Table 3

Genes putatively directly regulated by S. lividans AdpA in liquid rich mediuma
Geneb Geneb Geneb Gene nameb cis-elementc Scorec Positionc Fcd Classe
Probably directly activated by S. lividans AdpA:
SCO2921* Detected SGR4618 adbS3-orfa tttgcggaca 4.62 -260 0.196 c. e.
SCO0494 SLI0454 SGR6714 cchF tgtcgcgcca 4.36 -28 0.615 s. m.
SCO0929 SLI1160 SGR710 tggccggacg 5.19 -201 0.419 u. f.
SCO1565 SLI1668 SGR5973 glpQ1 cggccggaac 6.75 -82 0.531 c. e.
SCO1630 SLI1934 SGR1063 cvn9, rarA tgtcgggatc 6.71 -74 0.505 c. e.
SCO1674 SLI1979 SGR5829 chpC cggcggaatc 5.69 -154 0.564 c. e.
SCO1800 SLI2108 SGR5696 chpE cggccggacc 4.69 -65 0.256 c. e.
SCO1968 SLI2284 SGR5556 glpQ2 cattcagcct 3.75 -92 0.537 m. m.
SCO2792 SLI3139 SGR4742 adpA bldH gaaccggcca 8.09 -148 0.383 r.
SCO3323 SLI3667 SGR4151 bldN, adsA gttccggtca 6.38 -469 0.389 r.
SCO3579* SLI3822 SGR3340 wblA tggcccgaac 7.23 -135 0.31 r.
SCO3917* SLI4175 SGR3663 ctttcggcca 6.52 -72 0.504 u. f.
SCO4113 SLI4344 SGR3901 aaacccgtca 5.64 -52 0.568 u. f.
SCO4114* SLI4345 SGR3902 tggcgggatt 8.66 -117 0.487 c. p.
SCO4164 SLI4405 SGR3965 cysA gttgccgcca 5.70 -170 0.483 s. m.
SCO4295* SLI4532 SGR3226 scoF4 attctcgcca 7.13 -193 0.217 c. p.
SCO4761 SLI5031 SGR2770 groES aaccccgccg 3.31 -197 0.401 c. p.
SCO4762 SLI5032 SGR2769 groEL1 ttgccgtata 4.40 -44 0.44 c. p.
SCO4768 SLI5039 SGR2759 bldM aatctagccg 5.52 -292 0.586 r.
SCO5101 SLI5379 SGR2456 cggcgggaac 6.11 -28 0.584 u. f.
SCO6004 SLI6392 SGR1503 cggccgcatt 5.21 -292 0.603 c. e.
SCO6096* SLI6490 SGR1397 catcgcgcca 5.56 -147 0.557 c. e.
SCO7550 SLI7772 - glpQ3 gaaccggtca 5.88 -117 0.334 c. e.
Probably directly repressed by S. lividans AdpA:
SCO1684 SLI1989 SGR5819 gaatgcgcca 5.36 -161 1.626 u. f.
SCO1776* SLI2080 SGR5721 pyrG cttccggcca 7.25 -170 1.744 s. m.
SCO1821 SLI2130 SGR5674 moaA cggcccgaac 5.39 -61 1.679 s. m.
SCO1864 SLI2175 SGR5635 ectA atttcggaca 6.71 -203 2.903 c. p.
SCO1865 SLI2176 SGR5634 ectB cggccgggac 3.24 -78 3.154 c. p.
SCO1867 SLI2178 SGR5632 ectD gaagtggcca 4.62 -3 3.029 n. c.
SCO3123 SLI3480 SGR4383 prsA2 tgaccggaaa 6.21 # 1.891 s. m.
SCO3202 SLI3556 SGR4276 hrdD aatccggaca 7.75 -145 2.499 r.
SCO3811 SLI4062 SGR3768 dacA tatccggacg 5.34 -175 1.628 c. e.
SCO3945 SLI4193 SGR3646 cydA tgtcccgatt 6.39 -88 3.386 s. m.
SCO3947 SLI4195 SGR3644 cydCD catcccgccg 5.08 -30 2.653 s. m.
SCO3971 SLI4220 SGR3620 tggccggtac 7.78 -465 1.631 u. f.
SCO4215 SLI4452 - xlnR gatgaggccg 3.74 -294 1.964 r.
SCO5240 SLI5531 SGR2274 wblE tgtcccgatc 5.99 -170 2.246 u. f.
SCO5862 SLI6134 SGR1670 cutR tggccgaaaa 7.69 -99 1.927 r.
SCO6009 SLI6398 SGR1498 cttccagcca 6.53 -52 1.736 c. p.

aOrthologs of S. lividans AdpA-dependent genes (listed in Additional file 2: Table S2) were analysed in silico using the S. coelicolor genome database (version 1.2.3.0 of PREDetector software [39]). AdpA-binding sites upstream from S. coelicolor genes were identified and are presented in Additional file 5: Table S4. Table 3 presents a selected subset of this complete compilation.

bGene names for S. griseus (SGR) and annotated function are from the StrepDB database [7]. Ortholog gene names were identified using StrepDB. Genes identified in other Streptomyces as being directly AdpA-regulated are in bold, and those described as being AdpA-dependent are italicized [12-15,22]. * Binding sites in the promoters of these genes were identified in silico[22]. The SCO2921-ortholog was not annotated as a S. lividans CDS; however, our microarray data suggest that this CDS exists.

ccis-element, score, and binding site position as determined by analysing S. coelicolor genes with PREDetector [39]. When more than one putative AdpA-binding site was detected, only the one with the highest score was shown here. Other genes putatively directly regulated by S. lividans AdpA are listed in Additional file 5: Table S4. # site found in the SCO3122 CDS at position 1447 (total gene length 1449 nt).

dFold change (Fc) in gene expression in S. lividans adpA mutant relative to the parental strain with P-value < 0.05, as determined by Student’s t-test applying the Benjamini and Hochberg multiple testing correction (details in Additional file 2: Table S2).

eFrom a protein classification scheme for the S. coelicolor genome available on the Welcome Trust Sanger Institute database [37]: unknown function (u. f.), cell process (c. p.), macromolecule metabolism (m. m.), small molecule metabolism (s. m.), cell envelope (c. e.), extrachromosomal (e.), regulation (r.) and not classified (n. c.).

Guyet et al.

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

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