Download Autoinducer 2 Controls Biofilm Formation and

Supplementary Table S1. E. coli strains and plasmids used. Kanamycin (KmR) was used at 50 µg ml-1
for culturing the E. coli BW25113 isogenic mutants and at 100 µg ml-1 to maintain the pBS(Kan)-derived
plasmids. Chloramphenicol (CmR) at 30 µg ml-1 was used for the pCA24N-derived plasmids and 50 µg
ml-1 was used for pMMB206 or pMMB277.
Strains and plasmids
Strain
E. coli K-12 BW25113
Genotype/relevant characteristics
lacIq rrnBT14 lacZWJ16 hsdR514 araBA-DAH33 rhaBADLD78
(Baba et al. 2006)
E. coli K-12 BW25113
ydeI
E. coli K-12 BW25113
ydhM
E. coli K-12 BW25113
K-12 BW25113 ydeI  KmR
(Baba et al. 2006)
yeaQ
E. coli K-12 BW25113
yoaG
E. coli K-12 BW25113
yeaR
E. coli K-12 BW25113
yebV
E. coli K-12 BW25113
yodD
E. coli K-12 BW25113
yegP
E. coli K-12 BW25113
ygiW
E. coli K-12 BW25113
rpmG
E. coli K-12 BW25113
rpmE
E. coli K-12 BW25113
ybdB
E. coli K-12 BW25113
ybiI
E. coli K-12 BW25113
ybiX
E. coli K-12 BW25113
feaR
E. coli K-12 BW25113
nhoA
E. coli K-12 BW25113
sufE
E. coli K-12 BW25113
sufS
E.
coli K-12 BW25113
sufC
E. coli K-12 BW25113
tap
E. coli K-12 BW25113
fliD
E. coli K-12 BW25113
fliS
E. coli K-12 BW25113
yedF
E. coli K-12 BW25113
yeeF
E. coli K-12 BW25113
mglC
E. coli K-12 BW25113
mglA
E. coli K-12 BW25113
mglB
E. coli K-12 BW25113
galS
E. coli K-12 BW25113
hcaR
E. coli K-12 BW25113
luxS
E. coli K-12 BW25113
yhcN
E. coli K-12 BW25113
ibpB
E. coli K-12 BW25113
ibpA
Source
R
K-12 BW25113 ydhM  Km
(Baba et al. 2006)
R
K-12 BW25113 yeaQ  Km
(Baba et al. 2006)
R
K-12 BW25113 yoaG  Km
(Baba et al. 2006)
R
K-12 BW25113 yeaR  Km
(Baba et al. 2006)
K-12 BW25113 yebV  Km
R
(Baba et al. 2006)
R
K-12 BW25113 yodD  Km
(Baba et al. 2006)
R
K-12 BW25113 yegP  Km
(Baba et al. 2006)
K-12 BW25113 ygiW  Km
R
(Baba et al. 2006)
K-12 BW25113 rpmG  Km
(Baba et al. 2006)
K-12 BW25113 rpmE Km
(Baba et al. 2006)
R
R
K-12 BW25113 ybdB  Km
(Baba et al. 2006)
R
K-12 BW25113 ybiI  Km
(Baba et al. 2006)
K-12 BW25113 ybiX  Km
(Baba et al. 2006)
R
R
K-12 BW25113 feaR  Km
R
(Baba et al. 2006)
K-12 BW25113 nhoA  Km
(Baba et al. 2006)
R
K-12 BW25113 sufE  Km
(Baba et al. 2006)
R
K-12 BW25113 sufS  Km
(Baba et al. 2006)
K-12 BW25113 sufC  KmR
(Baba et al. 2006)
R
K-12 BW25113 tap  Km
(Baba et al. 2006)
K-12 BW25113 fliD  Km
(Baba et al. 2006)
R
R
K-12 BW25113 fliS  Km
R
(Baba et al. 2006)
K-12 BW25113 yedF  Km
R
(Baba et al. 2006)
R
(Baba et al. 2006)
K-12 BW25113 yeeF  Km
K-12 BW25113 mglC  Km
(Baba et al. 2006)
K-12 BW25113 mglA Km
(Baba et al. 2006)
R
R
K-12 BW25113 mglB  Km
(Baba et al. 2006)
R
K-12 BW25113 galS  Km
(Baba et al. 2006)
K-12 BW25113 hcaR  Km
(Baba et al. 2006)
R
K-12 BW25113 luxS  Km
(Baba et al. 2006)
R
K-12 BW25113 yhcN  Km
(Baba et al. 2006)
R
K-12 BW25113 ibpB  Km
(Baba et al. 2006)
K-12 BW25113 ibpA  Km
(Baba et al. 2006)
R
R
R
E. coli K-12 BW25113
tnaA
E. coli K-12 BW25113
tnaB
E. coli K-12 BW25113
glnG
E. coli K-12 BW25113
yjaA
E. coli K-12 BW25113
yjcB
E. coli TG1
Plasmids
pBS(Kan)
pBS(Kan) -TOM-Green
K-12 BW25113 tnaA  KmR
(Baba et al. 2006)
K-12 BW25113 tnaB  Km
(Baba et al. 2006)
R
R
K-12 BW25113 glnG  Km
(Baba et al. 2006)
R
K-12 BW25113 yjaA  Km
(Baba et al. 2006)
K-12 BW25113 yjcB  Km
R
(Baba et al. 2006)
supE hsdΔ5 thi Δ(lac-proAB) F' [traD36 proAB lacI
lacZΔM15]
+
q
(Sambrook et al. 1989)
pMMB206
Empty vector; KmR
pBS(Kan) plac::TOM-Green; expresses the evolved TOMGreen from Burkholderia cepacia G4
Empty vector, AmpR
pMMB206-TOMGreen
pMMB277
pMMB206 ptac-lacUV5::TOM-Green; expresses the evolved
TOM-Green from Burkholderia cepacia G4
Empty vector; CmR
pMMB277-IsoILR1GSHI*
pBS(Kan)-EchA
F108L/I219L/C248I
pCA24N
pMMB277 ptac:: IsoILR1-GSHI*; expresses IsoILR1 from
Rhodococcus AD45 and GSHI* from E. coli
pBS(Kan) plac::EchA F108L/I219L/C248I; expresses the
evolved EchA F108L/I219L/C248I from Agrobacterium
radiobacter AD1
Empty vector; CmR
(Kitagawa et al. 2005)
pCA24N-ygiW
pCA24N pT5-lac::ygiW; expresses YgiW derived from E. coli
(Kitagawa et al. 2005)
pCA24N-ychH
pCA24N-yhcN
pCA24N-galS
pCA24N pT5-lac::ychH; expresses YchH derived from E. coli
pCA24N pT5-lac::yhcN; expresses YhcN derived from E. coli
pCA24N pT5-lac::galS; expresses GalS derived from E. coli
(Kitagawa et al. 2005)
(Kitagawa et al. 2005)
(Kitagawa et al. 2005)
(Canada et al. 2002)
(Canada et al. 2002)
(Rui et al. 2004a)
(Rui et al. 2004a)
(Morales et al. 1991)
(Rui et al. 2004b)
(Rui et al. 2004a)
Additional reference:
Morales, V.M., Bäckman, A. and Bagdasarian, M. (1991) A series of wide-host-range low-copy-number
vectors that allow direct screening for recombinants. Gene 97, 39-47.
Supplementary Table S2. Primers used for qRT-PCR and verification of isogenic mutants.
Gene
Forward Primer
Reverse Primer
rpoA
5’-CGCGGTCGTGGTTATGTG-3’
5’-GCGCTCATCTTCTTCCGAAT-3’
gshA
5’-AAAACCGAGTGCGGTATGTATTA-3’
5’-AGCCTCTTACCGTCTTTCTCAAT-3’
tauA
5’-GTTTATCTCCACCACCCACTACA-3’
5’-GTTCAGAATCGGTCAACACCTT-3’
ibpB
5’-CGTAACTTCGATTTATCCCCACT-3’
5’-CTAAATCTTCCTGACGGAAACCT-3’
yfiD
5’-CAGTAAGCAAACTGGGTGACATT-3’
5’-CAGAGAGTTAAAGCGAACTGCAT-3’
sufS
5’-ATTACTCATGTCTCCAACGTGCT-3’
5’-TTCACATAAAGAATGCCAATTCC-3’
mglA
5’-TACTTGTTGGAAATGAGCGGTAT-3’
5’-AAATCGATCTCTTTACCCTGGAA-3’
tnaB
5’-TAATTGGTGGAGGTATGTTTGCT-3’
5’- TAATGTTCCAGGTGTTACCGATT -3’
ydeI
5'-GTCTTTGACTCAACGCGGATGTCAGGT-3’
5'-AGTTCCTTGTGCGCGCTATTCTAACGA-‘3
yhcN
5'-TGATATGGGTCACGAAACAAAGGCCCA-3’
5'-TGTTCATCTGGGAGAGAAAACGCGTCG-3’
yjaA
5'-GACCCCATGCCGAACTCAGAAGTGAAA-3’
5'-GGCGGTTGGGTTCTATAAGAAGGTGGG-3’
yodD
5'-CTCCTGTGGCTTTGTGCCAGTGTAGAA-3’
5'-GGAACATTTGCTTCGCGTAAACGGGTG-3’
R
Km
5’-CAGTCATAGCCGAATAGCCT-3’
Supplementary Table S3. E. coli genes significantly induced or repressed (P < 0.05) with 1 mmol l-1
cis-DCE mineralization for 2 h by whole E. coli cells expressing (i) eight genes encoding evolved toluene
ortho-monooxygenase, glutathione S-transferase, and -glutamylcysteine synthetase vs. no cloned genes
(two independent experiments were performed using two independent biological replicates) and (ii) six
genes encoding evolved toluene ortho-monooxygenase and evolved epoxide hydrolase vs. evolved
toluene ortho-monooxygenase (no evolved EH). Raw data for the four DNA microarrays are available
using GEO series accession number GSE 13698. Primarily, genes differentially-expressed above 3-fold
for the 8-gene microarrays and above 2-fold for the EH microarrays are shown although some related
genes are shown for completeness. N/D: not detected. Asterisks (*) indicate the selection of possible
stress related genes for further phenotypic study.
Gene
b#
Fold changes
GST/GSH vs. no
EH vs.
gene
no EH
1st
2nd
Sulfate metabolism
tauA
b0365
10.6
tauB
b0366
9.2
tauC
b0367
3.7
tauD
b0368
4.0
cbl
b1987
5.3
cysK
b2414
cysA
b2422
cysP
b2425
cysN
b2751
cysD
b2752
iscS
b2530
gshA
b2688
sbp
b3917
Stress-related genes
bolA
b0435
glxA2
b0505
glxA3
b0506
gloA
b1651
dps
b0812
grxA
b0849
sulA
b0958
8.6
7.0
2.5
3.0
6.1
1.0
1.1
1.1
1.1
1.1
3.2
2.6
2.8
2.6
4.0
2.3
13.9
4.0
6.5
2.8
7.0
3.5
8.0
5.3
21.1
7.0
2.0
-1.1
1.3
-1.1
1.1
1.2
1.4
1.1
3.0
-1.1
1.1
1.3
3.2
2.5
1.1
2.6
-1.4
1.4
1.1
2.8
3.5
3.7
1.4
2.8
2.0
2.1
1.4
3.0
2.3
msyB
b1051
6.5
2.6
1.7
bshA
ariR
osmB
marR
marA
b1112
b1166
b1283
b1530
b1531
4.0
-1.9
8.6
2.0
1.9
7.5
-2.0
7.5
2.5
2.1
2.3
2.3
-1.7
2.8
3.7
slyB
slyA
nemA
b1641
b1642
b1650
2.0
1.6
2.1
2.5
2.1
1.2
2.0
1.9
3.5
Lee et al., Texas A & M
Gene
Taurine transport system periplasmic protein
Taurine ATP-binding component of a transport system
Taurine transport system permease protein
Alpha-ketoglutarate-dependent taurine dioxygenase
Transcriptional regulator cys regulon, accessory circuit affecting
cysM
Cysteine synthase A, O-acetylserine sulfhydrolase A
ATP-binding component of sulfate permease A protein
Thiosulfate binding protein
ATP-sulfurylase, subunit 1, probably a GTPase
ATP:sulfurylase (ATP:sulfate adenylyltransferase), subunit 2
Cysteine desulfurase
Gamma-glutamate-cysteine ligase
Periplasmic sulfate-binding protein
Possible regulator of murein genes
Ureidoglycolate hydrolase, conversion of glyoxylate
Repressor of allantoin and glyoxylate utilization operons
Glyoxalase I, nickel isomerase
Global regulator, starvation conditions
Glutaredoxin1 redox coenzyme for ribonucleotide reductase
Suppressor of lon, inhibitor of cell division and FtsZ ring
formation
Acidic protein suppresses mutants lacking function of protein
export
YcfR, stress response protein, biofilm related.
Indole inducing acid resistance gene
Osmotically inducible lipoprotein
Multiple antibiotic resistance protein; repressor of mar operon
Multiple antibiotic resistance; transcriptional activator of
defense systems
Putative outer membrane lipoprotein
Transcriptional activator for hemolysin (MarR family)
N-ethylmaleimide reductase, induced due to lipid peroxidation
4
osmE
yfiD
mdaB
glgS
slyD
dnaK
b1739
b2579
b3028
b3049
b3349
b0014
3.7
1.6
3.5
4.3
1.1
6.1
2.0
3.5
4.9
3.0
2.0
5.3
1.3
4.6
1.7
1.6
2.1
1.1
dnaJ
clpB
grpE
hspQ
hsp15
hslJ
hslO
hslV
b0015
b2592
b2614
b0966
b3400
b1379
b3401
b3932
3.2
4.9
3.5
3.5
7.5
3.5
4.0
3.2
2.6
4.6
6.1
4.9
6.1
3.5
3.0
2.6
1.1
1.0
1.6
1.6
2.1
1.3
1.9
1.1
htpG
htpX
ibpB*
ibpA*
groS
groL
b0473
b1829
b3686
b3687
b4142
b4143
5.3
3.0
8.6
9.8
8.0
5.3
2.8
7.5
9.8
9.8
6.1
4.6
-1.2
2.1
2.0
2.3
1.5
-1.1
cpxP
b3914
ytfE
b3913
b3914
b4209
3.2
3.0
2.1
7.0
6.5
2.0
2.6
2.6
3.2
chpS
osmY
csrA
b4224
b4376
b2696
3.2
3.2
2.5
2.8
2.6
2.8
1.4
1.7
2.1
3.2
2.8
9.8
5.3
4.3
3.5
13.0
6.1
N/D
N/D
N/D
N/D
Activator of ntrL gene
Stress-induced alternate pyruvate formate-lyase subunit
Modulator of drug activity B
Glycogen biosynthesis, rpoS dependent
FKBP-type peptidyl prolyl cis-trans isomerase (rotamase)
Chaperone Hsp70; DNA biosynthesis; autoregulated heat shock
proteins
Chaperone with DnaK; heat shock protein
Heat shock protein
Heat shock protein; protein repair
Heat shock protein
Heat shock protein
Heat shock protein HslJ
Hsp33; redox regulated chaperone, heat shock locus
Heat shock protein HslVU, proteasome-related peptidase
subunit
Chaperone Hsp90, heat shock protein
Heat shock protein, integral membrane protein
Heat shock protein
Heat shock protein
Chaperone protein GroEL (Hsp60)
GroEL, chaperone Hsp60, peptide-dependent ATPase, heat
shock protein
Periplasmic protein combats stress
Periplasmic protein combats stress
Hypothetical protein, ytfE mRNA are increased in cells treated
with NO
Component of a toxin-antitoxin system
Hyperosmotically inducible periplasmic protein
Carbon storage regulator, post-translational activator of flhDC
expression
CsrB regulatory RNA
CsrC regulatory RNA
Small RNA regulates as an antisense RNA for ompA mRNA
Global regulatory RNA OxyS
1.9
1.0
1.4
3.0
3.0
1.9
5.7
2.3
4.3
1.5
2.5
4.9
4.9
1.4
1.0
3.0
1.4
1.5
2.8
4.3
3.5
4.3
3.2
1.6
1.2
4.6
2.8
8.0
1.7
2.1
2.0
2.0
2.1
-1.2
1.6
2.0
1.3
2.3
1.9
2.3
1.6
1.1
1.3
2.1
2.5
Aspartate 1-decarboxylase
Repressor of frmRAB
Component of Sec-independent translocase
ATPase of high-affinity potassium transport system, B chain
ATPase of high-affinity potassium transport system, A chain
Outer membrane protease, receptor for phage OX2
Macrolide-specific ABC-type efflux carrier
Putative carrier/transport protein
Quinone oxidoreductase
Fermentative D-lactate dehydrogenase, NAD-dependent
Murein lipoprotein
L-serine deaminase
Putative periplasmic binding transport protein
dTDP-glucose 4,6 dehydratase
Phosphohistidine phosphatase
csrB
b4408
csrC
b4457
sraD
b4442
oxyS
b4458
Other metabolism
panD
b0131
yaiN
b0357
ybeC
b0627
kdpB
b0697
kdpA
b0698
ompX
b0814
macB
b0879
yccA
b0970
wrbA
b1004
ldhA
b1380
lpp
b1677
sdaA
b1814
fliY
b1920
rfbB
b2041
sixA
b2340
Lee et al., Texas A & M
5
smpA
b2617
-1.1
pstS
b3728
1.9
miaA
b4171
2.5
RNA and ribosomal genes
rrsH
b0201
2.8
rrsG
b2591
2.8
rrfH
b0205
3.0
rmf
b0953
4.3
rpsV
b1480
8.6
rplY
b2185
2.1
raiA
b2597
3.2
1.6
4.6
4.6
2.0
1.6
1.3
Small membrane protein A
Periplasmic phosphate-binding protein
Isopentenylpyrophosphate tRNA-adenosine transferase
4.9
4.6
5.3
5.3
3.2
3.5
6.1
1.1
1.2
1.4
1.5
2.0
1.9
2.1
rnpB
b3123
yhbY
b3180
rplU
b3186
rplO
b3301
rpmF
b1089
rpmA
b3185
rpmD
b3302
rpmG* b3636
rpmB
b3637
rpmE* b3936
gcvB
b4443
Unknown function
ybbN
b0492
ybgC
b0736
yccV
b0966
yccJ
b1003
ycfJ
b1110
ycfQ
b1111
ycgZ
b1164
ymgA
b1165
ymgC
b1167
ychH* b1205
yciN
b1273
ycjX
b1321
yedI
b1586
ydhM* b1649
ydhD
b1654
yeaQ* b1795
yoaG* b1796
b1797
yeaR*
b1836
yebV*
dsrB
b1952
3.0
1.1
2.5
2.5
1.1
1.7
2.1
2.3
2.1
2.3
1.4
5.3
2.5
3.7
4.3
2.1
3.5
3.5
4.3
4.6
4.0
4.9
1.0
2.5
2.0
1.1
1.9
2.0
-1.2
2.6
2.8
2.0
N/D
16S rRNA
16S rRNA
5S rRNA
Ribosome modulation factor
30S ribosomal subunit protein S22, stationary-phase-induced
50S ribosomal subunit protein L25
Stationary phase translation inhibitor and ribosome stability
factor
RNase P, RNA component; M1 RNA
Possible RNA-binding protein
50S ribosomal subunit protein L21
50S ribosomal subunit protein L15
50S ribosomal subunit protein L32
50S ribosomal subunit protein L27
50S ribosomal subunit protein L30
50S ribosomal subunit protein L33
50S ribosomal subunit protein L28
50S ribosomal subunit protein L31
Regulatory RNA
3.0
1.5
3.5
3.2
4.3
3.0
-1.3
-1.3
-2.3
5.3
2.1
3.2
4.6
3.5
2.1
3.5
-1.1
1.3
3.0
3.5
2.6
2.3
4.9
1.7
4.0
3.0
-1.3
-1.2
-2.0
2.3
2.6
1.5
3.5
2.8
3.7
2.0
1.3
1.9
1.6
1.9
1.1
2.1
1.6
1.2
1.1
1.6
2.3
2.1
2.0
1.3
2.0
1.3
1.6
3.5
2.6
2.8
3.0
3.5
2.0
1.7
5.7
4.6
1.6
4.0
3.0
2.1
1.9
2.1
1.9
2.0
1.5
1.3
2.0
1.4
1.7
yodD*
yodC
yeeX
yegP*
elaB
b1953
b1957
b2007
b2080
b2266
Lee et al., Texas A & M
Hypothetical protein
Hypothetical protein
Hypothetical protein
Hypothetical protein
Hypothetical protein
Hypothetical protein
Hypothetical protein in ariR (ymgB) operon
Hypothetical protein in ariR (ymgB) operon
Hypothetical protein in ariR (ymgB) operon
Hypothetical protein
Hypothetical protein
Hypothetical protein
Hypothetical protein
Hypothetical protein
Hypothetical protein
Hypothetical protein
Hypothetical protein
Hypothetical protein; responds to nitric oxide
hypothetical protein
hypothetical protein; transcription is regulated by RpoS and
DsrA RNA
Hypothetical protein
Hypothetical protein
Hypothetical protein
Hypothetical protein
Hypothetical protein
6
ypeC
b2390
yfhL
b2562
b3024
ygiW*
yqjC
b3097
yhbY
b3180
yhgI
b3414
b4250
b4250
Repressed genes
b0309
b0309
ybcU
b0557
ycjT
b1316
manZ
b1819
yeeF
b2014
b2857
b2857
ygeW
b2870
malK
b4035
soxS
b4062
Indole-related genes
trpE
b1264
trpL
b1265
tnaC
b3707
tnaA
b3708
3.5
1.1
4.9
2.5
1.1
2.3
-1.1
4.9
1.9
3.0
2.3
2.5
4.0
-1.1
N/D
2.0
1.7
2.0
2.5
2.1
2.3
Hypothetical protein
Hypothetical protein
Hypothetical protein (b3024)
Hypothetical protein
Possible RNA-binding protein
Hypothetical protein
Hypothetical protein
-1.1
-3.0
-1.4
1.0
-1.2
1.1
-1.4
-1.9
2.1
-1.3
-1.4
-1.9
-1.3
-1.9
-2.5
-1.7
-1.4
2.6
-2.1
-1.2
-2.6
-4.6
-2.5
-2.3
-3.0
-2.0
-2.0
Hypothetical protein
Hypothetical protein
Hypothetical protein
PTS enzyme IID, mannose-specific
Putative amino acid/amine transport protein
Hypothetical protein
Putative carbamoyl transferase
ATP-binding component of transport system for maltose
Regulation of superoxide response regulon
-2.0
-8.0
-1.5
-1.5
-1.6
-1.9
1.3
-1.1
-1.3
-1.9
-2.0
-1.7
Anthranilate synthase component I
trp operon leader peptide
Tryptophanase leader peptide
Tryptophanase
Lee et al., Texas A & M
7
Supplementary Table S4. E. coli genes induced in exponentially-growing cells (turbidity at 600 nm of
1) upon addition of 2 mmol l-1 H2O2 for 10 min to K12 BW25113 (more than 4 fold), to BW25113 ygiW
(more than 10 fold), and to BW25113 ychH (more than 10 fold) in LB medium at 37°C. Some genes with
less significant fold changes are shown for completeness. +H2O2 represents treatment with H2O2. Raw data
for the six DNA microarrays are available using GEO series accession number GSE 13698. Pounds (#)
indicate newly identified induced stress genes with H2O2 treatment. Triangles () indicate the selection of
possible stress related genes for further phenotypic study.
Fold changes
WT+ H2O2 ygiW+H2O2 ychH+H2O2
vs. WT
vs. ygiW
vs. ychH
stress, metabolism, transport
entF
b0586
8.0
9.2
13.0
entD
b0583
6.5
6.5
4.0
entC
b0593
5.3
7.5
21.1
entE
b0594
8.6
9.2
27.9
entB
b0595
8.0
5.7
18.4
entA
b0596
8.0
7.0
18.4
grxA
b0849
5.3
11.3
27.9
poxB
b0871
7.5
22.6
11.3
#
b0958
6.5
3.2
6.1
sulA
#
b0231
7.5
5.3
9.2
dinP
b1061
4.3
2.8
10.6
dinI#
7.5
1.9
5.3
dinD# b3645
4.0
4.0
4.3
dinF# b4044
fhuE
b1102
9.2
12.1
32.0
bshA
b1112
1.9
13.9
32.0
ariR
b1166
5.3
9.2
9.8
8.6
8.6
18.4
umuD# b1183
11.3
8.0
12.1
umuC# b1184

b1463
12.1
14.9
17.1
nhoA

b1679
13.0
34.3
36.8
sufE

b1680
8.0
18.4
19.7
sufS
sufD
b1681
8.0
13.0
12.1

b1682
8.6
13.9
13.9
sufC
sufB
b1683
7.0
8.0
7.0
sufA
b1684
4.9
9.2
11.3
7.5
1.6
4.0
sbmC# b2009
cirA
b2155
6.1
4.6
16.0
9.2
8.0
13.9
recN# b2616
#
b2698
4.6
4.9
5.7
recX
#
b4458
7.0
4.9
14.9
oxyS
Unknown function
7.5
6.5
18.4
ybdB b0597
ybiJ
b0802
4.6
8.0
16.0

b0803
5.3
4.6
6.5
ybiI

b0804
8.6
5.7
18.4
ybiX
ymgC b1167
5.3
13.0
12.1
yedR
b1963
1.1
21.1
10.6

b3238
6.5
8.6
13.0
yhcN
yjcB
b4060
-1.9
34.3
9.2
Gene
b#
Lee et al., Texas A & M
Description
ATP-dependent serine activating enzyme
4'-phosphopantetheinyl transferase EntD
Isochorismate synthase EntC
2,3-dihydroxybenzoate-AMP ligase
Isochorismatase
2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
Glutaredoxin 1
Pyruvate dehydrogenase/oxidase
SOS cell division inhibitor
DNA polymerase IV, stress inducible
DNA-damage-inducible protein I
DNA-damage-inducible protein
DNA-damage-inducible protein F
FhuE receptor precursor
YcfR, stress response biofilm regulator
Indole inducing acid resistance gene
DNA repair protein UmuD
DNA repair protein UmuC
N-hydroxyarylamine O-acetyltransferase
SufE protein
Selenocysteine lyase, PLP-dependent
SufD protein
Probable ATP-dependent transporter SufC
SufB protein
SufA protein
DNA gyrase inhibitory protein, SOS inducible
Colicin I receptor precursor
DNA repair protein RecN
Regulatory protein RecX, DNA repair protein
Global regulatory RNA OxyS
Hypothetical protein YbdB
Hypothetical protein YbiJ precursor
Hypothetical protein
Hypothetical protein YbiX
Hypothetical protein in ariR (ymgB) operon
Hypothetical protein YedR
Hypothetical protein YhcN precursor
Hypothetical protein YjcB
8
Supplementary Table S5. E. coli genes repressed in exponentially-growing cells (turbidity at 600 nm of
1) upon addition of 2 mmol l-1 H2O2 for 10 min to BW25113 (more than 4 fold), to BW25113 ygiW (more
than 10 fold), and to BW25113 ychH (more than 10 fold) in LB medium at 37°C. Some genes with less
significant fold changes are shown for completeness. +H2O2 represents treatment with H2O2. Raw data for
the six DNA microarrays are available using GEO series accession number GSE13698. Triangles ( )
indicate the selection of possible stress related genes for further phenotypic study.
Gene
b#
+H2O2
WT
vs. WT
Metabolism and transport
aldA b1415
1.0
mglC b2148
-2.1
mglA b2149
-1.1
mglB b2150
-1.1
galS
b2151
2.6
yhaO b3110
-1.6
tdcB b3117
-1.3
garP b3127
1.5
garD b3128
-1.2
agaY b3137
-6.5
dctA b3528
-1.1
lldP
b3603
-2.5
tnaC b3707
-2.3
tnaB b3709
-1.7
rbsA b3749
-1.3
rbsC b3750
-1.6
malG b4032
-4.6
malF b4033
-4.0
malE b4034
-2.6
malK b4035
-3.2
malM b4037
-10.6
actP b4067
-3.2
Unknown function
ykgE b0306
-1.4
ykgF b0307
-1.9
ykgG b0308
-2.1
ychS b1228
-6.5
yedE b1929
-1.4
yedF b1930
-1.7
yeiN b2165
-1.4
yeiC b2166
1.4
yqeF b2844
1.2
yqeC b2876
1.9
yhaM b3109
-2.5
yihL
b3872
1.7
yihM b3873
1.2
yihN b3874
1.0
-4.0
yjaA b4011
yjcH b4068
-1.9
yjjM b4357
1.9
Lee et al., Texas A & M
Fold changes
ygiW+H2O2 ychH+H2O2
vs. ygiW
vs. ychH
Description
-19.7
-21.1
-34.3
-26.0
-12.1
-18.4
-10.6
-21.1
-16.0
-1.4
-16.0
-13.0
-14.9
-36.8
-21.1
-10.6
-2.1
-4.6
-6.5
-11.3
-2.1
-2.5
-2.0
-39.4
-19.7
-4.6
-3.7
3.2
-14.9
-2.3
-5.3
-2.8
-3.2
-11.3
-3.2
-13.9
-2.1
-4.3
-17.1
-24.3
-13.9
-27.9
-14.9
-19.7
Aldehyde dehydrogenase A
Methyl-galactoside transport and galactose taxis
Galactoside transport ATP-binding protein MglA
D-galactose-binding periplasmic protein precursor
Mgl repressor and galactose ultrainduction factor
Putative transport protein (HAAAP family)
Threonine dehydratase catabolic
Probable galactarate transporter
D-galactarate dehydratase
Tagatose-bisphosphate aldolase AgaY
Aerobic C4-dicarboxylate transport protein
L-lactate permease
Tryptophanase leader peptide
Low affinity tryptophan permease
Ribose transport ATP-binding protein RbsA
Ribose transport system permease protein RbsC
Maltose transport system permease protein MalG
Maltose transport system permease protein MalF
maltose transport protein, chemotaxis
Maltose/maltodextrin transport ATP-binding protein MalK
Maltose operon periplasmic protein precursor
Acetate permease
-14.9
-7.5
-4.9
-3.5
-14.9
-12.1
-10.6
-12.1
-12.1
-6.1
-12.1
-13.0
-12.1
-10.6
-1.1
-4.3
-10.6
-16.0
-16.0
-11.3
2.5
-13.0
-9.2
-7.5
-9.8
-2.1
-10.6
1.6
-3.2
-7.0
-8.6
-1.5
-16.0
-2.1
Hypothetical protein YkgE
Putative electron transport protein YkgF
Hypothetical protein YkgG
Hypothetical protein
Hypothetical protein YedE
Hypothetical protein YedF
Hypothetical protein
Putative kinase
Probable acetyl-CoA acetyltransferase
Hypothetical protein YqeC
Hypothetical protein
Hypothetical transcriptional regulator YihL
Hypothetical protein YihM
Hypothetical protein YihN
Hypothetical protein YjaA
Hypothetical protein YjcH
Putative transcriptional regulator
9
Supplementary Table S6. E. coli genes induced more than 10 fold (P < 0.05) in exponentially-growing
cells (turbidity at 600 nm of 1) upon addition of 2 mmol l-1 H2O2 for 10 min in BW25113 vs. BW25113
ygiW and BW25113 vs. BW25113 ychH in LB medium at 37°C. Some genes with less significant fold
changes are shown for completeness. +H2O2 represents treatment with H2O2. Raw data for the six DNA
microarrays are available using GEO series accession number GSE 13698. Deltas ( ) indicate the
selection of possible stress related genes for further phenotypic study.
Fold changes
Gene
b#
WT
WT+H2O2
vs.
vs.
ygiW+H2O2
ychH+H2O2
Transcription, metabolism, and transport
fepE
b0587
1.3
13.0

b1384
11.3
1.7
feaR
aldA
b1415
21.1
1.7
16.0
12.1
mglC b2148
29.9
10.6
mglA b2149

b2150
24.3
3.7
mglB

b2151
10.6
4.3
galS
fruB
b2169
13.9
4.3

b2537
10.6
1.6
hcaR
srlA
b2702
11.3
3.0
srlE
b2703
9.2
2.6
dctA
b3528
13.0
2.8
dppD b3541
4.0
9.2
dppC b3542
4.9
9.2
tnaC b3707
12.1
1.6

b3708
4.3
1.6
tnaA
24.3
6.1
tnaB b3709
rbsA
b3749
13.0
1.1
fadB
b3846
17.1
1.9
malK b4035
10.6
6.5
acs
b4069
9.8
3.2
treC
b4239
12.1
6.1
gntP
b4321
13.0
3.2
Unknown function
b0268
14.9
4.0
yagE
b0380
9.8
2.5
yaiZ
5.7
168.9
ychH b1205
9.2
13.9
yedE b1929
7.0
9.8
yedF b1930

B2014
-1.9
7.0
yeeF
b2166
9.2
11.3
yeiC
11.3
2.5
yqeF b2844
477.7
1.2
ygiW b3024
b3081
12.1
2.3
ygjL
b4047
-1.3
11.3
yjbL
+H2O2
Lee et al., Texas A & M
Description
Ferric enterobactin (enterochelin) transport
Regulatory protein for 2-phenylethylamine catabolism
Aldehyde dehydrogenase A
Methyl-galactoside transport and galactose taxis
Galactoside transport ATP-binding protein MglA
D-galactose-binding periplasmic protein precursor
Mgl repressor and galactose ultrainduction factor
PTS system, fructose-specific IIA/FPr component
Bifunctional: transcriptional activator of Hca cluster (LysR family)
PTS family enzyme IIC, glucitol/sorbitol-specific
PTS system, glucitol/sorbitol-specific IIBC component
Aerobic C4-dicarboxylate transport protein
Dipeptide transport ATP-binding protein DppD
Dipeptide transport system permease protein DppC
Tryptophanase leader peptide
Tryptophanase
Low affinity tryptophan permease
Ribose transport ATP-binding protein RbsA
3-Hydroxyacyl-CoA dehydrogenase
Maltose/maltodextrin transport ATP-binding protein malK
Acetyl-coenzyme A synthetase
Trehalose-6-phosphate hydrolase
Gluconate transport protein, GNT III system (GntP family)
CP4-6 prophage; putative synthase
Hypothetical protein YaiZ
Hypothetical protein YchH
Hypothetical protein YedE
Hypothetical protein YedF
Hypothetical protein YeeF
Putative kinase
Probable acetyl-CoA acetyltransferase
Protein YgiW precursor
2,4-Dienoyl-CoA reductase [NADPH]
Hypothetical protein
10
Supplementary Table S7. E. coli genes repressed more than 10 fold (P < 0.05) in exponentiallygrowing cells (turbidity at 600 nm of 1) upon 2 mmol l-1 H2O2 for 10 min in BW25113 vs. BW25113
ygiW and BW25113 vs. BW25113 ychH in LB medium at 37°C. Some genes with less significant fold
changes are shown for completeness. +H2O2 represents treatment with H2O2. Raw data for the six DNA
microarrays are available using GEO series accession number GSE 13698. Deltas ( ) indicate the
selection of possible stress related genes for further phenotypic study.
Fold changes
Gene
b#
WT
WT+H2O2
vs.
vs.
ygiW+H2O2
ychH+H2O2
metabolism and others
sotB
b1528
-12.1
-2.8
flxA
b1566
-1.7
-52.0
aer
b3072
-1.1
-18.4
glpD
b3426
-10.6
-6.5
b3868
-5.7
2.6
glnG
tsr
b4355
-2.5
-32.0
Flagella and chemotaxis
flgB
b1073
-3.7
-104.0
flgC
b1074
-3.5
-68.6
flgD
b1075
-4.6
-111.4
flgE
b1076
-3.5
-42.2
flgF
b1077
-3.5
-84.4
flgG
b1078
-3.5
-59.7
flgK
b1082
-3.0
-111.4
b1885
-3.5
-222.9
tap
tar
b1886
-3.2
-128.0
cheW
b1887
-3.2
-78.8
cheA
b1888
-3.2
-68.6
motB
b1889
-2.1
-90.5
motA
b1890
-3.0
-181.0
fliZ
b1921
-2.8
-84.4
fliA
b1922
-4.6
-128.0
fliC
b1923
-3.0
-73.5

b1924
-3.0
-168.9
fliD
b1925
-3.0
-137.2
fliS
fliT
b1926
-3.2
-104.0
fliE
b1937
-2.8
-119.4
Unknown function
ymdA
b1044
-1.4
-34.3
ycgR
b1194
-1.9
-111.4
ydjR
b1742
-1.1
-32.0
ynjH
b1760
-1.1
-26.0
ypdD
b2383
-2.1
-11.3
yhjH
b3525
-2.3
-119.4
b4060
-84.4
-9.2
yjcB
yjcZ
b4110
-3.5
-64.0
+H2O2
Lee et al., Texas A & M
Description
Sugar efflux transporter
Qin prophage
Aerotaxis receptor
sn-Glycerol-3-phosphate dehydrogenase (aerobic)
Response regulator for glutamine
Methyl-accepting chemotaxis protein I
Flagellar basal-body rod protein FlgB
Flagellar basal-body rod protein FlgC
Basal-body rod modification protein FlgD
Flagellar biosynthesis, hook protein
Flagellar biosynthesis, cell-proximal portion of basal-body rod
Flagellar basal-body rod protein FlgG
Flagellar hook-associated protein 1
Methyl-accepting chemotaxis protein IV
Methyl-accepting chemotaxis protein II
Chemotaxis protein CheW
Chemotaxis protein CheA
Chemotaxis MotB protein
Chemotaxis MotA protein
FliZ protein
RNA polymerase sigma factor for flagellar operon
Flagellar biosynthesis; flagellin, filament structural protein
Flagellar hook-associated protein 2
Flagellar protein FliS
Flagellar protein Flit
Flagellar hook-basal body complex protein FliE
Hypothetical protein YmdA precursor
Hypothetical protein YcgR
Hypothetical protein YdjR
Hypothetical protein YnjH precursor
Putative PTS family Hpr component (N-terminal)
Hypothetical protein YhjH
Hypothetical protein YjcB
Hypothetical protein YjcZ
11