase alpha
oadA
Citrate synthase
Heme
transport
protein HutA
VP0842
VPBB_A0827
complex
subunit
fadB
alpha
Q87MM5
8
VIPARK5030_
Fatty acid oxidation
E1EF47
24.34
50
subunit
Q87RF5
7
15
Oxaloacetate
E1D6T7
18.56
284.3
VP1388
protein
6
VP10329_191
VP1389
protein
Putative
VPBB_A1448
50.59
"Peptidase, insulinase
family
Putative
uncharacterized
VP2206
64.20
4
48.21
9
77.24
0
78.55
6
105.7
46
VP10329_121
64.57
36
7
0.1977
0.4656
0.0437
0.1690
0.4365
0.2992
0.001
metabolic process
2
0.020
tricarboxylic acid cycle
4
2.13
transporter activity
E-07
receptor activity
2.15E-
fatty acid beta-oxidation
05
0.004
proteolysis
9
0.000
hydrolase activity, acting
2
on carbon-nitrogen (but
protein
E1DBF1
Q87FE3
not peptide) bonds
"Oligoendopeptidase,
PepF/M3 family
Toxin
secretion
ATP-binding protein
VIPARAQ403
67.95
7_2676
8
VPA1736
Fatty acid oxidation
L0HXD2
complex
subunit
fadJ
alpha
L0HY24
3-ketoacyl-CoA
Iron-regulated
Q87LK9
fadI
thiolase
outer
membrane virulence
VP2602
protein homolog
78.10
9
76.79
6
46.39
6
71.94
8
0.3873
0.3532
0.3436
0.3251
0.1459
0.003
proteolysis
6
2.6E-0
proteolysis
5
0.000
fatty acid beta-oxidation
1
0.000
fatty acid beta-oxidation
8
0.000
transporter
2
activity,receptor activity
0.001
transferring alkyl or aryl
0
(other than methyl) groups
0.000
protein transport
transferase activity,
F3RTF4
Q87P87
A6AYD5
Homocysteine
synthase
Agglutination protein
Catalase-peroxidase
VP10329_121
45.74
31
6
VP1631
katG
Biopolymer transport
Q87JU6
protein ExbB-related
VPA0152
protein
F3S0P9
D-alanyl-D-alanine
carboxypeptidase
Putative
Q87M39
50.70
5
82.17
7
49.20
0
VP10329_108
42.20
76
4
0.2559
0.1343
0.4656
0.0637
0.3076
2
0.033
9
0.004
hydrogen peroxide
catabolic process
protein transporter activity
1
0.003
2
proteolysis
pilus
assembly
VP2419
transmembrane
52.72
3
0.1096
0.013
protein secretion
9
protein
phosphoenolpyruvate-depe
Phosphoenolpyruvate
Q87SA3
-protein
VP0521
phosphotransferase
Q87L24
Phosphoribulokinase
D-amino
L0HU11
acid
dehydrogenase small
subunit
VP2792
dadA
83.77
4
32.75
8
46.43
3
0.3565
0.3945
0.4613
0.020
1
0.028
2
0.042
0
ndent sugar
phosphotransferase system
carbohydrate metabolic
process
D-alanine catabolic
process
E1EF46
Q87PG7
Q87K27
L0I2K8
L0HW43
3-ketoacyl-CoA
fadA
thiolase
Putative
stress
protein
Putative
alcohol
dehydrogenase
Cyclohexadienyl
dehydratase
Uncharacterized
protein
VP1535
VPA0071
VPBB_2914
VPBB_2322
41.40
6
35.33
0
40.77
6
28.95
8
86.211
0.3631
0.2582
0.4831
0.3532
0.4875
0.009
fatty acid beta-oxidation
3
0.020
0
0.0011
0.003
ciliary or bacterial-type
flagellar motility
ethanol oxidation
transporter activity
0
0.047
lipid metabolic process
5
Putative
Q87JV2
glycerophosphoryl
diester
VPA0146
26.66
6
0.4656
0.028
lipid metabolic process
4
phosphodiesterase
E1D737
Q87H59
A6B3F3
"Exodeoxyribonuclea
se V, gamma subunit
Putative
stomatin-like protein
"ABC
transporter,
ATP-binding protein
recC
VPA1106
A79_1175
132.3
33
29.59
6
28.66
1
0.4365
0.2421
0.3499
0.016
3
0.003
exodeoxyribonuclease V
activity
membrane
8
0.033
ATP catabolic process
9
methylmalonate-semialdeh
A6B1P9
L0HV38
Q87I45
Q87HT7
F3RNI4
短链脱氢酶
mmsA
Uncharacterized
protein
Aldehyde
GGDEF
family
protein
Cell division protein
ZapD
1
0.1754
44.08
VPBB_1962
VPA0761
dehydrogenase
54.50
VPA0869
zapD
0
52.38
7
72.33
4
28.62
1
0.2333
0.4742
0.2884
0.4529
0.005
yde dehydrogenase
0
(acylating) activity
0.010
0
0.026
0
0.006
0
0.047
phosphorelay signal
transduction system
cellular aldehyde
metabolic process
intracellular signal
transduction
barrier septum assembly
6
Pyridoxamine
5'-phosphate
L0HZ08
oxidase-related
VPBB_A0398
putative heme iron
20.19
1
0.1127
0.040
3
pyridoxal phosphate
biosynthetic process
utilization protein
Q87IE2
Putaive Fe-regulated
VPA0664
74.20
0.1871
0.037
siderophore
protein B
6
TonB
transmembrane transport
system
biopolymer transport
L0I331
8
component
VPBB_A0140
Chromosome
28.15
1
0.0817
0.000
3
no GO
segregation ATPase
A6B121
Q87H91
UPF0229
protein
A79_6085
Uncharacterized
A79_6085
VPA1074
protein
Periplasmic
L0I1J4
hemin-binding
VPBB_A0392
protein
L0I2C0
F3RPL8
L0I0Q7
Q87NJ7
Putative nonspecific
acid phosphatase
Short
chain
dehydrogenase
Putative
exported
protein
Uncharacterized
protein
Putative
F3RSV7
uncharacterized
protein
Q87KC8
Q87G54
L0HZB2
SpoOM-related
protein
Uncharacterized
protein
Iron-regulated
protein A
VPBB_A0642
49.93
7
35.65
2
30.23
6
37.15
7
VP10329_176
27.23
40
7
VPBB_A0097
VP1871
49.13
5
51.78
4
VP10329_198
25.84
30
5
VP3049
30.311
VPA1463
VPBB_1761
20.78
6
45.38
8
0.1585
0.2992
0.0847
0.2443
5.24E08
0.0011
0.0441
1
0.006
6
no GO
no GO
no GO
no GO
0.1500
0.0110
no GO
0.2679
0.0111
no GO
0.4571
0.3311
0.1837
0.0299
0.2208
0.033
1
0.018
3
0.007
7
0.026
4
0.021
2
no GO
no GO
no GO
no GO
no GO
a. Protein information including accession numbers, gene names, MW and Gene Ontology (GO) was taken from the UniProtKB
b. iTRAQ ratio of VPP compared with VPW
c. Statistical analysis of iTRAQ ratio of VPP compared with VPW was performed using unpaired t-test.