Download Additional File 1: Microarray results for WT and expressing DctD250 rpoN WT/

Additional File 1: Microarray results for WT and ΔrpoN S. Typhimurium LT2 strains
expressing DctD250
Locus Taga
Gene Symbol
Function
54
Known σ -dependent operons and sRNA genes:
STM0368
prpB
Proprionate catabolism (putative)
STM0369
prpC
STM0370
prpD
STM0371
prpE
WT/ΔrpoNb
45
25
72
21c
STM0830
STM0829
STM0828
glnH
glnP
glnQ
Glutamine high-affinity transporter
7.1
2.4
2.9
STM2355
argT
Lysine/arginine/ornithine transport
3.5
STM_R0152
tke1
GlmY sRNA
0.9
STM_R0167
sraJ
GlmZ sRNA
1.1
STM4007
glnA
Glutamine synthetase
STM4006
glnL
STM4005
glnG
Predicted σ54-dependent operons:
STM0462
glnK
Nitrogen regulatory protein pII
STM0463
amtB
Ammonium transport (putative)
48
3.5
3.6
3.6
190
STM0577
STM0576
STM0575
STM0574
STM0573
STM0572
PTS system (putative)
67
3.8
3.5
59
18
23
STM0649.S
STM0650
STM0651
STM0652
STM0653
Hydrolase (putative)
ybeL
11
42
8.8
1.2
1.2
STM0665
STM_R0126
STM0664
STM0663
STM0662
gltI
sroC
gltJ
gltK
gltL
Glutamate/aspartate transporter
1.8
0.81
1.3
1
1.9
STM1285
STM1284
yeaG
yeaH
Serine protein kinase (putative)
2.5
2.5
STM1303
astC
Arginine/ornithine/glutamine metabolism
2.4
Locus Taga
STM1304
STM1305
STM1306
STM1307
STM1690
STM1689
STM1688
STM1687
STM1686
Gene Symbol
astA
astD
astB
astE
pspA
pspB
pspC
pspD
pspE
Function
WT/ΔrpoNb
2.4
2.6
3.3
2.4
Phage shock proteins
17
0.9
4
1.3
1.5
Amino acid transport (putative)
100
11
18
3.3
1.2
Nitric oxide reductase
16
7.1
STM2360
STM2359
STM2358
STM2357
STM2356
ubiX
STM2840
STM2841
ygbD
STM2842
STM2843
hypF
hydN
Hydrogenase maturation proteins
13
14
STM2853
STM2852
STM2851
STM2850
STM2849
STM2848
STM2847
STM2846
STM2845
STM2844
hycA
hycB
hycC
hycD
hycE
hycF
hycG
hycH
hycI
Hydrogenase 3
26
12
170
1.9
96
25
30
6.4
12
9.4
STM2854
STM2855
STM2856
STM2857
STM2858
hypA
hypB
hypC
hypD
hypE
Formate-hydrogen lyase system
5.6
39
6.3
25
31
STM3521
STM3519
STM3518
RNA repair system (putative)
rtcB
rtcA
71
27
4.3
STM3568
rpoH
Heat shock sigma factor (σ32)
1.7
PTS system (putative)
39
37
60
STM3772
STM3771
STM3770
Locus Taga
STM3769.S
STM3768
STM3767
STM3766
Gene Symbol
Function
WT/ΔrpoNb
31
24
41
1.4
STM4172
zraP
Zinc resistance-associated protein
16
STM4173
STM4174
hydH
hydG
Zinc resistance two-component system
3.7
2.8
STM4244
pspG
Phage shock protein
1.4
STM4285
fdhF
Formate dehydrogenase
29
PTS system (putative)
16
1.7
66
13
43
25
STM4535
STM4536
STM4537
STM4538
STM4539
STM4540.S
Novel σ54-dependent operon:
STM2944
ygcB
CRISPR-associated proteins
STM2943
STM2942
STM2941
yghJ
STM2940
STM2939
ygcH
STM2938
STM2937
ygbF
Possible indirectly regulated σ 54-dependent operons:
STM0144
ppdD
Pilin biogenesis (putative)
STM0143
hofB
STM0142
hofC
0.78
3.3
2.2
STM0515
STM0516
STM0517
STM0518
STM0519
STM0520
STM0521
STM0523
STM0524
STM0525
Allantoin utilization
ybbV
allB
ybbY
glxK
1.1
1
2
1.6
2
1.8
1.3
3.2
1.4
0.99
STM0791
hutH
Histidine-ammonia lyase
3.8
allA
allR
gcl
gip
glxR
1.6
1.2
1.3
1.2
1.4
2.8
4.1
0.8
Locus Taga
STM1252
Gene Symbol
STM2038
STM2039
STM2040
STM2041
STM2042
STM2043
STM2044
STM2045
STM2046
STM2047
STM2048
STM2049
STM2050
STM2051
STM2052
STM2053
STM2054
STM2055
STM2056
STM2057
STM2058
pduA
pudB
pduC
pduD
pduE
pduG
pduH
pduJ
pduK
pduL
pduM
pduN
pduO
pduP
pduQ
pduS
pduT
pduU
pduV
pduW
pduX
STM2149
STM2150
STM2151
STM2152
Function
Cytoplasmic protein (putative)
WT/ΔrpoNb
3.1
Propanediol utilization
0.75
1.1
2
1.5
0.46
3.3
0.46
0.58
0.7
4.3c
2.5
0.87
1.4
1.4
1.5
1.7
1.8
0.94
0.61
2.1
1.6
stcD
stcC
stcB
stcA
Chaperone-usher fimbriae (putative)
1.5
3.2
1.9
0.82
STM2572
yfhH
Membrane transport protein (putative)
3.1
STM2773
STM2774
STM2775
STM2776
iroB
iroC
iroD
iroE
Siderophore production
2.1
0.95
4
1.2
STM2839
ygaA
EBP activator for STM2840 operon (putative)
3.2
STM2859
fhlA
EBP activator for fdhF/hyc/hyp operons
3.5
STM2899
STM2898
STM2897
STM2896
STM2895
STM2894
STM2893
STM2892
STM2891
invF
invG
invE
invA
invB
invC
invI
invJ
spaO
Cell invasion proteins
2
5.9
1.7
1.8
1
1.9
0.9
2
1.9
Locus Taga
STM2890
STM2889
STM2888
STM2887
STM2886
STM2885
STM2884
STM2883
STM2882
Gene Symbol
spaP
spaQ
spaR
spaS
sicA
sipB
sipC
sipD
sipA
Function
WT/ΔrpoNb
1.6
0.69
2.7
1.4
0.71
1.1
1.1
1.2
1.7
STM3253
PTS system/sugar metabolism (putative)
1.5
STM3254
1.8
STM3255
1
STM3256
3.7
STM3257
2.9
STM3258
1.4
STM3259
1.1
STM3260
2
STM3261
1.3
STM3262
1
a
Locus tags for all genes within operons in which at least one gene was up-regulated ≥3-fold (p-value
<0.02) by RpoN in the microarray analysis; up-regulated genes are in black type and genes below the
3-fold cut off are in grey type). The up-regulated operons are grouped as known, predicted, novel, or
possible indirectly regulated, as defined in Results.
b
Both WT and ΔrpoN strains contain pPBHP92 expressing DctD250. Signal ratios below the 3-fold
cutoff for up-regulation are displayed in grey.
c
above 3-fold cutoff, but p-value >0.02