Identified members of the Streptomyces lividans AdpA regulon involved in differentiation and secondary metabolism

Guyet, Aurélie; Benaroudj, Nadia; Proux, Caroline; Gominet, Myriam; Coppée, Jean-Yves; Mazodier, Philippe

doi:10.1186/1471-2180-14-81

Table 3 Genes putatively directly regulated by S. lividans AdpA in liquid rich medium ^a

From: Identified members of the Streptomyces lividans AdpA regulon involved in differentiation and secondary metabolism

Gene^b	Gene^b	Gene^b	Gene name^b	cis-element^c	Score^c	Position^c	Fc^d	Class^e
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.).

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