Table S1. Catabolic and transport genes that are up-regulated in the absence of Hfq
ORF or
operona
PA0119
Gene
PA0129
Functiona
Predicted Hfq binding motifsc
putative dicarboxylate transporter
Fold change hfqvs wtb
10
bauD
amino acid permease
4.5
PA0153PA0154
PA0162
pcaHG
protocatechuate degradation
ATAACGCGAATAACAGGAGCCCGACatg (pcaH)
opdC
histidine porin OpdC
9.7 (pcaH),
4.0 (pcaG)
3.6
PA0226PA0228
PA0297PA0299
PA0300
pcaF
protocatechuate degradation
11
spuABC
glutamine biosynthesis
spuD
polyamine transport protein
7.6 (spuA), 5.6
(spuB), 6.4 (spuC)
4.5
ACAACAAGACGAGACCCGACCGatg (PA0226)
CAGAAGGGGAGCGACGAatg (pcaF)
ATAACATCTACAAACAACGGGTGTCTCatg (spuA);
AATAGAAGAGGTGTGACatg (spuC)
CAACAAAAATGGAGCTACCCCGCatg
PA0301PA0304
spuEFGH
polyamine transport proteins
AAAAGGCCCGGAACAGGAGTCGGACatg (spuE)
AACAGCCTGAAAAAGCGCatg (spuG)
AAAGAACTGGAGGGCAAGGTatg (spuH)
AAGAAACCAGAAGAGAGGCTACAACCgtg (PA0440)
dht
putative oxidoreductases for glutamate
biosynthesis
dihydropyrimidinase
4.8 (spuE), 7.8
(spuF), 7.3 (spuG),
5.7 (spuH)
129 (-39), 99 (-40)
45
PA0443PA0444
PA0783
95 (-43), 11 (-44)
putP
putative transporter and N-carbamoyl-betaalanine amidohydrolase
sodium/proline symporter
AAAAAACAATTTCAAGAACCGGCAACGACCGGTCAGCCTGCGAGGAAA
GACGGCatg
AATAACTAAAAGAATTCTGGAGAGGCCCatgCAACAGAGCAGA (PA0443)
3.6
ATAAAAACAAGCAATAGGGGAGTCCCTatg
PA0866
aroP2
aromatic amino acid transport protein
84
ACAACAATAAATTTCCACTTGCGTGAGATAATTCAatg
PA0870PA0872
PA1019
phhABC
phenylalanine metabolism
mucK
cis.cis-muconate transporter
2.5 (phhB), 2.3
(phhC)
3.2
AACAACAAAGACCCCGCGGCCACAAGCCGCTCATGGAGTCCGTatg
(phhA)
AGAACAAGAATAatg
PA1071PA1073
braDEFG
branched-chain amino acid transport proteins
CCGGAGGTGGAAAAAGTatg (braE)
PA1074
braC
branched-chain amino acid transport protein
9.9 (braD), 3.2
(braF), 8.0 (braE),
4.3 (braG)
3.2
PA1338
ggt
gamma-glutamyltranspeptidase precursor
11
GATAACAATAAATAGGGAAAGCCCatg
PA1763
hypothetical protein
6.6
AAAAACAAGAACAATCTCTGGGGATAGCGCCatg
PA1891PA1897
hypothetical proteins
TAAGGAAGAGGAGATAAATatg (PA1897)
PA0439PA0440
PA0441
PA1978
erbR
glycerol metabolism activator
13 (-91), 9.6 (-92),
18 (-93), 19 (-94),
19 (-95), 31 (-96),
36 (-97)
22
PA1979PA1980
eraSR
two component regulator for quinoprotein
ethanol dehydrogenase
5.7 (eraS), 7.2
(eraR)
AATAAAAATGCGTTCATCGCCCGCCTCCGCGAGGCCCGATGGAAGCGC
CGAatg
AAGAACAATTAAAGGGTCTCAACGatg
AAGAAGGAGCAACCGCAatgAGGAAT
ACAACAATGACAACACACAAGAAGAGTGGAGCACTatgAAGAAG
CATAACGACAATAACGAGGTGCAGGCCatg
PA1981PA1982
PA1983PA1984
PA1991PA1992
PA2003
exaA
quinoprotein ethanol dehydrogenase
29 (-81), 58 (exaA)
atgACAACAAGAAC (exaA)
exaBC
ethanol utilization
AGGAATGAAGTGatgAACAAGAACAAC (exaB)
ercS
ethanol utilization
12 (exaB), 12
(exaC)
5.6 (-91), 5.1 (ercS)
bdhA
3-hydroxybutyrate dehydrogenase
6.1
AGAAACAGCatg
13
AATAAGAACCTCAGGTACCTTGCGatg
PA2079
probable major facilitator superfamily (MFS)
transporter
probable amino acid permease
6.0
AAGAACCCCAATAAGATTCCAGAGGACATCCAGatgAAC
PA2210
probable MFS transporter
21
AAGAACAACAATAAAAGAGGTACGACCCatg
branched chain aminoacid assimilation
3.2 (bkdA1), 6.2
(bkdA2), 6.0
(bkdB), 4.1 (lpdV)
35
CAACGCCAGGAGCTCGGGGTatg (bkdA2)
4.1 (-64), 3.8 (-65),
5.5 (-66)
197 (catB), 87
(catC), 98 (catA)
11
AGAAAGACGAAACCGTGATGATCCAGAGAGGACCCCACCatg (PA2264)
PA2006
PA2247PA2250
bkdA1A2B
lpdV
PA2262
putative 2-ketogluconate transporter
PA2264PA2266
PA2507PA2509
PA2511
gluconate dehydrogenase (PA2265)
AACAATAAGAATGGTCTGTCAGatg (PA1991)
ACAAGAACAAGACAAGCTCAGGAGATACCCGACCatg
catBCA
catechol degradation
antR
transcriptional regulator
PA2512PA2514
PA2515PA2518
antABC
anthranilate degradation
xylXYZL
toluate degradation
PA2519
xylS
transcriptional regulator
80 (antA), 67
(antB), 152 (antC)
16 (xylX), 6.6
(xylY), 3.9 (xylZ),
7.2 (xylL)
15
PA2760
oprQ
outer membrane protein Q
5.0
AACAACCAGGAACAATAAGatgTTGAAGAAAAGG
PA3186
oprB
glucose/carbohydrate outer membrane porin
5.7
AAatgTACAAGAACAAGAAAACCAGA
PA3366
amiEBCRS
aliphatic amidase
PA3569PA3570
PA3709
mmsAB
branched chain aminoacid assimilation
7.2 (amiE), 12
(amiB), 4.7 (amiC),
4.7 (amiR), 2.1
(amiS)
5.0 (mmsA), 7.3
(mmsB)
30
AAAAAATAACAACAAGAGGTGATATCCatg (amiE)
CAGAAGGAGTTTCATCCatg (amiB)
AGCGACAGTCACAGGAGAGGAAACGGatg (amiC)
AACAATAACAAGAGGGGTATCGTCatg (amiS)
AACAATAAAAGCCGGCCTGGCCGGTGCAGGAGGGTTCatg (mmsA)
PA4023PA4025
PA4091PA4092
PA4121PA4123
PA4124PA4125
eutPBC
ethanolamine utilization
GATAACAACAAGATTGAGGTGAAAAACCCatg (eutP);
hpaAC
hydroxyphenylacetate degradation
hpcC
hydroxyphenylacetate degradation
hpcBD
hydroxyphenylacetate degradation
57 (eutP), 4.5
(eutB), 2.1 (eutC)
16 (hpaA), 9.8
(hpaC)
29 (-21), 20 (-22),
90 (-23)
12 (hpcB), 17
(hpcD)
probable MFS transporter
GACAACAACAAGCAGAGGCAAACGCCatg (catA)
CAGACAGAGGAGAAACGACCGatg (catC)
AAAACAGAGCGCCAGCAGAGCGCACCCCCAGCCTTGCCGTGTCGAGTG
CCGAACCatgATGAGG
CATAACGACAACGCACAAGGGTGAGAACGCatg (antA)
GAACAATAACAACGGAGGCCCCGGCCatg (xylX)
ATAACAACAACGATAGCAGCCTGAGTGTCCTGCCCatg (xylS)
AGACAACAATAAGAGCCCCCACAAGGGGCGGGAGAGCCGCAatg
AGATAACAACAATGACTGGAGACGATGatg (hpaA)
CCAGGAGACACCACCACAatg (PA4121)
AATGAGGAACCGACCatg (PA4122)
PA4126PA4128
PA4137
hpcG
PA4209
phzM
CACAAAAAGTACAAGATCatg (PA4126)
putative porin
8.5 (-26), 11
(hpcC), 11 (-28)
989
phenanzine specific methyltransferase
37
AACGAGAGAGAATAAAAGatgAATAATTCGAAT
4.7
AGACAATCAAAATAACCAGAGGTCACTCCatg
PA4498
putative binding protein component of ABC
transporter
putative metallopeptidase
3.8
AGACGAGGAGAACAACAAatg
PA4500
putative ABC transporter protein
19
TAGAAAAAGAAAAAATGAGGTTTGCatg
77 (opdD), 28 (02), 15 (-03), 20 (04), 11 (-05), 11 (06)
6.5
AACGACAACAATAAAGGGAGCAATCAGgtg (opdD)
8.0 (-08), 16 (-09),
24 (-10), 20 (-11),
53 (-12)
26
GAAGAGACTGAAAAatg (PA4912)
AAGAGGAGCTGTCatg (PA4909)
PA4496
hydroxyphenylacetate degradation
PA4501PA4506
opdD
glycine-glutamate dipeptide uptake
PA4588
gdhA
glutamate dehydrogenase
PA4908PA4912
putative ABC transporter proteins
PA4913
probable binding protein component of ABC
transporter
probable oxidoreductase
PA4986
PA5112
estA
CAAAAAATTGTTCACAAAACTAGAAACCGGTGAGAAAAatg
32
AAACACAACAACAACATCGTAGTTACGAGCGCCAACATCATCCTCAGG
AGCAACACCCCatg
AACAACAAGAAGGACGCCAACCgtg
esterase
2.8
GACAATAAAAACAAATCATGGAGTAAGAGAatg
putative permease of ABC transporter
2.9 (-52), 5.0 (-53),
4.9 (-54), 3.2 (-55)
3.5
AATAACAAGAGGAAAATCCatg (PA5152 first gene in operon)
7.4
AACAATCATAAAAAAAGCCTCGTGAGAGGCCTGCTTGCTCAGCGTGAG
GAGATACACCCatg
atgGCCCGCGAGCAGCAAC (PA5523)
PA5152PA5155
PA5309
pauB4
FAD-dependent oxidoreductase
PA5380
gbdR
PA5522PA5523
PA5542
pauA6
Transcriptional regulator for glycine betaine
catabolism
glutamylpolyamine synthetase
PA5543PA5545
AAGAACAACAACCAAGGGAAGAATCGatg
hypothetical proteins
hypothetical proteins
3.2 (-22), 4.3
(pauA6)
7.6
12 (-45), 30 (-44),
8.3 (-43)
AATAATCAGGATTTCACACatg
CATAAGGAAAACGTCCatg
GACAACAACGATAAGAACAGGAGACTTCCCatg (PA5545)
a
Gene numbers and functions are taken from the Pseudomonas genome database [61]
b
data derived from Sonnleitner et al [31]
c
A-rich sequences are highlighted in bold; start codons are in lower case letters.