Supplementary Table 1. Primer sequences used for validation of the RT-qPCR
expression profile.
Primer name
RT_Cg_16S_F
RT_Cg_16S_R
RT_cg0878_F
RT_cg0878_R
RT_cg0933_F
RT_cg0933_R
RT_cg1271_F
RT_cg1271_R
RT_cg1748_F
RT_cg1748_R
RT_cg1791_F
RT_cg1791_R
RT_cg2322_F
RT_cg2322_R
RT_cg2610_F
RT_cg2610_R
RT_cg2618_F
RT_cg2618_R
RT_cg2623_F
RT_cg2623_R
RT_cg2628_F
RT_cg2628_R
RT_cg2833_F
RT_cg2833_R
RT_cg3420_F
RT_cg3420_R
RT_cg3423_F
RT_cg3423_R
Primer sequence 5′→3′
ACCCTTGTCTTATGTTGCCAG
TGTACCGACCATTGTAGCATG
AATCTGCCGTGAAGAGGATC
GGCACTGGGAGGTAACTG
CCAATCCGATAAGACAGTCCTG
GTAGGTGTGAATATGCTCGGG
GATGAGTTGAGCCCAGACTTC
GTACCCATTTTCACTCCGAGG
CCCTTAAACCTCTGCATCCG
TTCCGTAGACATCGTTTCACC
CTACGATCCTGAGAACCACAAC
CGTTTAGGACCTTTGCCATTG
TGATCCACGCTCTGAAATCC
GCAGCGAAAACACCATCAAG
CGTGTTCTACGCCCAAAATG
CCCGACAGTTCCTCTTCATAG
ACAAAGAGAACCGTGGAACC
TCTGACATTCCGGTTTCCAC
CGGACTGTTGCTTTTGGATAAG
AGGTACTGGCGTGCATATTC
GAGTTGGACATGCACATTCG
ATGGTTGGAGTTCGGCAC
TGAACAAGCTCACCGAAGG
GGACTTCTCTGCATCTTCAACG
GACCTAAGCGATACCCAACTC
TTCCGCCCGTATTTTCTGG
TCATTGAGGAAATCGCAGGC
ATCTGGAACATGGCACCC
Note
16S rRNA gene
for normalization
whcE
cg0933
sigE
cg1748
gapA
trxB
cg2610
vanK
pcaI
pcaC
cysK
sigM
trxC
Supplementary Table 2. Transcriptional regulators based on a transcriptome
comparison of Corynebacterium glutamicum ATCC 13032 with the wild-type strain
cultivated under the no stress condition and the H2O2-adapted strain cultivated in
MCGC containing 10 mM H2O2.
Gene
Gene
Protein
IDa
nameb
family
Carbon metabolism
Response
cg0090
citB
regulator
Annotationc
Activator of citrate transporter genes citH and
tctCBA
Dual regulator (global regulator) functioning as
cg0350
glxR
Crp
network hub
Dual regulator (master regulator) of carbon
cg0444 ramB
HTH_3
metabolism
Activator of propionate utilization genes
cg0800 prpR
HTH_3
prpD2B2C2
Repressor of ribose uptake and uridine
cg1410 rbsR
LacI
utilization genes
Repressor of uridine utilization and ribose
cg1547
uriR
LacI
uptake genes
cg1738 acnR
TetR
Repressor of aconitase gene acn
cg1935 gntR2
GntR
Dual regulator involved in carbon metabolism
Repressor (master regulator) involved in carbon
cg2115 sugR
DeoR
metabolism
cg2118
fruR
DeoR
Repressor of fructose PTS system genes
cg2746
COG2508 putative sugar diacid utilization regulator
cg2783 gntR1
GntR
Dual regulator involved in carbon metabolism
Dual regulator (master regulator) of carbon
cg2831 ramA
LuxR
metabolism
cg3224
lldR
GntR
Repressor involved in carbon metabolism
Amino acid and vitamin biosynthesis and anaerobic respiration
cg0313
lrp
AsnC
Activator of amino acid exporter genes brnFE
Activator of serine hydroxymethyltransferase
cg0527
glyR
ArsR
gene glyA
Activator of pyridoxal phosphate synthase
cg0897 pdxR
GntR
genes
Repressor of NAD biosynthesis genes nadACcg1218
nrtR
NrtR
cg1214
Dual regulator (master regulator) of anaerobic
cg1340 arnR
ArnR
respiration
cg1425
lysG
LysR
Activator of amino acid exporter gene lysE
cg1486
ltbR
IclR
Repressor of leucine and tryptophan
Repressor of arginine and glutamate
cg1585 argR
ArgR
biosynthesis genes
Repressor of ribonucleotidereductase genes
cg2112 nrdR
NrdR
nrdHIE
Repressor of biotin uptake and biosynthesis
cg2309 bioQ
TetR
genes
cg2894 cgmR
TetR
Repressor of MFS-type transporter gene
Expression
ratiod
1.99
0.76
1.55
2.09
2.12
2.22
2.29
1.63
2.15
0.98
2.12
1.74
1.43
1.74
2.23
0.43
1.18
0.56
0.95
2.33
1.74
2.11
2.47
1.70
1.50
cg3202
farR
GntR
cg3261
GntR
Aromatic compound catabolism
cg0500 qsuR
LysR
cg1308 rhcR
TetR
cg2615 vanR
PadR
cg2624 pcaR
IclR
cg2627 pcaO
LuxR
cg2641 benR
LuxR
cg2965
AraC
cg3352 genR
IclR
cg3388
-
IclR
cg2893
Repressor of arginine and glutamate
biosynthesis genes
Regulator of conserved hypothetical protein
Activator of quinate/ shikimate pathway genes
Repressor of resorcinol pathway genes
Repressor of vanillate pathway genes
Repressor of protocatechuate pathway genes
Activator of protocatechuate pathway genes
Activator of catechol pathway genes
Activator of phenol pathway gene
Activator of gentisate pathway genes
Activator of putative hydroxyquinol pathway
genes
0.92
1.17
1.76
2.22
3.38
4.09
3.64
3.71
2.30
2.04
1.91
Macroelement metabolism
cg0012
ssuR
ROK
cg0112
ureR
MarR
cg0156
cysR
ROK
cg0986
amtR
cg2888
phoR
TetR
Response
regulator
TetR
cg3253 mcbR
Metal homeostasis
Cg0317
arsR2
ArsR
Cg1120
ripA
AraC
Cg1704
arsR1
ArsR
Cg2103 dtxR
Cg2500
znr
Cg2502
zur
Sigma factors
cg0309
sigC
DtxR
ArsR
FUR
cg0696
sigD
SigD
cg0876
sigH
SigH
cg1271
sigE
SigE
cg2092
sigA
SigA
cg2102
sigB
SigB
cg3420
sigM
SigM
SigC
Activator of sulfonate and sulfonate ester
utilization
putative repress or urease genes
Dual regulator of assimilatory sulfate reduction
genes
Repressor of nitrogen metabolism
0.91
2.53
1.33
1.22
Activator of phosphate metabolism
1.44
Repressor of sulfur metabolism
1.70
Repressor of arsenitepermease and arsenate
reductase genes
Repressor of iron protein genes
Repressor of arsenitepermease and arsenate
reductase genes
Dual regulator of iron metabolism
Putative repressor of zinc uptake regulator gene
Repressor of zinc uptake system genes
ECF sigma factor of unknown function
ECF sigma factor of probably involved in the
adaptation to microaerobic environments
ECF sigma factor controlling the heat and
oxidative stress response
ECF sigma factor involved in responses to cells
surface stresses
Primary (housekeeping) sigma factor
Nonessential primary-like sigma factor
involved in gene expression during the
transition phase, under oxygen deprivation and
during environmental stress responses
ECF sigma factor controlling the expression of
disulfide stress-related genes
1.89
0.68
1.34
1.40
0.81
1.08
1.98
1.46
2.12
0.09
0.74
0.66
1.79
Anti-sigma factors
cg0877
rhsA
RhsA
cg1272 cseE
CseE
SOS and stress response
cg0215 cspA
Cold
cg0337 whcA
WhiB
cg0695 whcB
WhiB
Anti-sigma factor of SigH
Anti-sigma factor of SigE
1.80
1.89
Repressor of malate synthase gene aceB
0.88
Repressor of oxidative stress response genes
1.68
Stationary phase-specific regulator
0.52
Dual regulator of genes involved in cell
Response
cg0862 mtrA
morphology, antibiotics susceptibility and
1.41
regulator
osmoprotection
cg0878 whcE
WhiB
Activator of thioredoxin genes
0.13
Hydrogen peroxide-sensitive MarR-type
cg1324
rosR
RosR
1.89
transcriptional regulator
putative stress-responsive transcriptional
cg1325
1.77
regulator
cg1552 qorR COG1733 Repressor of quinoneoxidoreductase gene qor2
1.25
Repressor of iron–sulfur cluster biogenesis
cg1765
sufR
ArsR
0.63
genes
cg2109 oxyR
LysR
Hydrogen peroxide sensing regulator
1.35
Dual regulator (master regulator) of SOS
cg2114
lexA
LexA
1.51
response
cg2152
clgR
HTH_3
Activator of proteolysis and DNA repair genes
1.62
Repressor of heat shock response genes with
cg2516 hrcA
HrcA
2.08
CIRCE elements
Repressor of heat shock response genes with
cg3097 hspR
MerA
1.91
HAIR elements
a
Gene ID according to the accession number BX927147 was used.
b,c
Gene name and annotation was obtained form the CoryneRegNet database
(www.coryneregnet.de), and Brinkrolf et al., 2010, and Schröderand Tauch, 2010.
d
Expression ratios are from a comparison of the H2O2-adapted strain under the oxidative
stress condition vs. the wild-type strain under the no stress condition.
Supplementary Table 3. Oxidation-reduction related genes from the transcriptome
results.
Gene
IDa
Gene
nameb
Protein
IDc
cg0031
-
YP_224316.1
cg0065
cg0131
-
YP_224345.1
YP_224397.1
cg0204
iolG
YP_224460.1
cg0207
cg0211
cg0237
cg0238
cg0251
cg0253
cg0274
cg0310
cg0319
cg0326
cg0344
oixA
katA
arsX
nuoL
fabG1
YP_224463.1
YP_224467.1
YP_224488.1
YP_224489.1
YP_224502.1
YP_224504.1
YP_224523.1
YP_224555.1
YP_224563.1
YP_224569.1
YP_224585.1
cg0402
rmlCD
YP_224633.1
cg0404
-
YP_224635.1
cg0423
murB
YP_224653.1
cg0476
murB2
YP_224698.1
cg0490
cg0497
cg0517
cg0612
proC
hemA
hemY
dkg
YP_224712.1
YP_224719.1
YP_224738.1
YP_224819.1
cg0618
fdhF
YP_224823.1
cg0624
-
YP_224828.1
cg0637
betB
YP_224839.1
cg0639
-
YP_224841.1
cg0700
guaB3
YP_224897.1
cg0795
-
YP_224984.1
cg0828
cg0965
folA
YP_225012.1
YP_225135.1
Annotationd
Reductase related to
diketogulonatereductase
Haem peroxidase superfamily
putative oxidoreductase
putative oxidoreductasemyo-inositol 2dehydrogenase
hypothetical oxidoreductase
putative oxidoreductase
putative oxidoreductase
L-Gulonolactone oxidase
Quinone oxidoreductase
Flavodoxinreductase
putative oxidoreductase
catalase
Arsenate reductase
NADH-quinoneoxidoreductase chain 5
3-Oxoacyl-(acyl-carrier protein) reductase
dTDP-4-dehydrorhamnose 3,5-epimerase,
dTDP-dehydrorhamnosereductase
Nitroreductase family
UDP-Nacetylenolpyruvoylglucosaminereductase
Probable UDP-Nacetylenolpyruvoylglucosamine reductase
Pyrroline-5-carboxylate reductase
Glutamyl-tRNAreductase
putative protoporphyrinogen oxidase
2,5-diketo-D-gluconic acid reductase
putative formate dehydrogenase
oxidoreductase protein
Secreted oxidoreductase
putative betaine aldehyde dehydrogenase
(BADH) oxidoreductase
Ferredoxinreductase
IMP dehydrogenase/ GMP reductase C
terminus
FAD-dependent pyridine nucleotidedisulphideoxidoreductase
putative dihydrofolatereductase
Dihydrofolatereductase
Expression
ratioe
2.62
2.39
2.02
2.15
2.32
1.90
1.03
0.77
1.85
1.71
2.14
2.11
1.93
2.06
2.32
1.30
0.74
1.72
1.00
1.32
2.14
2.15
1.42
1.39
2.30
1.92
2.23
1.38
2.54
1.55
1.58
cg1068
cg1080
-
cg1118
-
cg1150
cg1192
cg1236
cg1239
tpx
-
cg1244
-
cg1300
cydB
cg1301
cydA
cg1309
rhcH
cg1310
cg1341
cg1342
cg1343
cg1344
rhcM1
narI
narJ
narH
narG
cg1423
-
cg1528
dkgX
cg1580
argC
cg1680
-
cg1703
-
cg1711
cg1769
ctaA
cg1771
qor
cg1773
ctaB
cg1781
cg1783
'soxA
soxA
cg1800
ribG
cg1848
-
cg1881
-
YP_225228.1 Probable oxidoreductase
YP_225238.1 putative multicopper oxidase
Pyrimidine reductase, riboflavin
YP_225273.1
biosynthesis
YP_225302.1 NADPH-dependent FMN reductase
YP_225338.1 Aldo/ketoreductase
YP_225377.1 Thiol peroxidase
YP_225380.1 Similar to ketopantoatereductase
Arsenate reductase or related protein,
YP_225386.1
glutaredoxin family
Cytochrome d terminal oxidase
YP_225440.1
polypeptide subunit
YP_225441.1 Cytochrome d ubiquinol oxidase subunit I
2-polyprenyl-6-methoxyphenol
YP_225448.1 hydroxylase and related FAD-dependent
oxidoreductase
YP_225449.1 Maleylacetatereductase
YP_225476.1 Nitrate reductase gamma subunit
YP_225477.1 Nitrate reductase delta subunit
YP_225478.1 Nitrate reductase beta subunit
YP_225479.1 Nitrate reductase alpha subunit
putative oxidoreductase (related to arylYP_225550.1
alcohol dehydrogenases)
putative 2,5-diketo-D-gluconic acid
YP_225642.1
reductase
N-acetyl-gamma-glutamyl-phosphate
YP_225681.1
reductase
YP_225770.1 Short-chain dehydrogenase/reductase
FAD-dependent pyridine nucleotideYP_225793.1
disulphideoxidoreductase
YP_225801.1 Oxidoreductase
YP_225854.1 Cytochrome oxidase assembly protein
Probable NADPH: quinonereductase,
YP_225856.1
zeta-crystallin
Polyprenyltransferase (cytochrome
YP_225857.1
oxidase assembly factor)
YP_225864.1 Sarcosine oxidase-fragment
YP_225865.1 Sarcosine oxidase-N-terminal fragment
putative bifunctional riboflavin-specific
YP_225881.1
deaminase/reductase
Coenzyme F420-dependent N5,N10methylene
YP_225927.1
tetrahydromethanopterinreductase or
related flavin-dependent
Predicted iron-dependent peroxidase,
YP_225955.1
secreted protein
1.93
1.64
2.21
2.03
2.16
0.43
0.97
1.53
2.42
2.50
2.42
2.32
1.85
2.20
2.12
2.30
1.67
2.16
2.11
2.30
1.81
2.29
1.05
1.83
2.14
2.20
2.46
2.05
1.54
2.13
cg2078
msrB
YP_226139.1
cg2163 dapB
cg2192
mqo
cg2194 gor/mtr
YP_226215.1
YP_226243.1
YP_226245.1
cg2237
thiO
YP_226279.1
cg2329
-
YP_226360.1
cg2383
cg2406
cg2409
metF
ctaE
ctaC
YP_226413.1
YP_226434.1
YP_226437.1
cg2517
hemN
YP_226535.1
cg2543
glcD
YP_226558.1
cg2586
cg2591
proA
dkgA
YP_226599.1
YP_226604.1
cg2613
mdh
YP_226625.1
cg2639
benC
YP_226650.1
cg2674
-
YP_226677.1
cg2685
-
YP_226686.1
cg2736
bcp
YP_226730.1
cg2780
ctaD
YP_226765.1
cg2781
nrdF
YP_226766.1
cg2786
nrdE
YP_226771.1
cg2795
-
YP_226778.1
cg2867
cg2919
gpx
-
YP_226832.1
YP_226877.1
cg2958
butA
YP_226913.1
cg2966
-
YP_226920.1
cg2999
-
YP_226947.1
cg3004
gabD1
YP_226951.1
Peptide methionine sulfoxidereductaserelated protein
Dihydrodipicolinatereductase
Malate: quinoneoxidoreductase
putative glutathione reductase
putative D-amino acid oxidase/
flavoproteinoxidoreductase
Coenzyme F420-dependent N5,N10methylene
tetrahydromethanopterinreductase
5,10-methylenetetrahydrofolate reductase
Cytochrome c oxidase subunit 3
Cytochrome c oxidase chain II
putative anaerobic coproporphyrinogen III
oxidase
Probable glycolate oxidase (FAD-linked
subunit) oxidoreductase
Gamma-glutamyl phosphate reductase
2,5-diketo-d-gluconic acid reductase
Malate dehydrogenase oxidoreductase
protein
Benzoate dioxygenasereductase
AlkylhydroperoxidaseAhpD family core
domain
putative short-chain
dehydrogenase/reductase
Probable bacterioferritin comigratory
oxidoreductase
Probable cytochrome c oxidase
polypeptide subunit
Ribonucleoside-diphosphatereductase 2
beta chain
Ribonucleoside-diphosphatereductase
alpha chain
NADPH quinonereductase or related Zndependent oxidoreductase
Glutathione peroxidase
putative oxidoreductase
L-2,3-Butanediol
dehydrogenase/acetoinreductase
2-Polyprenyl-6-methoxyphenol
hydroxylase or related FAD-dependent
oxidoreductase
putative ferredoxinreductase
Probable succinate-semialdehyde
dehydrogenase oxidoreductase
0.96
2.27
1.59
2.35
2.30
2.21
2.20
2.30
1.71
1.72
2.23
1.14
1.42
1.62
4.55
0.82
0.90
1.68
1.02
1.63
1.32
1.91
2.24
2.56
0.22
2.25
1.86
2.23
NADH ubiquinone oxidoreductase subunit
cg3024 mrpA YP_226967.1 5 (chain L)/Multisubunit
1.96
Na+/H+antiporter, A subunit
NADH-ubiquinone
cg3026 mrpD YP_226969.1 oxidoreductase/Multisubunit
1.96
+ +
Na /H antiporter, D subunit
putative ferredoxin/ferredoxin-NADP
cg3049
fprA
YP_226992.1
1.68
reductase
2-polyprenylphenol hydroxylase or related
cg3092
YP_227029.1
1.47
flavodoxinoxidoreductase
Phosphoadenosinecg3116
cysH
YP_227054.1
0.60
phosphosulfatereductase
cg3118
cysI
YP_227056.1 Sulfite reductase (hemoprotein)
0.83
cg3119
cysJ
YP_227057.1 Probable sulfite reductase (flavoprotein)
1.01
cg3136
YP_227073.1 Nitroreductase
1.68
cg3223
ldh
YP_227152.1 NADPH-dependent FMN reductase
1.48
cg3236 msrA YP_227165.1 Peptide methionine sulfoxidereductase
2.01
cg3287 copO
Secreted multicopper oxidase
1.76
Probable oxidoreductase protein;
cg3290
YP_227216.1
1.77
NADPH: quinonereductase
cg3332
YP_227255.1 putative quinoneoxidoreductase
1.94
putative FAD-dependent pyridine
cg3339 merA YP_227261.1 nucleotide-disulphideoxidoreductase,
1.89
similar to mercuric reductases
cg3344
YP_227266.1 Nitroreductase
2.26
Probable gentisate 1,2-dioxygenase
cg3351 genD YP_227273.1
2.15
oxidoreductase
putative NADH-dependent
cg3370
YP_227291.1
2.18
flavinoxidoreductase
putative NDAH-dependent
cg3374
cye1
YP_227295.1
2.34
flavinoxidoreductase
cg3380
YP_227300.1 putative oxidoreductase protein
2.13
cg3386 rhcM2 YP_227305.1 Maleylacetatereductase
2.17
NADPH quinonereductase or Zncg3405
YP_227324.1
1.61
dependent oxidoreductase
cg3422
trxB
YP_227339.1 Thioredoxinreductase
1.98
a
Gene ID according to the accession number BX927147 was used.
b, c, d
Gene name, protein ID, and annotation were obtained from the CoryneRegNet database
(www.coryneregnet.de) and Brinkrolf et al., 2010 and Schröder and Tauch, 2010.
e
Expression ratios from a comparison of the H2O2-adapted strain under the oxidative stress
condition vs. the wild-type strain under the no stress condition.
Supplementary Table 4. List of genes showing a ≥ 3-fold increase in comparison with the
H2O2-adapted and wild-type strains.
1
2
3
4
5
6
7
8
9
10
11
12
13
Gene
IDa
cg0311
cg1328
cg1748
cg1912
cg1925
cg1932
cg1938
cg1974
cg2003
cg2156
cg2600
cg2608
cg2609
Gene
nameb
ppp2
tnp1d
folC
valS
14
cg2610
-
15
16
17
18
19
20
cg2614
cg2615
cg2616
cg2617
cg2618
cg2619
vanR
vanA
vanB
vanK
-
21
cg2622
pcaJ
22
cg2623
pcaI
23
cg2624
pcaR
24
cg2625
pcaF
25
cg2626
pcaD
26
cg2627
pcaO
27
cg2628
pcaC
28
29
30
31
32
33
cg2629
cg2630
cg2631
cg2633
cg2634
cg2635
pcaB
pcaG
pcaH
catC
catB
No
Annotationc
Secreted protein
putative Copper chaperone
putative secreted protein
hypothetical protein
hypothetical protein
Probable protein phosphatase
hypothetical protein
putative lysin
hypothetical protein
hypothetical protein
Transposase (ISCg1d)
Folylpolyglutamate synthase
putative valine-tRNA ligase
ABC-type dipeptide/oligopeptide/nickel transport
system, secreted component
Bacterial regulatory proteins, TetR family
Putative transcriptional regulator PadR-like family
Probable vanillateO-demethylaseoxygenase subunit
Probable VanillateO-demethylase
Vanillate transporter Vank
Predicted permease
Probable succinyl-CoA:3-ketoacid-coenzyme A
transferase subunit acyl-CoA: acetate CoA
transferase beta subunit
Probable fesuccinyl-CoA:3-ketoacid-coenzyme A
transferase subunit or acyl-CoA:acetate CoA
transferase alpha subunit
Repressor of protocatechuate pathway genes. IclR
family
Putative Acetyl-CoA:Acetyltransferase
3-Oxoadipate enol-lactone hydrolase/4Carboxymuconolactonedecarboxylase
Activator of protocatechuate pathway genes. LuxR
family
3-oxoadipate enol-lactone hydrolase/4carboxymuconolactonedecarboxylase
3-Carboxy-cis,cis-Muconate Cycloisomerase
Protocatechuatedioxygenase alpha subunit
Protocatechuatedioxygenase beta subunit
Putative restriction endonuclease
Muconolactoneisomerase
Chloromuconatecycloisomerase
Expression
ratiod
3.12
3.06
3.40
3.22
3.40
3.02
3.23
3.20
3.03
3.25
3.50
3.98
3.29
4.20
3.51
3.38
3.89
3.39
4.11
3.96
4.35
4.45
4.09
4.35
3.35
3.64
3.97
3.74
4.17
3.90
3.84
4.57
3.75
34
cg2636
catA
Catechol 1,2-dioxygenase
4.05
Benzoate 1,2-Dioxygenase Alpha Subunit
35
cg2637 benA
4.21
(Aromatic ring hydroxylation dioxygenase A)
36
cg2638 benB Benzoate dioxygenase small subunit
3.87
37
cg2639 benC Benzoate dioxygenasereductase
4.55
38
cg2640 benD Benzoate diol dehydrogenase bend
4.23
39
cg2641 benR Activator of catechol pathway genes. LuxR family
3.71
40
cg2642 benK Putative Benzoate Transport Protein
3.96
41
cg2643 benE Benzoate Membrane Transport Protein
3.48
a
Gene ID according to the accession number BX927147 was used.
b,c
Gene name and annotation were obtained from the CoryneRegNet database
(www.coryneregnet.de) and Brinkrolf et al., 2010 and Schröder and Tauch, 2010.
d
Expression ratios from a comparison of the H2O2-adapted strain under the oxidative stress
condition vs. the wild-type strain under the no stress condition.
Supplementary Table 5. List of the open reading frames (ORFs) showing a ≤ 2-fold
decrease in comparison with those of the H2O2-adapted and wild-type strains.
1
2
3
Gene
IDa
cg0048
cg0092
cg0160
Gene
nameb
ppiA
-
4
cg0186
-
5
6
7
8
9
10
cg0282
cg0394
cg0440
cg0470
cg0482
cg0491
csbD
gpmA
-
11
cg0492
-
12
13
cg0493
cg0494
-
14
cg0527
-
15
16
17
18
19
20
21
22
23
24
25
26
cg0545
cg0573
cg0583
cg0587
cg0599
cg0600
cg0601
cg0602
cg0603
cg0608
cg0652
cg0674
pitA
rplL
fusA
tuf
rpsS
rplV
rpsC
rplP
rpmC
rplN
rpsM
rpsI
27
cg0737
-
28
29
30
31
32
33
34
cg0755
cg0775
cg0812
cg0867
cg0871
cg0878
cg0892
metY
dtsR1
whcE
-
No
Annotationc
Peptidyl-prolylcis-trans isomerase B
putative membrane protein
hypothetical protein
Methylated-DNA--protein-cysteine
methyltransferase
hypothetical protein
Glycosyltransferase
hypothetical protein
secreted protein
Phosphoglyceromutase 1
hypothetical protein
Extremely conserved possible DNA-binding
protein
Hypothetical protein
Extremely conserved hypothetical protein
Activator of serine hydroxymethyltransferase
gene glyA.ArsR family
putative low-affinity phosphate transport protein
Probable 50S ribosomal subunit protein L7/L12
Elongation factor G
Elongation factor TU
30S ribosomal protein S19
Ribosomal protein L22
30S ribosomal protein S3
50S ribosomal protein L16
50S ribosomal protein L29
50S ribosomal protein L14
Ribosomal protein S13
30S ribosomal protein S9
ABC-type transport system, secreted lipoprotein
component
O-Acetylhomoserine (Thiol)-Lyase
hypothetical protein
Acetyl/propionyl-CoA carboxylase beta chain
Ribosome-associated protein Y (PSrp-1)
hypothetical protein
Activator of thioredoxin genes
hypothetical protein
Expression
ratiod
0.42
0.49
0.47
0.42
0.25
0.43
0.19
0.40
0.34
0.08
0.10
0.12
0.32
0.43
0.21
0.23
0.47
0.16
0.45
0.27
0.36
0.10
0.46
0.48
0.35
0.31
0.13
0.35
0.32
0.32
0.29
0.43
0.13
0.19
35
cg0906
36
cg0924
37
38
cg0933
cg0958
39
cg0967
40
41
42
cg0989
cg1109
cg1111
43
cg1147
44
cg1236
45
cg1271
46
47
48
cg1283
cg1290
cg1291
49
cg1373
50
51
52
53
54
55
cg1408
cg1409
cg1479
cg1538
cg1556
cg1579
56
cg1615
57
cg1630
58
59
60
61
62
63
64
65
66
67
68
69
cg1633
cg1791
cg1811
cg1859
cg2027
cg2052
cg2079
cg2121
cg2167
cg2195
cg2235
cg2254
-
hypothetical protein
ABC-type cobalamin/Fe3+-siderophores transport
system, periplasmic component
DNA or RNA helicase of superfamily II
Secreted protein
3'-Phosphoadenosine 5'-phosphosulfate (PAPS)
cysQ
3'-phosphatase
rpsN 30S ribosomal protein S14
porB Anion-specific porin precursor
eno
Enolase (2-phosphoglycerate dehydratase)
Conserved protein/domain typically associated
ssuI
with flavoproteinoxygenases, DIM6/NTAB
family
tpx
Thiol peroxidase
ECF sigma factor involved in responses to cells
sigE
surface stresses
aroE1 putative shikimate / quinate 5-dehydrogenase
metE Homocysteinemethyltransferase
putative membrane protein
Glyoxalase/Bleomycin resistance/Dioxygenase
superfamily protein
putative membrane protein
pfkA 6-phosphofructokinase
glgP1 Putative glycogen phosphorylase
Dephospho-coa kinase
hypothetical protein
putative secreted protein
16S rRNA uridine-516 pseudouridylate synthase
or related pseudouridylate synthase
Putative signal transduction protein, FHA
domain
Predicted transcriptional regulator
gapA Glyceraldehyde-3-phosphate dehydrogenase
ihf
Putative integration host factor CihF
Putative secreted protein
hypothetical protein
putative secreted protein
hypothetical protein
ptsH Phosphocarrier protein HPR
rpsO Ribosomal protein S15
putative secreted or membrane protein
rplS 50S ribosomal protein L19
Ankyrin repeat protein
0.00
0.36
0.19
0.23
0.46
0.44
0.29
0.44
0.30
0.43
0.09
0.38
0.22
0.41
0.30
0.35
0.22
0.28
0.23
0.24
0.49
0.24
0.06
0.14
0.07
0.34
0.18
0.28
0.22
0.31
0.37
0.12
0.27
0.28
0.21
70
cg2274
71
72
73
74
75
76
77
78
79
80
81
82
83
84
cg2283
cg2291
cg2308
cg2320
cg2325
cg2362
cg2363
cg2411
cg2451
cg2458
cg2477
cg2480
cg2510
cg2518
85
cg2561
86
87
cg2573
cg2658
88
cg2661
89
90
91
92
93
cg2684
cg2686
cg2687
cg2701
cg2703
94
cg2704
95
96
97
98
99
100
101
102
103
cg2705
cg2735
cg2833
cg2835
cg2840
cg2853
cg2875
cg2880
cg2952
104
cg2958
105
106
107
cg3008
cg3009
cg3036
Predicted metal-binding, possibly nucleic acidbinding protein
hypothetical protein
pyk pyruvate kinase
putative secreted protein
Predicted transcriptional regulator
hypothetical protein
putative membrane protein
hypothetical protein
hypothetical protein HesB/YadR/YfhF family
hypothetical protein
pgp2 Predicted phosphatase, HAD family
hypothetical protein
hypothetical protein
bex Bex protein (GTP-binding protein Era homolog)
putative secreted protein
Secreted protein potentially involved into thiamin
thiX
biosynthesis
rpsT 30S ribosomal protein S20
rpi
Possible phosphopentoseisomerase
Putative dithiol-disulfide isomerase involved in
polyketide biosynthesis
Membrane protein DedA family
Bacterial regulatory proteins, TetR family
metB Cystathionine gamma-Synthase
putative membrane protein
Sugar permease
ABC-type sugar transport system, permease
component
malE1 Maltose-binding protein precursor
putative membrane protein
cysK O-acetylserine (thiol)-lyase
Predicted acetyltransferase
actA Butyryl-CoA:acetate coenzyme a transferase
Conserved hypothetical protein-fragment
hypothetical protein
HIT family hydrolase
putative secreted protein
L-2,3-Butanediol
butA
dehydrogenase/acetoinreductase
porA Porin
hypothetical protein
xthA Exodeoxyribonuclease III
-
0.32
0.46
0.45
0.26
0.23
0.47
0.27
0.40
0.22
0.08
0.32
0.37
0.49
0.43
0.36
0.40
0.49
0.05
0.49
0.29
0.37
0.45
0.45
0.12
0.12
0.30
0.37
0.04
0.41
0.32
0.47
0.04
0.27
0.33
0.22
0.27
0.03
0.26
108
109
cg3068
cg3147
fba Fructose-bisphosphatealdolase
0.25
‘bglY' Beta-glucosidase-fragment
0.22
3+
ABC-type cobalamin/Fe -siderophores transport
110 cg3148
0.24
system, ATPase component
111 cg3219
ldh L-lactate dehydrogenase
0.14
112 cg3257
hypothetical protein
0.14
113 cg3260
putative membrane protein
0.35
114 cg3343
putative secreted membrane protein
0.15
115 cg3409 thiD2 putative phosphomethylpyrimidine kinase
0.22
116 cg3432 rpmH 50S ribosomal protein l34
0.23
117 cg4000
hypothetical protein
0.08
118 cg4007
hypothetical protein
0.00
a
Gene ID according to the accession number BX927147 was used.
b,c
Gene name and annotation were obtained from the CoryneRegNet database
(www.coryneregnet.de) and Brinkrolf et al., 2010 and Schröder and Tauch, 2010.
d
Expression ratios from the comparison of the H2O2-adapted strain under the oxidative stress
condition vs. the wild-type strain under the no stress condition.
Supplementary Table 6. Validation of selected gene expression profile via RT-qPCR at 4,
12, and 22 h of batch culture.
Gene
IDa
Gene
nameb
Relative expressionc
4h
Up-regulated
in
RNA-seq
12 h
22 h
WT
H2O2d
HA
H2O2e
HA
+
H2O2f
WT
H2O2
HA
H2O2
HA
+
H2O2
WT
H2O2
HA
H2O2
HA
+
H2O2
cg1748
-
1.00
±0.07
2.00
±0.17
1.40
±0.16
1.00
±0.03
3.20
±0.09
4.80
±0.46
1.00
±.15
1.38
±0.16
3.50
±0.63
cg2610
-
1.00
±0.05
1.23
±0.13
1.37
±0.23
1.00
±0.03
1.55
±0.04
2.73
±0.10
1.00
±0.09
4.37
±0.11
11.93
±1.21
cg2618
vanK
1.00
±0.33
1.86
±0.48
1.90
±0.47
1.00
±0.06
4.36
±0.44
7.38
±0.76
1.00
±0.15
5.52
±0.94
7.74
±0.97
cg2622
pcaI
1.00
±0.20
5.46
±0.52
2.14
±0.18
1.00
±0.14
5.78
±0.73
9.72
±1.01
1.00
±0.18
7.55
±0.95
8.16
±1.10
cg2628
pcaC
1.00
±0.08
1.27
±0.20
1.38
±0.28
1.00
±0.17
1.87
±0.24
3.06
±0.10
1.00
±0.11
2.01
±0.31
1.28
±0.22
cg3420
sigM
1.00
±0.22
3.57
±0.14
2.15
±0.75
1.00
±0.16
2.63
±0.39
6.82
±0.89
1.00
±0.06
5.16
±0.23
7.44
±0.31
cg3422
trxB
1.00
±0.06
2.19
±0.14
1.23
±0.10
1.00
±0.09
1.84
±0.20
1.73
±0.18
1.00
±0.08
0.68
±0.04
0.94
±0.13
cg3423
trxC
1.00
±0.24
1.78
±0.37
1.44
±0.34
1.00
±0.27
1.90
±0.41
3.44
±0.75
1.00
±0.30
1.37
±0.36
2.34
±0.54
4h
Down-regulated
in
RNA-seq
12h
22h
WT
H2O2
HA
H2O2
HA
+
H2O2
WT
H2O2
HA
H2O2
HA
+
H2O2
WT
H2O2
HA
H2O2
HA
+
H2O2
0.43
±0.03
cg0878
whcE
1.00
±0.09
0.37
±0.01
1.00
±0.06
0.74
±0.09
0.54
±0.04
1.00
±0.09
0.24
±0.02
0.33
±0.03
cg0933
-
1.00
±0.30
0.61 0.46 ±0.2 1.00
±0.16
±0.05
1.70
±0.26
1.17
±0.18
1.00
±0.15
0.96
±0.16
0.88
±0.21
cg1271
sigE
1.00
±0.07
2.48
±0.21
0.83
±0.09
1.00
±0.13
2.32
±0.24
1.29
±0.21
1.00
±0.03
1.38
±0.20
1.02
±0.19
cg1791
gapA
1.14
±0.05
0.67
±0.05
0.31
±0.02
1.00
±0.06
0.88
±0.06
0.43
±0.03
1.00
±0.09
0.80
±0.07
0.71
±0.05
cg2833
cysK
1.00
±0.09
1.98
±0.2
1.05
±0.14
1.00
±0.06
0.87
±0.08
0.45
±0.03
1.00
±0.08
0.05
±0.01
0.11
±0.01
a
b
Gene ID according to the accession number BX927147 was used.
Gene name was obtained from the CoryneRegNet database (www.coryneregnet.de) and
references (Brinkrolf et al., 2010; Schröder and Tauch, 2010)
c
Relative expression resulted from cDNA synthesized using total RNA corresponding to 4,
12, and 22 h shown in Fig. 2.
d, e, f
WT and HA represent Corynebacterium glutamicum ATCC 13032 wild-type and the
H2O2-adapted strain, respectively; - or + H2O2 indicate growth condition under the absence or
presence of 10 mM H2O2, respectively.