SUPPLEMENTARY MATERIAL
Figure S1. Electrostatic potential surface representations of AraC/XylS family members. The electrostatic potentials were calculated
with the software DelPhi version 4 release 1.1 and the surfaces and images were generated with PyMOL. A) View on the side of the
proteins facing DNA. B) View on the opposite side of the protein, by rotation of the proteins by 180 degrees. Blue color indicates a
positive potential, red color indicates a negative potential and white color indicates a neutral potential.
Figure S2. Genetic context of predicted binding sites of the uncharacterized AraC/XlyS transcription factors.
Distance (in base pairs) from the hypothetical binding site is provided for each gene. In blue are genes with
a function related with the proposed biological role of the AraC/XylS transcription factor. In black, genes
with unknown or not obviously related function. In the majority of the cases, the function of these genes
was obtained by sequence similarity to other genes or by the annotation of the InterPro database for their
families.
Table S1. List of 62 well-characterized AraC/XylS-family transcriptional regulators with
known biological function
Proteina
Organism
Biol. proccessb
Regulatory function
Categoryc
Ref.d
AarP
(P43463)
Providencia
stuartii
Antibiotic
resistance
S+V
7768849,
10390241
Ada
(P06134)
Escherichia coli
(strain K12)
DNA damage
response
S+V
3529081
Ada
(P26189)
Salmonella
typhimurium
DNA damage
response
S+V
1904855
AdaA
(P19219)
Bacillus subtilis
DNA damage
response
S+V
8376346,
2120677
AdiY
(P33234)
Escherichia coli
(strain K12)
Acid resistance
S+V
8795195,
21034467
AggR
(P43464)
Escherichia coli
Cell adhesion
V
7913930
AlkR
(O31249)
Acinetobacter sp.
(strain ADP1)
Alkane
metabolism
M
9811637
AppY
(P05052)
Escherichia coli
(strain K12)
Phosphate
starvation
response
S
18383615
AraC
(P07642)
Erwinia
chrysanthemi
Plant
carbohydrates
metabolism
Regulates the transcription of 2'-Nacetyltransferase, which is capable of
acetylating both peptidoglycan and
certain aminoglycoside antibiotics.
Repairs O6-methylguanine and O4methylthymine and induces
transcription of genes involved in the
adaptive response to alkylation
damage in DNA
Repairs O6-methylguanine and O4methylthymine and induces
transcription of genes involved in the
adaptive response to alkylation
damage in DNA
Repairs O6-methylguanine and O4methylthymine and induces
transcription of genes involved in the
adaptive response to alkylation
damage in DNA
Regulates arginine-dependent acid
resistance, is involved in glutamatedependent response to acid stress,
and is associated with activation of
virulent strains of E. coli in the
stomage
Transcriptional activator of
aggregative adherence fimbria I
expression in enteroaggregative E. coli
Activates the expression the alkane 1monooxygenase that permits the use
of alkanes with at least twelve carbon
atoms as the sole source of carbon
and energy
Induces the synthesis of acid
phosphatase (AppA) and several other
polypeptides (such as AppBC) during
the deceleration phase of growth in
response to phosphate starvation. Also
involved in the stabilization of the
sigma stress factor RpoS during stress
conditions
Controls the expression of at least six
genes that are involved in the
transport and catabolism of Larabinose an aldopentose sugar found
in plant gums, pectins and bacterial
cell wall polysaccharides
M
3902795
Proteina
Organism
Biol. proccessb
Regulatory function
Categoryc
Ref.d
AraC
(P0A9E0)
Escherichia coli
(strain K12)
Plant
carbohydrates
metabolism
M
12596232
Caf1R
(P26950)
Yersinia pestis
Capsule
formation
V
1633857,
19103769
CfaD
(P25393)
Escherichia coli
Cell adhesion
V
1971911
ChbR
(P17410)
Escherichia coli
(strain K12)
Carbohydrates
metabolism
M
15066032
CsvR
(P43460)
EnvY
(P10805)
Escherichia coli
Cell adhesion
V
1685133
Escherichia coli
(strain K12)
Temperature
stress response
S
2536924
EutR
(P36547)
Escherichia coli
(strain K12)
Amine
metabolism
M+V
20234377
ExsA
(P26993)
Pseudomonas
aeruginosa
V
FapR
(P23774)
Escherichia coli
Type III
secretion
system
Cell adhesion
V
16714561,
9618447,
11119548
2077360
FeaR
(Q47129)
Escherichia coli
(strain K12)
Amine
metabolism
M
9043126
GadW
(P63201)
Escherichia coli
(strain K12)
Acid resistance
S+V
12730179
GadX
(Q9EYV5)
Escherichia coli
O127:H6
Cell adhesion,
Type III
secretion
system, Acid
resistance
S+V
17576759
HilD
(P0CL08)
Salmonella
typhimurium
Type III
secretion
system
Controls the expression of at least six
genes that are involved in the
transport and catabolism of Larabinose an aldopentose sugar found
in plant gums, pectins and bacterial
cell wall polysaccharides
Regulates the caf1M1A1 operon. The
caf operon products constitute a
fimbrial chaperone-usher system that
acts to assemble and export F1
capsule components
Transcriptional activator of the CFA/I
adhesin (cfAA) gene of enterotoxigenic
E. coli
Regulates the expression of the
chbBCARFG operon for the uptake and
metabolism of chitobiose (the major
breakdown product of chitin
degradation)
Transcriptional activator of the
fimbrial gene in enterotoxigenic E. coli
Regulates the temperature-dependent
expression of several E. coli envelope
proteins, most notably the porins
ompF and ompC and the lambda
receptor, lamB
Activates the transcription of the eut
operon, neccesary for uptake and
metabolism of ethanolamine. It was
suggested that the breakdown of
ethanolamine contributes to
disrupting gut functions, in particular
innate immune functions
Promotes the expresion of type III
secretion system in response of low
levels of Ca2+
Regulates the expression of the 987P
operon for the fimbrial protein in
enterotoxygenic E. coli
Regulates tynA/maoA and feaB/padA
genes necessary for 2phenylethylamine catabolism
GadW regulates the gadA and gadBC
genes that regulate acid tolerance and
virulence gene expression in response
to environmental cues within the
gastrointestinal tract
GadX regulates
perABC and gadA and gadB, that
regulate acid tolerance and virulence
gene expression in response to
environmental cues within the
gastrointestinal tract
Regulates the expression of the main
transcriptional regulator of the
Salmonella pathogenicity island 1
(SPI1) hilA
V
11442828
Proteina
Organism
Biol. proccessb
Regulatory function
Categoryc
Ref.d
HrpB
(P31778)
Type III
secretion
system
Regulates the hrp operon. hrp genes
encode a specialized type III secretion
system
V
12374732
InvF
(P69343)
Ralstonia
solanacearum
(Pseudomonas
solanacearum)
Salmonella
typhimurium
Type III
secretion
system
V
11296219
LacR
(O33813)
Staphylococcus
xylosus
Mammalian
carbohydrates
metabolism
M
9573174
LumQ
(Q51872)
Photobacterium
leiognathi
Riboflavin
synthesis
and/or
luminescence
M
17586644
MarA
(P0ACH5)
Escherichia coli
(strain K12)
Antibiotic
resistance
S+V
9333027,
11104814
MelR
(P0ACH8)
Escherichia coli
(strain K12)
Plant
carbohydrates
metabolism
M
16621812
MmsR
(P28809)
Pseudomonas
aeruginosa
Amino acid
metabolism
M
1339433
MsmR
(Q00753)
Streptococcus
mutans
Plant
carbohydrates
metabolism
M
1537846,
8432594
MxiE
(P0A2S7)
Shigella flexneri
Type III
secretion
system
V
16428428
OruR
(P72171)
PchR
(P40883)
Pseudomonas
aeruginosa
Pseudomonas
aeruginosa
Amino acid
metabolism
Iron stress
M
9401045
S+V
10722571,
15375116
PerA
(P43459)
Escherichia coli
O127:H6
Cell adhesion
V
7729884
PocR
(Q05587)
Salmonella
typhimurium
Carbohydrates
metabolism
M
8071226
PqrA
(Q52620)
Proteus vulgaris
Antibiotic
resistance,
Oxidative stress
response
Regulates the expression of genes
encoding the secreted effector
molecules Sip/Ssp ABCD, SigD, SptP
and SopE, necessary for type III
secretion system
Regulates the expression of lacPH
(lactose permease and the betagalactosidase) genes for lactose
utilization
Probably regulates the riboflavin
synthesis and/or luminescence. Is
encoded in the lux operon that is
linked to the luminescence genes in
some photobacterium species
Regulates the expression of the
mar regulon that confers resistance to
a variety of antibiotics
Transcriptional activator for the
expression of the melAB operon in
response to the availability of
melibiose
Regulates the expression of the
mmsAB operon. The operon contains
two structural genes involved in valine
metabolism
Regulates the expression of the msm
operon responsible for the transport
and metabolism of melibiose,
raffinose, and isomaltosaccharides
Controls transcription of a set of genes
encoding proteins that transit through
the type III secretion system
apparatus.
Regulates the expression of genes
involved in ornithine metabolism
Regulates the expression of pyoverdin
and pyochelin siderophores (iron
chelators) which contribute to
virulence
Regulates the expression of the
eaeA gene that is associated with
attaching and effacing lesions and
encodes intimin, a 94-kDa outer
membrane protein
Regulates the expression of pdu and
cob operons that regulate the
meabolism of the L-fucose subproduct
anaerobic metabolite 1,2-propanediol
Confers multidrug resistance in a way
similar to that of the soxS and marA
genes in E. coli
S+V
7726514
Proteina
Organism
Biol. proccessb
Regulatory function
Categoryc
Ref.d
RafR
(P43465)
Pediococcus
pentosaceus
Plant
carbohydrates
metabolism
M
2180920
RamA
(P55922)
Enterobacter
cloacae
Antibiotic
resistance
S+V
21811569
RhaR
(P09378)
Escherichia coli
(strain K12)
M
8757746
RhaS
(P09377)
Escherichia coli
(strain K12)
M
8230210
RhrA
(Q9Z3Q6)
Rhizobium
meliloti (Ensifer
meliloti)
Plant
carbohydrates
metabolism
Plant
carbohydrates
metabolism
Activation of
siderophores,
Iron stress
BPI + S
11274118
RipA
(Q8NRR3)
Corynebacterium
glutamicum
Iron stress
response
S
21217007,
16179344
Rns
(P16114)
Rob
(P0ACI0)
Escherichia coli
Cell adhesion
V
2563591
Escherichia coli
(strain K12)
Antibiotic
resistance
S+V
7896685,
7793951
SirC
(Q8Z4A6)
Salmonella typhi
Type III
secretion
system
V
10322010
SoxS
(P0A9E2)
Escherichia coli
(strain K12)
Oxidative stress
response
S+V
1653416,
7726514
TcpN
(P0C6D6)
Vibrio cholerae
Pilus formation
V
1352761
TetD
(P28816)
Escherichia coli
Antibiotic
resistance
S+V
6094472,
9333027
ThcR
(P43462)
Rhodococcus
erythropolis
(Arthrobacter
picolinophilus)
Escherichia coli
Organosulfur
compound
metabolism
Regulates the raffinose operon.
Raffinose is a trisaccharide composed
of galactose, fructose, and glucose
found in many plants
Is Involved in resistance to multiple
antibiotics through the expression
regulation of the OmpF porin and the
efflux pump AcrAB
Regulates the rhaBAD operon that
encode enzymes for catabolism of
rhamnose
Regulates the rhaBAD operon that
encode enzymes for catabolism of
rhamnose
Regulates the transcription of the
rhbABCDEF operon involved in
biosynthesis of rhizobactin 1021, a
siderophore produced under iron
stress. Also regulates the rhtA gene
which encodes an membrane receptor
protein for rhizobactin 1021
Under iron limitation, RipA acts as a
repressor of several genes encoding
prominent iron-containing proteins
(e.g. aconitase and succinate
dehydrogenase)
Regulates the expression of the CS1
and CS2 adhesins
Regulates the expression of genes that
confer multiple antibiotic resistance.
Overexpression causes antibiotic
resistance, organic solvent tolerance
and heavy metal resistance
Regulates the expression of the
invasion-associated type III secretion
system encoded within the SPI-1
plasmid
Regulates the transcriptional
activation of a complex oxidative
stress regulon in response to
superoxide-generating agents
Regulates the tcp gene cluster,
associated with the biosynthesis and
assembly of the toxin-coregulated
pilus
Regulates the transcripcion of the mar
regulon that confers the multiple
antibiotic resistance phenotype
Regulates the transcription of the thc
operon for the degradation of the
thiocarbamate herbicide EPTC
M
7836301
Regulates the expression of the urease
operon, related with uropathogenic
strains of E. coli and Proteus mirabilis
V
11724879,
11119505
UreR
(P32326)
Urease
activation
Proteina
Organism
Biol. proccessb
Regulatory function
Categoryc
Ref.d
UreR
(Q02458)
Proteus mirabilis
(strain HI4320)
Urease
activation
V
7678244,
18202436
VirF
(P0A2T1)
Shigella flexneri
Type III
secretion
system
V
18202440
VirF
(P0C2V5)
Yersinia
enterocolitica
Type III
secretion
system
V
9841674,
9618447
VqsM
(Q9I1P2)
Pseudomonas
aeruginosa
Quorum sensing
V
16194239
XylR
(P0ACI3)
Escherichia coli
(strain K12)
M
9371449
XylS
(P07859)
M
18296514
XylS1
(Q04713)
Pseudomonas
putida
(Arthrobacter
siderocapsulatus)
Pseudomonas
putida
Plant
carbohydrates
metabolism
Benzene
derivatives
metabolism
M
8473862
XylS2
(Q05092)
Pseudomonas
putida
Benzene
derivatives
metabolism
M
1331988
XylS3
(Q05335)
Pseudomonas
putida
Benzene
derivatives
metabolism
M
8473862
Y4fK
(P55449)
Rhizobium sp.
(strain NGR234)
Nodulation
induction
BPI
9669339
YesN
(O31517)
Bacillus subtilis
M
17921311,
19651770
YesS
(O31522)
Bacillus subtilis
Plant
carbohydrates
metabolism
Plant
carbohydrates
metabolism
Regulates the expression of the urease
operon, related with uropathogenic
strains of E. coli and Proteus mirabilis
Primary regulator of plasmid-encoded
virulence genes. VirF activates the
second essential virulence plasmid
regulator VirB (type III secretion
system) and the actin nucleator
protein IcsA
Transcriptional activator of the
Yersinia Yop virulence regulon that
encodes 11 different secreted antihost
proteins called Yops, as well as a type
III secretion machinery that is required
for their secretion
Regulates dozens of genes which are
implicated in quorum sensing,
virulence and multidrug resistance
Regulatory protein for the xylBAFGHR
operon involved in the transport and
metabolism of D-xylose
Regulates the xylXYZLTEGFJQKIH
operon of TOL plasmid, required for
the degradation of toluene, m-xylene
and p-xylene
Regulates the xylXYZLTEGFJQKIH
operon of TOL plasmid, required for
the degradation of toluene, m-xylene
and p-xylene
Regulates the xylXYZLTEGFJQKIH
operon of TOL plasmid, required for
the degradation of toluene, m-xylene
and p-xylene
Regulates the xylXYZLTEGFJQKIH
operon of TOL plasmid, required for
the degradation of toluene, m-xylene
and p-xylene
Regulates the nod operon that
controls nodulation factors that
promote nitrogen fixation in symbiotic
bacteria-plant interaction
Probably activates the expression of
genes that regulate the metabolism of
plant cell wall polysaccharides
Probably regulates the pathway
involve in rhamnogalacturonan (plant
cell wall polysaccharides)
depolymerization
M
17449691
Benzene
derivatives
metabolism
a
Protein name and UniProt accession number in parenthesis.
b
General biological process. Multiple processes are separated by a comma.
c
Functional category: Bacteria-plant interaction (BPI), metabolism (M), stress response (S)
and virulence (V).
d
PubMed ID of references describing the biological function.
Table S2. Details of the analysis of the genetic context for predicted binding sites of the uncharacterized AraC/XlyS transcription factors.
PDB
structure
3mn2
3oio
Organism
Rhodopseudomonas
palustris TIE-1
Chromobacterium
violaceum ATCC 12472
-
3lsg
3oou
Chromobacterium
violaceum ATCC 12472
Fusobacterium
nucleatum subsp.
nucleatum ATCC 25586
Listeria innocua
Listeria innocua
-
-
+
-
-
1283534 / 1283555
3284826 / 3284847
2429687 / 2429708
1447985 / 1448006
2208002 / 2208023
2849441 / 2849462
GATCTGCCCGAGGGCG
CCACGC
AGGCGCACCAGCTCCT
TGACGA
GATGACGCCGTTTTCC
GCCTTC
TCTGGATTCATGATAG
TTCAAT
TCAAATAAAGGATCCC
CGAACT
AGACGAACAAATCGCC
CAAGCA
Gene 1
Locus: Rpal_1214 /
UniProtKB: B3QHJ6
Gene: ibeB / UniProtKB:
Q7NVV0
Locus: CV_3010 /
UniProtKB: Q7NTP4
Locus: FN0792 / Uniprot:
Q8RFC1
Locus: lin2190 / Uniprot:
Q929T4
Locus: 2833 / Uniprot:
Q7ANT9
Genome
start / end /
strand
1285065 / 1285718 / +
2430434 / 2431813 / +
3286108 / 3286602 / -
1448403 / 1450424 / +
2207728 / 2208621 / -
2849334 / 2849636 / +
Description
DSBA oxidoreductase /
protein disulfide
oxidoreductase activity
Lipoprotein / outer
membrane drug efflux
lipoprotein
oxidation-reduction
process / electron carrier
activity
urocanate hydratase
Aminoglycoside 3'phosphotransferase
IIA PTS Lactose / cellobiose
uptake / enzyme IIA
Distance
from
sequence
1510
726
1261
419
598
0
Gene 2
Locus: Rpal_1215 /
UniProtKB: B3QHJ7
Locus: CV_2243 /
UniProtKB: Q7NVU9
Gene: flaD / UniProtKB:
Q7NTP3
Locus: FN0793 / Uniprot:
Q8RFC0
tRNA
Locus: lin2834 / Uniprot:
Lin2834 protein
Genome
start / end /
strand
1285927 / 1286238 / +
2431827 / 2432282 / -
3286802 / 3287920 / -
1450652 / 1451851 / +
2208754 / 2208837 / +
2850081 / 2851184 / -
Description
hypothetical protein
conserved hypothetical
protein
ciliary or flagellar motility
/ structural molecule
activity
L-glutamato Transporter
tRNA
Family FtsW_RodA_SpoVE
Implicated in Cell division
Distance
from
sequence
2372
2140
1955
2668
731
619
Genome
strand of
Binding
Site
Binding
Site start /
end
Binding
Site
sequence
PDB
structure
3mn2
3oio
Gene 3
Locus: Rpal_1216 /
UniProtKB: B3QHJ8
Gene: nfnB / UniProtKB:
Q7NVU8
Genome
start / end /
strand
1286243 / 1287505 / +
3lsg
3oou
Locus: CV_3012 /
UniProtKB: Q7NTP2
Locus: FN0794 / Uniprot:
Q8RFB9
Locus: lin2191 / Uniprot:
Q929T3
Locus: lin2835 / Uniprot:
Q927F4
2432321 / 2432974 / -
3288132 / 3289388 / +
1451930 / 1452343 / -
2208964 / 2210244 / -
2851181 / 2852311 / -
Description
electron carrier activity /
flavin adenine
dinucleotide binding /
iron ion binding /
oxidoreductase activity
oxygen-insensitive
NAD(P)H nitroreductase
/ 6,7-dihydropteridine
reductase activity
proteolysis / serine-type
carboxypeptidase
activity
Unknown
DNA binding protein (HTH
motif)
Family FtsW_RodA_SpoVE
Implicated in Cell division
Distance
from
sequence
2688
2613
3285
3964
941
1719
Gene 4
Locus: Rpal_1213 /
UniProtKB: B3QHJ5
Gene: acrB / UniProtKB:
Q7NVV1
Locus: CV_3009 /
UniProtKB: Q7NTP5
Gene: hutH1 / Uniprot:
Q8RFC2
Locus: lin2189 / Uniprot:
Q929T5
Locus: lin2832 / Uniprot:
Q927F7
Genome
start / end /
strand
1281779 / 1285003 / +
2427309 / 2430437 / +
3284381 / 3286096 / -
1446836 / 1448386 / +
2207105 / 2207731 / -
2847990 / 2849297 / +
Enzyme, catalyzes: Lhistidine = urocanate +
NH3
Protein with structural
similarity with: Regulation
domain of Rob, multidrug
effect transporter
regulator and heme
binding protein2
PTS, cellobiose uptake /
enzyme IIC
Description
transporter activity /
acriflavin resistance
protein
transporter activity /
acriflavin resistance
protein B
peptidyl-histidine
phosphorylation /
regulation of transcription,
DNA-dependent
Distance
from
sequence
0
0
0
0
293
166
Gene 5
Locus: Rpal_1212 /
UniProtKB: B3QHJ4
Locus: CV_2240 /
UniProtKB: Q7NVV2
Locus: CV_3008 /
UniProtKB: Q7NTP6
Locus: FN0790 / Uniprot:
Q8RFC3
Gene: crcB2 / Uniprot:
Q929T6
Locus: lin2831 / Uniprot:
Q927F8
Genome
start / end /
strand
1280787 / 1281782 / +
2426145 / 2427305 / +
3283449 / 3284312 / +
1445384 / 1446547 / -
2206609 / 2206998 / -
2847548 / 2847853 / +
Description
efflux transporter, RND
family, MFP subunit /
transmembrane
transport
transmembrane
transport / probable
multidrug efflux protein
regulation of
transcription, DNAdependent / twocomponent response
Xylose repressor
Protein CrcB homolog 2
PTS Lactose / cellobiose
uptake / enzyme IIB
PDB
structure
3mn2
3oio
3lsg
3oou
regulator activity
Distance
from
sequence
1774
2404
536
1438
1026
1610
Gene 6
Locus: Rpal_1211 /
UniProtKB: B3QHJ3
Gene: fepB / UniProtKB:
Q7NVV3
Gene: fhiA / UniProtKB:
Q7NTP7
Locus: FN0789 / Uniprot:
Q8RFC4
Gene: crcB1 / Uniprot:
Q929T7
Gene: kdpA / Uniprot:
Q927F9
Genome
start / end /
strand
1280444 / 1280785 / +
2424881 / 2425849 / -
3281425 / 3283137 / +
1444526 / 1445368 / -
2206263 / 2206619 / -
2845522 / 2847207 / -
Description
Transcriptional
regulator, ArsR family /
sequence-specific DNA
binding transcription
factor activity / HTH
arsR-type DNA-binding
domain
high-affinity iron ion
transport /
ferrienterobactin-binding
periplasmic protein
precursor
protein secretion
Unknown
Protein CrcB homolog 1
Potassium-transporting
ATPase A chain,l
Distance
from
sequence
2771
3860
1708
2617
1404
2256