Supplementary material
Functional role of bdm in the flagella biogenesis in E. coli
Ji-Sun Kim1, Yu Jin Kim1, Sojin Seo, Maeng-Je Seong*, and Kangseok Lee*
1 These authors contributed equally to this work.
*Corresponding authors: Maeng-Je Seong, Tel: +82 2 820 5190, Fax: +82 2 825 4988, E-mail: or Kangseok Lee, Tel: +82 2 820 5241, Fax: +82 2 825 5206, E-mail:
Materials and methods
Vancomycin sensitivity determination plate assay
Overnight cultures grown in LB medium containing appropriate antibiotics were diluted 1 to 100 in same medium. Strains were grown to 0.6-0.7 at A600nm and serial dilutions of bacteria were applied to LB plates containing various concentrations of vancomycin. The number of colonies was counted after overnight incubation at 37 °C.
Propidium iodide (PI) membrane leakage assay and confocal fluorescence microscopy
E. coli cells were harvested, washed, and resuspended in Phosphate buffer (pH 7.2) with an optical density at OD600=0.6-0.7. Then, PI and DAPI were added and incubated for 30 min at room temperature in the dark to assess the integrity of the bacterial membrane. Fluorescence detected by laser scanning confocal microscopy (Carl Zeiss ZEN 2011, Germany). Bar, 5 μm.
Figure S1. Assessment of the membrane permeability of the bdm-deleted mutant. (a) WT and bdm cells were staind with propidium iodide (PI) and DAPI. Representative images were observed with a 40× water-immersion objective. Scale bars = 5 μm. (b) Vancomycin sensitivity of the WT and bdm was assayed by measuring CFU/ml on LB plates containing various concentrations of vancomycin (0-100 μg/ml). Approximate mumber of cells are shown on the left.
Table S1. Sequence of primers used in this study.
5′-bdm-D / AACCCCTAAATTAGGTTGCCGATCAAGCATAGCACCTTAGTGTAGGCTGGAGCTGCTTC
3′-bdm-D / GCAGACACCATAAATACACAGACACGGAGAATCACTATGCATATGAATATCCTCCTTA
FliC-F / TTATGGCACAAGTCATTAAT
FliC-R / AAGCATTTGCCGTTGCTCCA
Bdm-F / ATGTTTACTTATTATCAGGCAG
Bdm-R / TTAAAGCGTAGGGTGCTGGCCAC
rpsO 5’RT / GTACACTGGGATCGCTGAATT
rpsO 3’RT / GGCCCCCTTTTCTGAAACTCG
Table S2. Bdm dependent gene expression profile
Gene name / Gene product / WT versus bdm fold change (log value)bdm
flgA
tar
fliA
flgB
flgD
tap
yecR
flgL
flgE
flgH
flgC
flgF
motB
cheA
aer
flgM
flgG
flgI
puuA
ymgD
flhB
yecR
yfhH
fliC
ycgR
flgN
cheW
fliZ
fliM
fliE
puuD
flgK
cheR
fliG
fliN
motA
fliT
trg
fliF
puuC
fliO
flhA
fliQ
yfhL
fliP
cheZ
fliH
putA
puuB
fliS
cheY
fliI
yohJ
ycfR
flgJ
fliR
puuE
puuP
fliJ
yedR
fliD
fliL
bax
dsdX
asnA
yohK
lldP
carB
ydeA
putA
yhjH
ydjR
ivy
ynfM
deoA
putP
insI-2
carA
tsr
deoC
ypeC
pyrB
flhE
mscS
rcsA
proP
glnH
argO
fliK
garK
phoH
yedN_1
yjbA
dsdA
gltJ
glnP
nirB
gltI
astC
yjcB
glnQ
ydfZ
garR
yedN_2
helD
yghO
nirD
gltI
dinJ
pyrI
mhpR
osmC
dinJ
ydhA
deoD
yhcE_2
yeeY
ycgB
ompX
glcD
nirC
yhaC
garL
ybiJ
dadA
nupG
gltK
puuR
ydiV
dadX
ymdC
ndk
yhjX
yhaB
uraA
astA
deoB
rpsR
xapB
thiC
fimG
cytR
ftn
codB
purT
glmS
hepA
yaiY
rplQ
ynbD
fdrA
hipA
yfjB
yeiQ
rpsN
purL
mglA
yaiU
caiC
yneE
prmB
speD
ybaS
serA
ydiH
feaR
fimF
hcaR
garP
yqeH
yecG
cyaA
rpoB
rluA
thiF
fadL
kch
sdaB
oxc
caiB
ynbB
thrA
guaB
kdpD
gst
cysG
kdpB
yieP
rfbA
sdaC
potD
torR
copA
yedF
rcsC
yjiH
yccF
rplA
ypfG
folD
sapC
ttdB
fucO
gntT
feoA
ygbJ
dmsB
malF
wcaI
ydjJ
entA
frlA
fhuB
yhaL
eutT
xylG
cspA
pepT
cadC
ydiL
tdcF
mppA
rmuC
ibpB
gldA
nrfB
yihL
fdnG
yfcU
agaA
cpsG
fepC
yzgL
yjgL
ynfE
ybeD
yfeW
inaA
srlR
ykgH
agaB
yjjP
flhD
blr
grpE
yccM
yjbC
pmrD
napA
yhhI
tonB
rssB
fsaB
yciT
yncC
cspE
hupA
eutC
frvA
hslU
sucD
pflB
ccmC
cirA
nudD
yjbM
dppA
malE
fdhF
phoE
fhuD
yehD
yidF
agaV
htpG
ccmE
prpD
wzc
ypjC
fucA
yfcT
fes
ydjF
fepA
yjiL
tdcC
yjfF
dppF
feoB
dmsC
yicO
bcsG
yeaS
yfiA
exbB
wcaA
yiaY
eutL
fdhF
fhuF
fucR
nrdA
napD
ydhO
nikR
yqeB
ptsA
melR
yghZ
yebE
yghY
fepG
alkB
srlD
yahN
agaD
ygeK
malP
fhuA
ygeW
lamB
malS
chbB
yjiT
yjbI
xylE
yibD
ydjI
ypfE
ygcB
ydbJ
yejG
yfaD
cpxP
srlB
yhgG
degQ
treB
yjiZ
fucP
csiE
yhgG
yzgL
add
ygjH
stpA
cspC
srlE
eutP
nrfE
aldB
gntK
groL
exbD
ygjK
ycjN
pps
yqeI
yhcC
yehC
katG
ccmB
galP
b4506
dnaJ
abgR
gatY
malK
idnK
yjbG
narH
wcaF
pepE
ilvC
yeaT
yeiR
fnr
hslV
yieM
yjjM
eutB
yeeL
ydcI
napF
napG
ytfK
ygjK
yjdK
pdhR
ccmA
ydcH
yqeJ
yjfO
glpX
clpB
frlB
ygcO
yfaH
yfcC
rihA
yjjM
ydjH
tnaB
yjfN
nrdE
groS
rssA
cmtB
yjdO
ycjM
ygiP
narJ
nrdI
yecH
yobF
yeiA
glpK
ygcP
narI
rpiR
entF
ygcN
ybdO
yehB
yhdH
yfeW
tnaC
glpD
elbA
malM
aegA
rbsR
nikA
glpF
gntU
sanA
fsaA
aspA
ogt
gatZ
yjbE
srlA
gmd
uxaB
garD
tdcD
mbhA
alsE
napB
wza
nrdF
hypD
ygfJ
dnaK
nikC
murP
yhbU
hypC
napH
nikB
fhlA
napC
glpT
nrdH
ompF
yiaI
fcl
ybiW
yfeU
gatZ
ibpA
yggM
hypA
aphA
cdd
yjdP
hypB
alsC
rbsK
hypE
udp
yhbV
ycdZ
ygeV
oppF
oppA
ansB
gatR_2
yhjA
fxsA
ybiY
tdcA
mhpE
glpQ
udp
oppD
tdcB
ccmD
tdcE
nikE
yqeC
nikD
rpiB
oppC
ykgG
dctA
oppB
glpA
ykgE
ykgF
sra
yjjW
yjjI
alsB
tnaA
glpB
alsA
rbsB
rbsC
glpC
dcuC
rbsA
gatA
gatD
gatC
gatB
/ biofilm-dependent modulation protein
assembly protein for flagellar basal-body periplasmic P ring
methyl-accepting chemotaxis protein II
RNA polymerase, sigma 28 (sigma F) factor
flagellar component of cell-proximal portion of basal-body rod
flagellar hook assembly protein
methyl-accepting protein IV
predicted protein
flagellar hook-filament junction protein
flagellar hook protein
flagellar protein of basal-body outer-membrane L ring
flagellar component of cell-proximal portion of basal-body rod
flagellar component of cell-proximal portion of basal-body rod
protein that enables flagellar motor rotation
fused chemotactic sensory histidine kinase
fused signal transducer for aerotaxis sensory component,
anti-sigma factor for FliA (sigma 28)
flagellar component of cell-distal portion of basal-body rod
predicted flagellar basal body protein
gamma-Glu-putrescine synthase
predicted protein
predicted flagellar export pore protein
hypothetical protein
predicted DNA-binding transcriptional regulator
flagellar filament structural protein (flagellin)
protein involved in flagellar function
export chaperone for FlgK and FlgL
purine-binding chemotaxis protein
predicted regulator of FliA activity
flagellar motor switching and energizing component
flagellar basal-body component
gamma-Glu-GABA hydrolase
flagellar hook-filament junction protein 1
chemotaxis regulator
flagellar motor switching and energizing component
flagellar motor switching and energizing component
proton conductor component of flagella motor
predicted chaperone
methyl-accepting chemotaxis protein III, ribose and galactose sensor receptor
flagellar basal-body MS-ring and collar protein
gamma-Glu-gamma-aminobutyraldehyde dehydrogenase, NAD(P)H-dependent
flagellar biosynthesis protein
predicted flagellar export pore protein
flagellar biosynthesis protein
predicted 4Fe-4S cluster-containing protein
flagellar biosynthesis protein
chemotaxis regulator
flagellar biosynthesis protein
fused DNA-binding transcriptional regulator; proline dehydrogenase
gamma-Glu-putrescine oxidase, FAD/NAD(P)-binding
flagellar protein potentiates polymerization
chemotaxis regulator transmitting signal to flagellar motor component
flagellum-specific ATP synthase
conserved inner membrane protein
predicted protein
muramidase
flagellar export pore protein
GABA aminotransferase, PLP-dependent
putrescine importer
flagellar protein
predicted inner membrane protein
flagellar filament capping protein
flagellar biosynthesis protein
conserved protein
predicted transporter
asparagine synthetase A
predicted inner membrane protein
L-lactate permease
carbamoyl-phosphate synthase large subunit
predicted arabinose transporter
multifunctional: proline dehydrogenase (in membrane);
EAL domain containing protein involved in flagellar function
conserved protein
inhibitor of vertebrate C-lysozyme
predicted transporter
thymidine phosphorylase
proline:sodium symporter
IS30 transposase
carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
methyl-accepting chemotaxis protein I, serine sensor receptor
2-deoxyribose-5-phosphate aldolase, NAD(P)-linked
conserved protein
aspartate carbamoyltransferase, catalytic subunit
flagellar protein
mechanosensitive channel
DNA-binding transcriptional co-regulator with RcsB
proline/glycine betaine transporter
glutamine transporter subunit; periplasmic binding component of ABC superfamily
arginine transporter
flagellar hook-length control protein
glycerate kinase I
conserved protein with nucleoside triphosphate hydrolase domain
predicted protein, C-ter fragment (pseudogene)
predicted phosphate starvation inducible protein
D-serine ammonia-lyase
glutamate and aspartate transporter subunit; membrane component of ABC superfamily
glutamine transporter subunit; membrane component of ABC superfamily
nitrite reductase, large subunit, NAD(P)H-binding
glutamate and aspartate transporter subunit
succinylornithine transaminase, PLP-dependent
predicted inner membrane protein
glutamine transporter subunit; ATP-binding component of ABC superfamily
conserved protein
tartronate semialdehyde reductase
predicted protein, N-ter fragment (pseudogene)
DNA helicase IV
predicted DNA-binding transcriptional regulator
nitrite reductase, NAD(P)H-binding, small subunit
glutamate/aspartate periplasmic binding protein
damage-inducible protein J
aspartate carbamoyltransferase, regulatory subunit
DNA-binding transcriptional activator, 3HPP-binding
osmotically inducible, stress-inducible membrane protein
predicted antitoxin of YafQ-DinJ toxin-antitoxin system
predicted lipoprotein
purine-nucleoside phosphorylase
predicted protein, C-ter fragment (pseudogene)
predicted DNA-binding transcriptional regulator
conserved protein
outer membrane protein
glycolate oxidase subunit, FAD-linked
nitrite transporter
predicted protein
alpha-dehydro-beta-deoxy-D-glucarate aldolase
predicted protein
D-amino acid dehydrogenase
nucleoside
glutamate and aspartate transporter subunit; membrane component of ABC superfamily
DNA-binding transcriptional repressor
conserved protein
alanine racemase 2, PLP-binding
predicted hydrolase
multifunctional nucleoside diphosphate kinase; apyrimidinic endonuclease
predicted transporter
predicted protein
uracil transporter
arginine succinyltransferase
phosphopentomutase
30S ribosomal subunit protein S18
xanthosine transporter
thiamin (pyrimidine moiety) biosynthesis protein
minor component of type 1 fimbriae
DNA-binding transcriptional dual regulator
ferritin iron storage protein (cytoplasmic)
cytosine transporter
phosphoribosylglycinamide formyltransferase 2
L-glutamine:D-fructose-6-phosphate aminotransferase
RNA polymerase-associated helicase protein
predicted inner membrane protein
50S ribosomal subunit protein L17
predicted phosphatase, inner membrane protein
predicted acyl-CoA synthetase with NAD(P)-binding Rossmann-fold domain
regulator with hipB
NAD kinase
predicted dehydrogenase, NAD-dependent
30S ribosomal subunit protein S14
phosphoribosylformyl-glycineamide synthetase
fused methyl-galactoside transporter subunits;ATP-binding components of ABC superfamily
predicted protein
predicted crotonobetaine CoA ligase:carnitine CoA ligase
conserved inner membrane protein
N5-glutamine methyltransferase
S-adenosylmethionine decarboxylase
predicted glutaminase
D-3-phosphoglycerate dehydrogenase
predicted protein
DNA-binding transcriptional regulator
minor component of type 1 fimbriae
DNA-binding transcriptional regulator
predicted (D)-galactarate transporter
conserved protein with bipartite regulator domain
universal stress protein
adenylate cyclase
RNA polymerase, beta subunit
pseudouridine synthase for 23S rRNA (position 746) and tRNAphe(position 32)
thiamin (thiazole moiety) biosynthesis protein
long-chain fatty acid outer membrane transporter
voltage-gated potassium channel
L-serine deaminase II
predicted oxalyl-CoA decarboxylase
crotonobetainyl CoA:carnitine CoA transferase
predicted CDP-diglyceride synthase
fused aspartokinase I ; homoserine dehydrogenase I
IMP dehydrogenase
fused sensory histidine kinase in two-component regulatory system with KdpE
glutathionine S-transferase
fused siroheme synthase 1,3-dimethyluroporphyriongen III dehydrogenase/siroheme ferrochelatase
potassium translocating ATPase, subunit B
predicted transcriptional regulator
glucose-1-phosphate thymidylyltransferase
predicted serine transporter
polyamine transporter subunit;periplasmic-binding component of ABC superfamily
DNA-binding response regulator in two-component regulatory system with TorS
copper transporter
conserved protein
hybrid sensory kinase in two-component regulatory system with RcsB and YojN
conserved inner membrane protein
conserved inner membrane protein
50S ribosomal subunit protein L1
predicted protein
bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase
predicted antimicrobial peptide transporter subunit
L-tartrate dehydratase, beta subunit
L-1,2-propanediol oxidoreductase
gluconate transporter, high-affinity GNT I system
ferrous iron transporter, protein A
predicted dehydrogenase, with NAD(P)-binding Rossmann-fold domain
dimethyl sulfoxide reductase, anaerobic, subunit B
maltose transporter subunit
predicted glycosyl transferase
predicted oxidoreductase, Zn-dependent and NAD(P)-binding
2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
predicted fructoselysine transporter
fused subunits of iron-hydroxamate transporter
predicted protein
predicted cobalamin adenosyltransferase in ethanolamine utilization
fused subunits of D-xylose transporter
major cold shock protein
peptidase T
DNA-binding transcriptional activator
conserved protein
predicted L-PSP (mRNA) endoribonuclease
murein tripeptide (L-ala-gamma-D-glutamyl-meso-DAP) transporter subunit
predicted recombination limiting protein
heat shock chaperone
glycerol dehydrogenase, NAD
nitrite reductase, formate-dependent, penta-heme cytochrome c
predicted DNA-binding transcriptional regulator
formate dehydrogenase-N, alpha subunit, nitrate-inducible
predicted export usher protein
predicted truncated N-acetylgalactosamine-6-phosphate deacetylase
phosphomannomutase
iron-enterobactin transporter subunit
predicted protein
hypothetical protein
oxidoreductase subunit
conserved protein
putative beta-lactamase
conserved protein
DNA-bindng transcriptional repressor
predicted inner membrane protein
N-acetylgalactosamine-specific enzyme IIB component of PTS
predicted inner membrane protein
DNA-binding transcriptional dual regulator with FlhC
beta-lactam resistance membrane protein
heat shock protein
predicted 4Fe-4S membrane protein
23S rRNA pseudouridine synthase
polymyxin resistance protein B
nitrate reductase, periplasmic, large subunit
predicted transposase
membrane spanning protein in TonB-ExbB-ExbD complex
response regulator of RpoS
fructose-6-phosphate aldolase 2
predicted DNA-binding transcriptional regulator
predicted DNA-binding transcriptional regulator
DNA-binding transcriptional repressor
HU, DNA-binding transcriptional regulator, alpha subunit
ethanolamine ammonia-lyase, small subunit (light chain)
PTS family enzyme IIA, fructose-specific
molecular chaperone and ATPase component of HslUV protease
succinyl-CoA synthetase, NAD(P)-binding, alpha subunit
pyruvate formate lyase I
heme exporter subunit, membrane component of ABC superfamily
ferric iron-catecholate outer membrane transporter
GDP-mannose mannosyl hydrolase
predicted protein
dipeptide transporter
maltose transporter subunit
formate dehydrogenase-H, selenopolypeptide subunit
outer membrane phosphoporin protein E
iron-hydroxamate transporter subunit
predicted fimbrial-like adhesin protein
predicted DNA-binding transcriptional regulator
N-acetylgalactosamine-specific enzyme IIB component of PTS
molecular chaperone HSP90 family
periplasmic heme chaperone
2-methylcitrate dehydratase
protein-tyrosine kinase
predicted protein
L-fuculose-1-phosphate aldolase
predicted outer membrane export usher protein
enterobactin/ferric enterobactin esterase
predicted DNA-binding transcriptional regulator
iron-enterobactin outer membrane transporter
predicted ATPase, activator of (R)-hydroxyglutaryl-CoA dehydratase
L-threonine/L-serine transporter
predicted sugar transporter subunit
dipeptide transporter
fused ferrous iron transporter, protein B
dimethyl sulfoxide reductase, anaerobic, subunit C
predicted xanthine/uracil permase
predicted inner membrane protein
neutral amino-acid efflux system
cold shock protein associated with 30S ribosomal subunit
membrane spanning protein in TonB-ExbB-ExbD complex
predicted glycosyl transferase
predicted Fe-containing alcohol dehydrogenase
predicted carboxysome structural protein with predicted role in ethanolamine utilization
formate dehydrogenase-H, selenopolypeptide subunit
ferric iron reductase involved in ferric hydroximate transport
DNA-binding transcriptional activator
ribonucleoside diphosphate reductase 1, alpha subunit
assembly protein for periplasmic nitrate reductase
predicted lipoprotein
DNA-binding transcriptional regulator, Ni-binding
conserved protein with NAD(P)-binding Rossman fold
fused predicted PTS enzymes Hpr component
DNA-binding transcriptional dual regulator
aldo-keto reductase
conserved protein
predicted dienlactone hydrolase (pseudogene)
iron-enterobactin transporter subunit
oxidative demethylase of N1-methyladenine or N3-methylcytosine DNA lesions
sorbitol-6-phosphate dehydrogenase
neutral amino-acid efflux system
N-acetylgalactosamine-specific enzyme IID component of PTS
predicted DNA-binding transcriptional regulator
maltodextrin phosphorylase
ferrichrome outer membrane transporter
conserved protein
maltose outer membrane porin (maltoporin)
alpha-amylase
N,N -diacetylchitobiose-specific enzyme IIB component of PTS
conserved protein
conserved protein
D-xylose transporter
predicted glycosyl transferase
predicted aldolase
predicted carboxysome structural protein with predicted role in ethanol utilization
conserved protein, member of DEAD box family
predicted protein
predicted protein
conserved protein
periplasmic protein combats stress
glucitol/sorbitol-specific enzyme IIA component of PTS
putative transcriptional regulator
serine endoprotease, periplasmic
fused trehalose(maltose)-specific enzyme IIBC component of PTS
predicted transporter
L-fucose transporter
stationary phase inducible protein
predicted DNA-binding transcriptional regulator
hypothetical protein
adenosine deaminase
conserved protein
DNA binding protein, nucleoid-associated