Table 2

AdpA-binding sites identified in silico in the promoter regions of S. lividans AdpA-dependent genesa
S. coelicolor gene (S. lividans gene)b Putative AdpA-binding sitec Position (bp) with respect to translation start sitec Strand locationd Scorese Sites in EMSA probesf
cchA/cchB* TGGCCGGATT# -425# CS 9.30 +
TGGCGACATT# -254# CS 5.19 +
GGGCCGATTC (G7th) -101 CS 4.99 +
TGGCTCGAAT (C10th) -86 NCS 6.91 +
ramR GTGCCGGTTC -464 NCS 3.37 -
TGGCGCGAAA -384 NCS 6.42 +
CGGCCGAAAA -358 NCS 5.85 +
GGGCGGGTTC -280 NCS 5.08 +
TGGCCAGGAC -279 CS 3.86 +
GGGCGGATAA -184 NCS 3.87 +
TGTCGTGTTC -95 CS 4.83 -
CGGCGGAACA -81 NCS 3.15 -
TGGCCCGAAC -30 CS 7.23 -
SCO0774/SCO0775* CGGCGCGTTC -268 (-226) CS 4.25 -
(i.e. SLI0755/SLI0756) GGACGGGAAC -253 (-211) NCS 3.37 +
GGGCGCGATC -207 (-165) CS 4.53 +
TGGCGCGATC -170 (-128) NCS 6.90 +
CGGCCAGTCT -110 (-68) CS 3.06 +
TGGCCGAACT -84 (-42) CS 6.20 -
CGGCCAGATC -79 (-37) NCS 5.84 -
SCO6197/SCO6198* GGTCCGGACA -499 (-547~) CS 4.98 -
(i.e. SLI6586/SLI6587) TGACCAGAAG -414 (-462~) CS 3.82 +
TGGCCGAGTT -362 (-410~) CS 5.06 +
GTTCCTGCAA -297 (-345~) NCS 3.50 +
GGGCTGAAAC -271 (-319~) NCS 4.77 +
TGGCTGAATT -116 (-164) CS 7.85 +
hyaS TGGCCGGATC -130 (-129) NCS 8.90 +
CGGCCATTTC -124 (-123) CS 3.05 +
TGTCCAGAAG -101 (-100) NCS 4.48 +

aIn silico analysis of the S. coelicolor genome using PREDetector software (version 1.2.3.0, the S. lividans database was not available at the time this analysis was performed) [39] to analyse orthologs of S. lividans AdpA-dependent genes. The S. coelicolor AdpA-binding sites identified were checked for their conservation and location using the S. lividans genome StrepDB database [7] (see legend c).

bGenes are named according to the StrepDB database [7]. *binding sites located between S. coelicolor genes transcribed in the opposite orientation.

cPutative S. coelicolor AdpA-binding sites were found in silico with PREDetector [39]; #putative site located in the upstream from the CDS of cchB. The site location given corresponds to the position of first nucleotide most distant from the translation start point of the first gene named. The positions of some sites are not the same for the S. lividans orthologs as indicated in brackets (S. lividans StrepDB database [7]). ~ putative sites are in the CDS of SLI6587. Predicted CDS diverge between SLI6586 and SLI6587 locus and their orthologs SCO6197 and SCO6198, resulting in a smaller intergenic region in S. lividans.

dCS, coding strand; NCS, non coding strand with reference to the first gene named in the S. coelicolor gene column.

eScores given by PREDetector software for S. coelicolor genes [39].

fSites present (+) or absent (-) in the S. lividans DNA probes used in EMSA experiments.

Guyet et al.

Guyet et al. BMC Microbiology 2014 14:81   doi:10.1186/1471-2180-14-81

Open Data