Additional file 9 Summary of His10-MrpC2 and FruA-His6 binding to DNA fragments in EMSAs
Ranka
MXAN
1
2
3
4
5
6
4360
6247
4064
5802
0524
5125
mrpC
Position of
peak relative
to ORF starta
568
-71
-241
-370
-97
-247
12
14
4147
3117
rpoE1
fruA
-23
-330
19
3993
bsgA
-47
27
1710
pkn8
-204
50
268
383
6947
5208
6500
cheW6a
socA1
pktA1
-55
-61
-74
421
444
4149
2902
frzS
Mx3320
-163
-40
461
5123
mrpA
-171
655
5783
pilA
-173
a
Gene
Characteristicsb
high rank
high rank, down-regulated
high rank
high rank
high rank, up-regulated
high rank, up-regulated,
known to be bound by
MrpC/2 and involved in
development
A and S motility regulation
up-regulated, known to be
bound by MrpC/2 and
involved in development
weakly up-regulated,
known to be involved in
development
up-regulated, known to be
involved in development
S motility
bypass of C-signaling
known to be involved in
development
S motility
up-regulated, known to be
involved in development
up-regulated, known to be
involved in development
S motility
Apparent number
of His10-MrpC2
binding sitesc
2
2
Nt
3
2
>4
Motifs bound by
His10-MrpC2d
1
1
1
1
2
Nt
Binding by
FruA-His6
alonee
+
+
Nt
+
-
Cooperative binding
by His10-MrpC2 and
FruA-His6e
+
+
Nt
+
+
+
4
2
Nm
1
Nt
+
Nt
2
1
+
+
1
1
-
+
1
2
2
1
Nm
1
+
+
+
+
1
1
Nm
Nm
+
+
+
2
Nm
+
+
1
Nm
-
-
From Additional file 3. Note that the ChIP-seq peak at -330 relative to the fruA start codon is at -98 relative to the predicted start codon of
MXAN_3116, as listed in Additional file 3.
b
From Additional files 3, 6, and 7. See the text or Additional file 6 for references.
c
From Figure 4 and Additional file 10. Nt, not tested.
From Figure 5. Nt, not tested; Nm, no match.
e
From Figure 6 and Additional file 10. Nt, not tested. Note that cooperative binding was not observed at a low concentration of His10-MrpC2 for
MXAN_5802.
d