The genome-scale DNA-binding profile of BarR, a β-alanine responsive transcription factor in the archaeon Sulfolobus acidocaldarius

Liu, Han; Wang, Kun; Lindås, Ann-Christin; Peeters, Eveline

doi:10.1186/s12864-016-2890-0

Table 1 Locations of BarR genomic binding regions as determined by ChIP-seq

From: The genome-scale DNA-binding profile of BarR, a β-alanine responsive transcription factor in the archaeon Sulfolobus acidocaldarius

Peak summit coordinate	Growth condition^a	Fold enrich-ment^b	Nearest ORF	Annotation	Peak summit location^c	In vitro binding^d	Predicted binding motif	Gene regulation^e
19904	w/o	N.A./5.3	Saci_0028	Hypothetical protein	intra-5’	N.A.	-	N.A.
46668	both	4.9/8.7	Saci_0061	Lysine arginine ornithine transport system kinase	intra-3’	++	+	-
554848	w/o	N.A./4.4	Saci_0695	Translation initiation factor IF-2	intra	N.A.	+	N.A.
577211	both	4.8/12.7	Saci_0720	Nicotinamide-nucleotide adenylyltransferase	intra-5’ (operon)	+	+	N.A.
674867	both	11.1/13.8	Saci_0839	Reverse gyrase	intra	++	+	-
676039	w/o	N.A./4.3	Saci_0839	Reverse gyrase	intra	N.A.	+	N.A.
850922	w	4.2/N.A.	Saci_1050	ParA, chromosome partitioning ATPase	intra-5’	+	+	-
918486	both	3.6/5.4	Saci_1115	Alcohol dehydrogenase	intra	+	+	N.A.
999186	both	4.0/11.9	Saci_1182	Major facilitator superfamily permease	intra	N.A.	+	N.A.
1421788	both	3.0/7.3	Saci_1664	Protein kinase	intra	N.A.	+	N.A.
1431591	w/o	N.A./5.5	Saci_1674	Gluconolactonase	intra-5’	++	+	-
1563444	w/o	N.A./3.7	Saci_1796	Hypothetical protein	intra-3’	N.A.	+	N.A.
1563826	w/o	N.A./9.2	Saci_1796	Hypothetical protein	inter-3’	++	+	-
1598826	w	3.9/N.A.	Saci_1833	Hypothetical protein	intra-3’	N.A.	+	N.A.
1773917	w/o	N.A./5.8	Saci_1964	Hypothetical protein	intra-5’	N.A.	+	N.A.
1840150	w/o	N.A./4.4	Saci_2025	ATPase	inter-3’	N.A.	+	N.A.
1889870	w/o	N.A./6.4	Saci_2073	Major facilitator superfamily permease	inter-3’	N.A.	+	N.A.
1964012	w/o	N.A./3.6	Saci_2136	BarR	intra-3’	+*	+	+*
1964490	both	4.3/6.6	Saci_2137	Aminotransferase	inter-5’	+*	+	+*
2000304	w/o	N.A./3.7	Saci_2166	Uroporphyrin-III methyltransferase	intra-5’	N.A.	+	N.A.
2166455	both	2.2/7.2	Saci_2319	Hypothetical protein	inter	++	+	+**

^aGrowth condition in which the binding region was detected above the significance level: both = detected in absence and presence of exogenously added β-alanine, w = detected only in the presence of β-alanine, w/o = detected only in the absence of β-alanine, ^bfold-enrichment value in the presence of β-alanine/in the absence of β-alanine against input sample, ^clocation of the peak summit with respect to the nearest gene: intra = intragenic, inter = intergenic, 5’ = within 150 bp (intragenic) or 300 bp (intergenic) of the 5’ end of the gene, 3’ = within 150 bp (intragenic) or 300 bp (intergenic) of the 3’ end of the gene. “Operon” means that the gene for which the peak summit is located within 150 bp of the 5’ end, is a second or next gene that is part of an operon, ^dEMSA results, with “+” indicating the observation of binding and “++” indicating the observation of high-affinity binding, ^eqRT-PCR results. N.A. = not analyzed; an asterisk indicates that this result was previously published [17]; a double asterisk indicates that it is not the nearest ORF that is regulated. All gene annotations were manually curated

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ISSN: 1471-2164

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