Supporting Information
Comprehensive
provide
profiling
insights
of
of
proteome
industrial
changes
Penicillium
chrysogenum during pilot and industrial penicillin G
fermentation
Jing-Sheng Cheng1,2,3, Yan Zhao1,2,3, Bin Qiao1,2,3, Hua Lu1,2,4, Yao Chen4,
Ying-Jin Yuan1,2,3
1. Key Laboratory of Systems Bioengineering (Tianjin University),
Ministry of Education;
2. Department of Pharmaceutical Engineering, School of Chemical
Engineering and Technology, Tianjin University, Tianjin 300072, P. R.
China;
3. Collaborative Innovation Center of Chemical Science and Engineering
(Tianjin), Tianjin, 300072, People’s Republic of China
4. Hebei Zhongrun Pharmaceutical Co., Ltd, China, Shijiazhuang
Pharmaceutical Group Co., Ltd. (CSPC), Shijiazhuang, Hebei province
050041, P. R. China
1
Table S1. The identified intracellular proteins of P. chrysogenum under industrial fermentation
Sopt
No.
GI
Signal peptide
Biological process
Molecular function
1#
211582307
MGSSVPALSA LNGPTYVTA (1-19)
oxidation reduction
2#
211582307
MGSSVPALSA LNGPTYVTA (1-19)
oxidation reduction
3#
211592932
MVLAARCGQA AALLRQRCIA (1-20)
4#
211591091
nitrogen
process
unknown
5#
211591532
glycolysis
6#
211583774
gluconeogenesis
7#
211583774
gluconeogenesis
9#
10#
12#
13#
211583413
211583413
211586918
211586918
proteolysis
proteolysis
proteolysis
proteolysis
15#
211586335
histidine biosynthetic
oxidation reduction
16#
17#
42#
43#
127#
222#
232#
18#
211592083
211582027
211582027
211582027
211582027
211582027
211582027
211586109
proteolysis
protein folding; response to stress
protein folding; response to stress
protein folding; response to stress
protein folding; response to stress
response to stress; protein folding
response to stress; protein folding
hydrogen
peroxide
catabolic
MHVLALVTGL VGVANA(1..16)
compound
metabolic
process;
2
electron carrier activity; oxidoreductase
activity, acting on the aldehyde or oxo
group of donors
electron carrier activity; oxidoreductase
activity, acting on the aldehyde or oxo
group of donors
ATP
binding;
carbamoyl-phosphate
synthase activity
hydrolase activity
oxoglutarate
dehydrogenase
(succinyl-transferring) activity; thiamin
pyrophosphate binding
ATP binding; biotin binding; pyruvate
carboxylase activity
ATP binding; biotin binding; pyruvate
carboxylase activity
serine-type peptidase activity
serine-type peptidase activity
metallopeptidase activity; zinc ion binding
metallopeptidase activity; zinc ion binding
NAD or NADH binding; histidinol
dehydrogenase
activity;
phosphoribosyl-AMP
cyclohydrolase
activity; phosphoribosyl-ATP diphosphatase
activity; zinc ion binding
metallopeptidase activity; zinc ion binding
ATP binding; unfolded protein binding
ATP binding; unfolded protein binding
ATP binding; unfolded protein binding
ATP binding; unfolded protein binding
ATP binding; unfolded protein binding
ATP binding; unfolded protein binding
catalase activity; heme binding
MM
PI
Score
Expect
COV
NP
114799
5.05
73
0.024
14%
12
114799
5.05
123
2.60E-07
21%
17
128738
5.32
73
0.026
16%
15
139325
5.78
279
6.60E-23
39%
32
119581
6.22
204
2.10E-15
36%
28
131892
6.1
241
4.20E-19
28%
33
131892
6.1
103
2.60E-05
15%
16
78670
78670
98916
98916
5.07
5.07
5.15
5.15
126
130
81
138
1.30E-07
5.30E-08
0.0039
8.30E-09
27%
27%
12%
26%
20
17
9
19
93035
5.34
126
1.30E-07
29%
17
99394
79544
79544
79544
79544
79544
79544
79912
5.33
4.87
4.87
4.87
4.87
4.87
4.87
5.37
99
120
271
245
90
60
114
101
6.80E-05
5.30E-07
4.20E-22
1.70E-19
0.0005
0.48
2.10E-06
4.20E-05
20%
27%
46%
42%
23%
23%
28%
23%
17
17
28
25
13
11
16
14
process; oxidation reduction
hydrogen
peroxide
catabolic
process; oxidation reduction
hydrogen
peroxide
catabolic
process; oxidation reduction
hydrogen
peroxide
catabolic
process; oxidation reduction
19#
211586109
MHVLALVTGL VGVANA(1..16)
29#
211586109
MHVLALVTGL VGVANA (1..16)
233#
211586109
MHVLALVTGL VGVANA (1..16)
21#
211588557
22#
211591261
tricarboxylic acid cycle
23#
211591261
tricarboxylic acid cycle
24#
211592785
methionine biosynthetic process
25#
211592785
methionine biosynthetic process
26#
211592785
methionine biosynthetic process
27#
211592785
methionine biosynthetic process
30#
211587433
proteolysis
31#
211588888
metabolic process
32#
211592078
ATP synthesis coupled electron
transport
228#
211592078
ATP synthesis coupled electron
transport
33#
211587397
ATP synthesis coupled electron
transport
34#
211592918
protein folding
3
catalase activity;
heme binding
79912
5.37
185
1.70E-13
35%
20
catalase activity;
heme binding
79912
5.37
124
2.10E-07
16%
11
79912
5.37
83
0.0028
15%
9
86528
5.4
132
3.30E-08
32%
18
85870
5.97
183
2.60E-13
29%
17
85870
5.97
240
5.30E-19
40%
22
87540
6.12
202
3.30E-15
29%
23
87540
6.12
113
2.60E-06
23%
13
87540
6.12
115
1.70E-06
24%
16
87540
6.12
232
3.30E-18
43%
28
81477
5.36
80
0.0048
24%
16
77933
5.65
149
6.60E-10
25%
14
80608
6.05
130
5.30E-08
31%
15
80608
6.05
68
0.078
21%
10
147309
5.88
52
3
13%
12
72603
5.58
107
1.00E-05
29%
16
catalase activity; heme binding
pyridoxal phosphate binding; transaminase
activity
4 iron, 4 sulfur cluster binding; aconitate
hydratase activity
4 iron, 4 sulfur cluster binding; aconitate
hydratase activity
5-methyltetrahydropteroyltriglutamate-hom
ocysteine S-methyltransferase activity; zinc
ion binding
5-methyltetrahydropteroyltriglutamate-hom
ocysteine S-methyltransferase activity; zinc
ion binding
5-methyltetrahydropteroyltriglutamate-hom
ocysteine S-methyltransferase activity; zinc
ion binding
5-methyltetrahydropteroyltriglutamate-hom
ocysteine S-methyltransferase activity; zinc
ion binding
metalloendopeptidase activity; zinc ion
binding
ATP binding; biotin binding; ligase activity
4 iron, 4 sulfur cluster binding; NADH
dehydrogenase
(ubiquinone)
activity;
electron carrier activity; iron ion binding
NADH
dehydrogenase
(ubiquinone)
activity; 4 iron, 4 sulfur cluster binding;
electron carrier activity; iron ion binding
4 iron, 4 sulfur cluster binding; NADH
dehydrogenase
(ubiquinone)
activity;
electron carrier activity; iron ion binding
ATP binding; unfolded protein binding
226#
227#
35#
36#
104#
225#
38#
39#
40#
211592918
211592918
211592606
211592047
211592047
211592047
211584281
211584281
211584281
protein folding
protein folding
proteolysis
41#
211585176
45#
6002489
carbohydrate metabolic process
46#
6002489
carbohydrate metabolic process
259#
6002489
carbohydrate metabolic process
MAARHSRKLL RPLLYTSAAA AAGA (1..24)
metabolic process
metabolic process
metabolic process
glycerol-3-phosphate
metabolic
process; oxidation reduction
47#
211582382
gluconeogenesis
231#
211582382
gluconeogenesis
48#
211583594
leukotriene biosynthetic process;
proteolysis
49#
211586940
unknown
51#
211587867
electron
transport
tricarboxylic acid cycle
chain;
53#
211587867
electron
transport
tricarboxylic acid cycle
chain;
54#
211587867
electron
transport
tricarboxylic acid cycle
chain;
52#
211592830
IMP biosynthetic process
4
ATP binding; unfolded protein binding
ATP binding; unfolded protein binding
dipeptidyl-peptidase activity
ATP binding
ATP binding
ATP binding
transketolase activity
transketolase activity
transketolase activity
glycerol-3-phosphate
dehydrogenase
activity
beta-N-acetylhexosaminidase
activity;
cation binding
beta-N-acetylhexosaminidase
activity;
cation binding
beta-N-acetylhexosaminidase
activity;
cation binding
ATP binding; oxidoreductase activity;
phosphoenolpyruvate carboxykinase (ATP)
activity
phosphoenolpyruvate carboxykinase (ATP)
activity; oxidoreductase activity; ATP
binding
leukotriene-A4
hydrolase
activity;
metallopeptidase activity; zinc ion binding
electron carrier activity; oxidoreductase
activity
FAD binding; electron carrier activity;
oxidoreductase activity, acting on the
CH-CH group of donors
FAD binding; electron carrier activity;
oxidoreductase activity, acting on the
CH-CH group of donors
FAD binding; electron carrier activity;
oxidoreductase activity, acting on the
CH-CH group of donors
IMP
cyclohydrolase
activity;
phosphoribosylaminoimidazolecarboxamide
72603
72603
78783
67030
67030
67030
74784
74784
74784
5.58
5.58
5.27
5.32
5.32
5.32
581
5.81
5.81
82
92
167
148
75
99
189
281
129
0.0032
0.00034
1.00E-11
8.30E-10
0.018
6.60E-05
6.60E-14
4.20E-23
6.60E-08
25%
20%
36%
39%
24%
37%
37%
47%
22%
15
13
20
19
11
12
21
24
13
76917
6.24
123
2.60E-07
19%
12
66840
5.32
76
0.014
18%
6
66840
5.32
140
5.30E-09
29%
12
66840
5.32
76
0.014
20%
9
66646
5.79
103
2.60E-05
27%
9
66646
5.79
66
0.14
36%
12
76263
5.87
83
0.0024
17%
12
70326
5.76
104
2.10E-05
36%
16
71710
6.55
177
1.00E-12
42%
22
71710
6.55
261
4.20E-21
44%
25
71710
6.55
197
1.00E-14
38%
21
65153
5.93
202
3.30E-15
57%
28
55#
211593224
carboxylic acid metabolic process
56#
211581378
alcohol metabolic process
57#
211581378
alcohol metabolic process
58#
211581814
MAAPQVIVVG GGLSGLSA (1..18)
230#
211581814
MAAPQVIVVG GGLSGLSA(1-18)
59#
60#
62#
63#
65#
66#
211588870
211588870
211586036
211586036
211589937
211587581
MKWSLLITHL SVAFAEA a(1..17)
MKWSLLITHL SVAFAEA a(1..17)
67#
211586717
carbohydrate metabolic process
69#
211587160
glycolysis
70#
211593078
microtubule-based
movement;
protein polymerization
71#
211583021
glucose catabolic process
72#
211593263
75#
211591342
77#
7387882
glycolysis
oxidation
reduction;
valine
metabolic process
cysteine biosynthetic process;
methionine biosynthetic process;
sulfate assimilation
proteolysis
proteolysis
protein folding
protein folding
metabolic process
unknown
78#
211592291
ATP synthesis
transport
coupled
79#
211587347
seryl-tRNA aminoacylation
proton
5
formyltransferase activity
isocitrate lyase activity
FAD binding; oxidoreductase activity,
acting on the CH-CH group of donors
FAD binding; oxidoreductase activity,
acting on the CH-CH group of donors
electron carrier activity;heme binding;
succinate dehydrogenase activity
succinate dehydrogenase activity; electron
carrier activity; heme binding
peptidase activity
peptidase activity
ATP binding; protein binding
ATP binding; protein binding
nucleotidyltransferase activity
FAD binding; oxidoreductase activity
intramolecular
transferase
activity,
phosphotransferases;
magnesium
ion
binding
magnesium ion binding; potassium ion
binding; pyruvate kinase activity
GTP binding; GTPase activity; structural
molecule activity
manganese ion binding; phosphoglycerate
mutase activity
ATP binding; hexokinase activity
methylmalonate-semialdehyde
dehydrogenase (acylating) activity
ATP binding; kinase activity;
adenylyltransferase (ATP) activity
sulfate
hydrogen ion transporting ATP synthase
activity,
rotational
mechanism;;
hydrogen-exporting
ATPase
activity,
phosphorylative
mechanism;;
proton-transporting
ATPase
activity,
rotational mechanism
ATP binding; serine-tRNA ligase activity
65935
7.23
172
3.30E-12
35%
24
65335
6.12
94
0.00021
20%
9
65335
6.12
187
1.00E-13
44%
18
66784
6.17
84
0.0021
18%
10
66784
6.17
100
5.40E-05
19%
10
52914
52914
61986
61986
55609
63086
5.58
5.58
5.61
5.61
5.38
6.22
98
114
162
170
110
106
8.30E-05
2.10E-06
3.30E-11
5.30E-12
5.30E-06
1.30E-05
17%
15%
34%
28%
23%
18%
11
11
22
15
9
14
60479
5.66
89
0.00068
20%
9
58936
6.35
160
5.30E-11
35%
14
50993
4.91
116
1.30E-06
40%
11
56843
5.17
119
6.60E-07
27%
12
54358
5.19
113
2.60E-06
26%
12
63244
7.56
114
2.10E-06
38%
15
64048
6.36
84
0.0022
27%
12
56134
5.69
169
6.60E-12
50%
19
53849
5.64
86
0.0013
34%
16
80#
211582852
81#
211581247
137#
211581247
82#
211590959
83#
211592892
84#
211582337
85#
88#
211593391
211593391
86#
211588550
87#
211591450
electron carrier activity; heme binding;
oxidoreductase activity
metabolic process
oxidation reduction; oxidoreductase
activity
oxidation reduction
oxidation reduction; oxidoreductase
activity
gluconeogenesis; glycolysis
oxidation
reduction;
proline
biosynthetic process
metabolic process
metabolic process
propionate
catabolic
process,
2-methylcitrate cycle
ketone body catabolic process
211589753
MFKSGLARSFGRAAFARTTPVARAFQPVR
S NALPALARFASSDA(1..44)
ATP synthesis coupled proton
transport (ATP synthesis; Hydrogen
ion transport; Ion transport;
Transport)
91#
211589753
MFKSGLARSFGRAAFARTTPVARAFQPVR
S NALPALARFASSDA(1..44)
ATP synthesis coupled proton
transport (ATP synthesis; Hydrogen
ion transport; Ion transport;
Transport)
92#
211584381
microtubule-based
movement;
protein polymerization
93#
211588090
proteolysis
94#
211582556
arginine biosynthetic process
95#
211582556
arginine biosynthetic process
96#
211586200
proteolysis
97#
211584913
protein transport; regulation of
89#
6
oxidoreductase activity
glucose-6-phosphate isomerase activity
1-pyrroline-5-carboxylate dehydrogenase
activity
oxidoreductase activity
oxidoreductase activity
2 iron, 2 sulfur cluster binding;
2-methylcitrate dehydratase activity
CoA-transferase activity
ATP binding; hydrogen ion transporting
ATP
synthase
activity,
rotational
mechanism; hydrogen-exporting ATPase
activity,
phosphorylative
mechanism;
proton-transporting
ATPase
activity,
rotational mechanism
ATP binding; hydrogen ion transporting
ATP
synthase
activity,
rotational
mechanism; hydrogen-exporting ATPase
activity,
phosphorylative
mechanism;
proton-transporting
ATPase
activity,
rotational mechanism
GTP binding; GTPase activity; structural
molecule activity
metallopeptidase
activity;
protein
dimerization activity
ATP binding; argininosuccinate synthase
activity
ATP binding; argininosuccinate synthase
activity
metalloendopeptidase activity; zinc ion
binding
Rab GDP-dissociation inhibitor activity
55366
5.69
84
0.002
27%
10
54046
5.85
162
3.30E-11
42%
12
54046
5.85
60
0.47
25%
6
54003
5.88
111
4.20E-06
44%
14
61256
5.82
75
0.018
25%
14
62610
6.84
120
5.30E-07
44%
16
52952
52952
6.3
6.3
124
196
2.10E-07
1.30E-14
41%
43%
16
16
61311
8.03
166
1.30E-11
40%
19
55778
8.29
152
3.30E-10
40%
16
55237
5.25
176
1.30E-12
58%
18
55237
5.25
206
1.30E-15
68%
25
50373
4.9
250
5.30E-20
49%
25
53000
5.04
164
2.10E-11
44%
14
47069
5.09
141
4.20E-09
57%
16
47069
5.09
141
4.20E-09
53%
16
53098
5.66
214
2.10E-16
48%
19
52104
5.33
115
1.70E-06
40%
13
GTPase activity
98#
211581925
metabolic process
99#
211590747
100#
211582351
101#
211582351
239#
211582351
249#
211582351
102#
211587749
103#
211587749
unknown
L-phenylalanine catabolic process;
oxidation
reduction;
tyrosine
metabolic process
L-phenylalanine catabolic process;
oxidation
reduction;
tyrosine
metabolic process
L-phenylalanine catabolic process;
tyrosine
metabolic
process;
oxidation reduction
L-phenylalanine catabolic process;
tyrosine
metabolic
process;
oxidation reduction
cell redox homeostasis; oxidation
reduction
cell redox homeostasis; oxidation
reduction
106#
211583598
cellular process
107#
211584789
glycolysis
108#
211584789
glycolysis
109#
211592754
110#
211592890
111#
211587647
isocitrate
metabolic
oxidation reduction
112#
211585478
one-carbon metabolic process
113#
211587647
isocitrate
metabolic
oxidation reduction
115#
16555763
isoprenoid biosynthetic process;
phosphorylation
cellular amino acid catabolic
process
process;
process;
oxidation reduction
7
catalytic activity; pyridoxal
binding
ATP binding; catalytic activity
phosphate
48353
5.53
128
8.30E-08
33%
11
52690
5.94
70
0.056
30%
10
homogentisate 1,2-dioxygenase activity
50358
5.91
184
2.10E-13
55%
16
homogentisate 1,2-dioxygenase activity
50358
5.91
171
4.20E-12
42%
13
homogentisate 1,2-dioxygenase activity
50358
5.91
104
2.10E-05
28%
9
homogentisate 1,2-dioxygenase activity
50358
5.91
104
2.10E-05
26%
10
54589
7.67
149
6.60E-10
37%
17
54589
7.67
177
1.00E-12
41%
15
51568
5.28
178
8.30E-13
46%
16
47250
5.26
124
2.10E-07
37%
11
47250
5.26
94
0.0002
30%
9
43627
5.52
102
3.30E-05
38%
12
50197
5.47
92
0.0003
35%
14
54375
8.42
148
8.30E-10
35%
13
49485
5.6
121
4.20E-07
37%
13
54375
8.42
161
4.20E-11
43%
25
49177
5.68
93
0.00025
26%
11
FAD binding; dihydrolipoyl dehydrogenase
activity; electron carrier activity
FAD binding; dihydrolipoyl dehydrogenase
activity; electron carrier activity
aminopeptidase activity; manganese ion
binding
magnesium ion binding; phosphopyruvate
hydratase activity
magnesium ion binding; phosphopyruvate
hydratase activity
ATP
binding;
diphosphomevalonate
decarboxylase activity; kinase activity
catalytic activity
NAD or NADH binding; isocitrate
dehydrogenase
(NADP+)
activity;
magnesium ion binding
adenosylhomocysteinase activity; binding
NAD or NADH binding; isocitrate
dehydrogenase
(NADP+)
activity;
magnesium ion binding
binding;
saccharopine
dehydrogenase
(NADP+, L-glutamate-forming) activity
116#
211593289
117#
211582350
118#
211582350
140#
211582350
182#
211582350
119#
211586702
metabolic process
243#
211586702
metabolic process
120#
211583718
metabolic process
antibiotic biosynthetic
penicillin biosynthetic
oxidation reduction
antibiotic biosynthetic
penicillin biosynthetic
oxidation reduction
antibiotic biosynthetic
penicillin biosynthetic
oxidation reduction
antibiotic biosynthetic
penicillin biosynthetic
oxidation reduction
antibiotic biosynthetic
penicillin biosynthetic
oxidation reduction
antibiotic biosynthetic
penicillin biosynthetic
oxidation reduction
antibiotic biosynthetic
penicillin biosynthetic
oxidation reduction
antibiotic biosynthetic
121#
124829
122#
3144
155#
3144
156#
3144
157#
3144
158#
3144
164#
3144
178#
3144
MNPTSSRAAVRSMATLTHAARA(1..22)
fumarate
metabolic
process;
tricarboxylic acid cycle
aromatic amino acid family
metabolic process
aromatic amino acid family
metabolic process
aromatic amino acid family
metabolic process
aromatic amino acid family
metabolic process
fumarate hydratase activity
58125
7.74
70
0.048
22%
9
fumarylacetoacetase activity
46621
6.01
146
1.30E-09
44%
13
fumarylacetoacetase activity
46621
6.01
120
5.30E-07
50%
12
fumarylacetoacetase activity
46621
6.01
103
2.60E-05
34%
12
fumarylacetoacetase activity
46621
6.01
112
3.30E-06
35%
10
41052
5.05
98
8.90E-05
45%
14
41052
5.05
75
0.018
39%
10
48013
5.7
77
0.011
21%
10
isopenicillin-N synthase activity; L-ascorbic
acid binding; iron ion binding
38050
5.42
149
6.60E-10
53%
12
isopenicillin-N synthase activity; L-ascorbic
acid binding; iron ion binding
38100
5.42
191
4.20E-14
55%
14
isopenicillin-N synthase activity; L-ascorbic
acid binding; iron ion binding
38100
5.42
215
1.70E-16
56%
16
isopenicillin-N synthase activity; L-ascorbic
acid binding; iron ion binding
38100
5.42
177
1.00E-12
54%
15
isopenicillin-N synthase activity; L-ascorbic
acid binding; iron ion binding
38100
5.42
198
8.30E-15
56%
15
isopenicillin-N synthase activity; L-ascorbic
acid binding; iron ion binding
38100
5.42
227
1.00E-17
55%
20
isopenicillin-N synthase activity; L-ascorbic
acid binding; iron ion binding
38100
5.42
87
0.0011
38%
8
isopenicillin-N synthase activity; L-ascorbic
38100
5.42
134
2.10E-08
54%
11
binding;
electron
carrier
activity;
oxidoreductase activity
oxidoreductase activity; electron carrier
activity; binding
Ligase; ATP binding
process;
process
process;
process
process;
process
process;
process
process;
process
process;
process
process;
process
process;
8
192#
3144
241#
3144
123#
211588892
124#
14194448
126#
211582533
129#
211582979
130#
211592030
134#
211592030
131#
211589003
penicillin biosynthetic
oxidation reduction
antibiotic biosynthetic
penicillin biosynthetic
oxidation reduction
antibiotic biosynthetic
penicillin biosynthetic
oxidation reduction
MASLTLPSLL RTSTRA(1..16)
process
process;
process
process;
process
oxidation reduction
oxidation
reduction;
pentose-phosphate shunt
transport
N-acetylglucosamine
process
N-acetylglucosamine
process
unknown
N-acetylglucosamine
process
N-acetylglucosamine
process
metabolic
metabolic
metabolic
132#
211592027
133#
211592027
135#
211592134
glycolysis; oxidation reduction
138#
211587149
oxidation reduction
139#
211587149
oxidation reduction
143#
211584596
MASRGLPRALRLARVAAPRSVVTAALPRPA
VAAAAALPRVSS(1..42)
145#
211584596
MASRGLPRALRLARVAAPRSVVTAALPRPA
metabolic
branched chain family amino acid
biosynthetic process; oxidation
reduction
branched chain family amino acid
9
acid binding; iron ion binding
isopenicillin-N synthase activity; L-ascorbic
acid binding; iron ion binding
38100
5.42
156
1.30E-10
43%
12
isopenicillin-N synthase activity; L-ascorbic
acid binding; iron ion binding
38100
5.42
192
3.30E-14
56%
14
46985
5.84
127
1.00E-07
38%
15
41958
5.45
207
1.00E-15
50%
17
56065
5.92
243
2.60E-19
54%
22
37873
5.38
163
2.60E-11
46%
19
40158
6.08
121
4.20E-07
58%
15
40158
6.08
82
0.0031
49%
13
44192
5.66
179
6.60E-13
58%
21
46132
5.75
125
1.70E-07
54%
13
46132
5.75
148
8.30E-10
56%
13
45382
8.49
149
6.60E-10
40%
14
38518
5.92
167
1.00E-11
35%
15
38518
5.92
93
0.00029
30%
12
44150
8.79
62
0.35
17%
7
44150
8.79
184
2.10E-13
39%
17
FAD binding; acyl-CoA dehydrogenase
activity; electron carrier activity
ATP binding; protein binding
NADP
or
NADPH
binding;
phosphogluconate
dehydrogenase
(decarboxylating) activity
transporter activity
glucosamine-6-phosphate
deaminase
activity
glucosamine-6-phosphate
deaminase
activity
unknown
N-acetylglucosamine-6-phosphate
deacetylase activity
N-acetylglucosamine-6-phosphate
deacetylase activity
pyruvate
dehydrogenase
(acetyl-transferring) activity
NAD or NADH binding; magnesium ion
binding; oxidoreductase activity, acting on
the CH-OH group of donors, NAD or
NADP as acceptor
NAD or NADH binding; magnesium ion
binding; oxidoreductase activity, acting on
the CH-OH group of donors, NAD or
NADP as acceptor
ketol-acid
reductoisomerase
coenzyme binding;
activity;
ketol-acid
activity;
reductoisomerase
VAAAAALPRVSS(1..42)
biosynthetic
reduction
process;
oxidation
144#
211589783
146#
211589494
148#
211581920
oxidation reduction
150#
211581920
oxidation reduction
151#
211581920
oxidation reduction
149#
152#
153#
160#
161#
211589225
211584011
211584011
211584785
211584785
162#
211593001
respiratory electron transport chain
163#
211581941
165#
211590565
anion transport
oxidation reduction; potassium ion
transport
166#
211586700
glycolysis
168#
169#
170#
171#
172#
211588765
211586963
211586963
211586963
211582080
173#
211584729
175#
211584478
oxidation reduction
(Belongs to the 14-3-3 family)
(Belongs to the 14-3-3 family)
(Belongs to the 14-3-3 family)
unknown
proteolysis involved in cellular
protein catabolic process
translation
176#
211584684
177#
179#
211590406
211591539
galactose metabolic process
MARLSFLLLGALSALSGVATA (1..21)
MKSFTLLTASALLGSAAA(1..18)
MKSFTLLTASALLGSAAA(1..18)
MAAPRLFRPTARLFSSRLAS
ALRSNLRQSACAPSILRRGYA (1..42)
coenzyme binding;
UDP-glucose
4-epimerase
activity;
coenzyme binding
isomerase activity
NAD or NADH binding; oxidoreductase
activity, acting on the CH-OH group of
donors, NAD or NADP as acceptor
NAD or NADH binding; oxidoreductase
activity, acting on the CH-OH group of
donors, NAD or NADP as acceptor
NAD or NADH binding; oxidoreductase
activity, acting on the CH-OH group of
donors, NAD or NADP as acceptor
acyltransferase activity
aspartic-type endopeptidase activity
aspartic-type endopeptidase activity
protein domain specific binding
protein domain specific binding
oxidoreductase activity, acting on NADH or
NADPH
voltage-gated anion channel activity
40587
5.73
124
2.10E-07
29%
11
39754
6.21
160
5.30E-11
50%
15
50347
6.25
147
1.00E-09
39%
17
50347
6.25
92
0.0003
35%
16
50347
6.25
206
1.30E-15
46%
20
43067
43589
43589
31338
31338
6.27
5.08
5.08
4.72
4.72
94
98
84
106
106
0.00021
8.30E-05
0.0019
1.30E-05
1.30E-05
56%
28%
31%
45%
39%
13
8
11
11
8
27024
5
166
1.30E-11
47%
13
38442
5.39
63
0.31
36%
7
37952
5.94
67
0.11
31%
6
39486
5.43
218
8.30E-17
71%
20
37330
29365
29365
29365
36513
6.14
4.76
4.76
4.76
5.58
162
115
160
69
72
3.30E-11
1.70E-06
5.30E-11
0.062
0.037
59%
35%
56%
26%
36%
15
9
13
7
11
threonine-type endopeptidase activity
28880
5.13
76
0.015
34%
8
structural constituent of ribosome
32517
4.79
71
0.042
50%
7
metabolic process
catalytic activity
39291
8.22
91
0.00045
33%
11
pentose-phosphate shunt
oxidation reduction
transaldolase activity
oxidoreductase activity
35589
36627
5.45
5.54
96
181
0.00015
4.20E-13
32%
56%
10
16
cell redox homeostasis
metabolic process
proteolysis
proteolysis
unknown
unknown
10
oxidoreductase activity
fructose-bisphosphate aldolase activity; zinc
ion binding
oxidoreductase activity
protein domain specific binding
protein domain specific binding
protein domain specific binding
FAD binding; electron carrier activity
181#
211590788
183#
211583384
MFSRAVRPALRAGGAAVARPAPANA(1..25)
184#
211581963
MVKAVVLGAA GGIG (1..14)
185#
186#
187#
211588997
211588997
211582639
ATP synthesis coupled proton
transport
glycolysis;
malate
metabolic
process; oxidation reduction
unknown
unknown
unknown
188#
211582045
unknown
189#
211590181
glycolysis; oxidation reduction
270#
211590181
glycolysis; oxidation reduction
284#
211590181
glycolysis; oxidation reduction
190#
211591374
unknown
191#
211587455
Tricarboxylic acid cycle
193#
211586927
265#
211586927
194#
211581603
195#
112941
197#
112941
198#
112941
267#
112941
pentose-phosphate shunt
response to oxidative
oxidation reduction
response to oxidative
oxidation reduction
metabolic process
antibiotic biosynthetic
penicillin biosynthetic
oxidation reduction
antibiotic biosynthetic
penicillin biosynthetic
oxidation reduction
antibiotic biosynthetic
penicillin biosynthetic
oxidation reduction
antibiotic biosynthetic
stress;
stress;
coenzyme
binding;
phosphogluconate
dehydrogenase (decarboxylating) activity
hydrogen ion transporting ATP synthase
activity, rotational mechanism
38923
7.83
82
0.003
34%
7
32415
6.04
112
3.30E-06
49%
13
L-malate dehydrogenase activity
34281
5.44
189
6.60E-14
52%
17
unknown
unknown
GTP binding; GTPase activity
S-formylglutathione hydrolase activity;
carboxylesterase activity
NAD
or
NADH
binding;
glyceraldehyde-3-phosphate dehydrogenase
(phosphorylating) activity
NAD
or
NADH
binding;
glyceraldehyde-3-phosphate dehydrogenase
(phosphorylating) activity
NAD
or
NADH
binding;
glyceraldehyde-3-phosphate dehydrogenase
(phosphorylating) activity
unknown
L-malate
dehydrogenase
activity;
nucleotide binding
34722
34722
94450
5.64
5.64
6.3
121
115
97
4.20E-07
1.70E-06
0.00011
45%
55%
15%
10
10
12
31360
5.89
67
0.096
37%
7
36149
6.23
112
3.30E-06
47%
11
36149
6.23
69
0.071
17%
6
36149
6.23
77
0.01
27%
7
35346
6.31
88
0.00091
28%
9
35821
8.44
123
2.60E-07
37%
11
heme binding; peroxidase activity
40284
8.29
88
0.00081
37%
11
peroxidase activity; heme binding
40284
8.29
72
0.035
25%
8
binding; oxidoreductase activity;
28712
5.33
93
0.00028
37%
10
process;
process
isopenicillin-N N-acyltransferase activity
40199
6.23
224
2.10E-17
42%
20
process;
process
isopenicillin-N N-acyltransferase activity
40199
6.23
203
2.60E-15
47%
17
process;
process
isopenicillin-N N-acyltransferase activity
40199
6.23
125
1.70E-07
39%
9
process;
isopenicillin-N N-acyltransferase activity
40199
6.23
99
6.90E-05
28%
10
11
196#
199#
211589756
211591049
201#
211584898
202#
211591714
203#
211582349
204#
205#
206#
208#
209#
210#
211586852
211586852
211586852
211582636
211589332
211589332
211#
211581829
214#
211593369
216#
211590405
219#
220#
221#
211585738
211584333
211589115
229#
543770
235#
211586726
237#
211590220
242#
211590370
245#
211589753
penicillin biosynthetic process
oxidation reduction
Unknown
Unknown
nucleoside metabolic process;
pyrimidine nucleotide biosynthetic
process
MSVSPNRTIAIVGVGSSISRSLALWLASVG
WNIALVSR (1..38)
MASRLAKSAIGASRLRPALPARGVPAVTAN
LTSSRQA(1-37)
metabolic process
aromatic amino acid family
metabolic process
cell redox homeostasis
cell redox homeostasis
cell redox homeostasis
unknown
unknown
unknown
ATP synthesis coupled proton
transport
cell redox homeostasis
superoxide metabolic process;
oxidation reduction
proteolysis
metabolic process
acetoin catabolic process
MSGARNITAALRRARVPRPSLAIRTVQFIT
PLTARTFS(1..38)
unknown
translation
MFKSGLARSFGRAAFARTTPVARAFQPVR
S NALPALARFA SSDA (1..44)
ATP synthesis
transport
coupled
proton
12
unknown
unknown
26106
24617
5.9
5.13
129
104
6.60E-08
2.10E-05
58%
51%
10
10
orotate phosphoribosyltransferase activity
26116
5.97
70
0.055
42%
8
oxidoreductase activity;binding
26386
5.83
112
3.30E-06
37%
8
catalytic activity
24869
6.45
145
1.70E-09
65%
11
antioxidant activity; oxidoreductase activity
antioxidant activity; oxidoreductase activity
antioxidant activity; oxidoreductase activity
O-methyltransferase activity
oxidoreductase activity
oxidoreductase activity
hydrogen ion transmembrane transporter
activity; hydrolase activity
oxidoreductase activity
superoxide dismutase activity; copper ion
binding; zinc ion binding
peptidase activity
ATP binding
triose-phosphate isomerase activity
acetate-CoA ligase activity; ATP binding;
AMP binding
thiamin
pyrophosphate
binding;
carboxy-lyase activity; magnesium ion
binding;
UDP-N-acetylmuramate
dehydrogenase
activity
structural constituent of ribosome
hydrogen-exporting
ATPase
activity,
phosphorylative
mechanism;
proton-transporting
ATPase
activity,
rotational mechanism; hydrogen ion
transporting
ATP synthase activity,
24769
24769
24769
24891
24295
24295
5.24
5.24
5.24
5.14
5.33
5.33
79
85
194
103
112
88
0.006
0.0015
2.10E-14
2.60E-05
3.30E-06
0.00081
35%
43%
68%
38%
49%
52%
6
9
17
9
9
8
26366
9.3
95
0.00017
35%
7
18359
5.37
106
1.30E-05
52%
9
15951
5.94
97
0.0001
64%
7
84115
79429
27202
5.17
5.05
5.29
92
143
122
0.0003
2.60E-09
3.30E-07
22%
31%
51%
12
17
11
74640
5.85
85
0.0018
12%
10
63489
5.68
79
0.0068
28%
11
59671
5.76
114
2.10E-06
32%
14
40006
11
79
0.0071
37%
8
55237
5.25
141
4.20E-09
51%
15
246#
211591628
248#
211581996
250#
211588099
252#
211585945
255#
256#
257#
258#
261#
211586201
211589998
211592526
211590561
211583872
262#
211582330
264#
211590742
266#
211593449
pentose-phosphate
non-oxidative branch
pentose-phosphate shunt
268#
211582340
nucleoside metabolic process
269#
211591187
273#
211585181
274#
134086007
275#
211589762
276#
211592809
280#
281#
282#
211589209
211582444
211593284
rotational mechanism; ATP binding
ATPase activator activity; chaperone
binding
response to stress
35970
5.35
98
7.60E-05
29%
9
39220
5.5
85
0.0016
38%
8
3625
5.67
74
0.023
35%
8
structural constituent of ribosome
33147
4.9
59
0.71
19%
5
catalytic activity; coenzyme binding
oxidoreductase activity; binding
catalytic activity
oxidoreductase activity; Binding
adenylylsulfate kinase activity; ATP binding
NADH
dehydrogenase
(ubiquinone)
activity
35273
28455
32504
27515
23642
5.83
5.48
5.47
6
6.02
74
108
109
129
99
0.022
8.30E-06
6.60E-06
6.60E-08
6.80E-05
34%
40%
37%
62%
52%
10
10
11
10
9
32594
7.74
147
1.00E-09
58%
13
ribose-5-phosphate isomerase activity
29001
5.76
86
0.0012
22%
7
6-phosphogluconolactonase activity
transferase activity, transferring pentosyl
groups
29063
5.51
65
0.16
28%
6
34143
6.11
82
0.0037
37%
9
GTPase activity; protein binding; GTP
binding
24362
6.45
101
4.20E-05
32%
8
guanylate kinase activity
21977
6.19
99
6.80E-05
41%
7
glutathione transferase activity
2 iron, 2 sulfur cluster binding; electron
carrier activity; iron ion binding;
ubiquinol-cytochrome-c reductase activity
24781
6.1
113
2.60E-06
32%
11
25836
8.59
118
8.30E-07
42%
10
threonine-type endopeptidase activity
22566
6.3
88
0.00089
29%
9
unknown
unknown
oxidoreductase activity
18643
18955
18697
4.88
4.99
4.9
172
65
90
3.30E-12
0.17
0.00048
68%
46%
55%
16
5
8
MPATTADTLSLVNRSVTVAPLVLLSVA
(1..27)
hexose metabolic process
ribosome biogenesis; translational
elongation
cellular metabolic process
metabolic process
metabolic process
oxidation reduction
sulfate assimilation
MASARSLMRLGSGRSVASATRSMAARTFS
S ASLQCAPKAS T (1-41)
oxidation reduction
shunt,
intracellular protein transport;
nucleocytoplasmic transport; signal
transduction
purine
nucleotide
metabolic
process
MSLSSASSTLLRTVAR (1..16)
electron transport chain; transport
proteolysis involved in cellular
protein catabolic process
unknown
unknown
cell redox homeostasis
carbohydrate binding; isomerase activity
MM: Molecular Mass; pI: Isoelectric point; NMP: Number Matched Peptide; COV: Coverage
13
Figure S1. The biomass and relative penicillin productions under the pilot
and industrial processes. Each value represented the mean value of four
independent replications
14
Figure S2. The intracellular proteome profiling of the industrial P. chrysogenum strain during the industrial process.
15
Figure S3. Heat map representation of the identified proteins related to signal
peptides in P. chrysogenum during fermentation. The observation counts were
first normalized by dividing the volume of each protein spot by the total
volume of all protein spots on the gel, then normalized to the volume of the
protein spot at fermentation time 2h, which was set to 1.0. The scale from
least to most abundant ranged from 0.5 (green color) to > 1.5 (red color).
16
Figure S4. Heat map representation of the identified proteins with molecular
function of NAD, FAD or NADH binding in P. chrysogenum during fermentation.
The observation counts were first normalised by dividing the volume of each
protein spot by the total volume of all protein spots on the gel, then normalised to
the volume of the protein spot at fermentation time 2h, which was set to 1.0. The
scale from least to most abundant ranged from 0.5 (green color) to > 1.5 (red
color).
17
Figure S5. The relative changes in the levels of the identified proteins associated
with glycolysis, pp pathways and TCA cycle. (A) Pilot process, (B) Industrial
process; The observation counts were firstly normalized by dividing the volume of
each protein spot by the total volume of all protein spots on the gel, then
normalized to the volume of the protein spot at 2h, which was set to 1.0.
18
Figure S6. The relative variations in the levels of proteins involved in amino acid
metabolic processes. (A) Pilot process, (B) Industrial process; The observation
counts were firstly normalized by dividing the volume of each protein spot by the
total volume of all protein spots on the gel, then normalized to the volume of the
protein spot at 2h, which was set to 1.0.
19
Figure S7. The relative alterations in the levels of proteins related to
oxidation reduction and response to stresses. (A) Pilot process, (B) Industrial
process; The observation counts were firstly normalized by dividing the
volume of each protein spot by the total volume of all protein spots on the gel,
then normalized to the volume of the protein spot at 2h, which was set to 1.0.
20
Figure S8. The relative changes in the levels of proteins involved in transport
process (A) Pilot process, (B) Industrial process; The observation counts
were firstly normalized by dividing the volume of each protein spot by the
total volume of all protein spots on the gel, then normalized to the volume of
the protein spot at 2h, which was set to 1.0.
21
Figure S9. The dynamic changes of proteins involved in cellular
structural molecule and signal transduction of P. chrysogenum during
industrial and pilot fermentation.
22