Curation Information

Publication: Identification and regulation of the N-acetylglucosamine utilization pathway of the plant pathogenic bacterium Xanthomonas campestris pv. campestris.;Boulanger A, Déjean G, Lautier M, Glories M, Zischek C, Arlat M, Lauber E;Journal of bacteriology 2010 Mar; 192(6):1487-97 [20081036]
TF: NagR [Q8P5C9, view regulon]
Reported TF sp.: Xanthomonas campestris pv. campestris str. ATCC 33913
Reported site sp.: Xanthomonas campestris pv. campestris str. ATCC 33913
Created by: Dinara Sagitova
Curation notes: -

Experimental Process

GUS reporter assays identified that the expression of nixA, nixC, nixD, nagK-IIA, and nagK-IIB was derepressed in the ΔnagR deletion mutant compared to the expression in the wild-type strain. The results of these assays were in agreement with the putative NagR boxes in the promoters of these genes. A new NagR consensus sequence (GTTGACARCGYTGTCANC) was identified by the authors based on the alignment of the four predicted NagR boxes. This NagR box differed at positions 1, 2, and 18 from the previously proposed NagR box (AATGACARCGYTGTCATT).

Transcription Factor Binding Sites

GTTGACAACGCTGTCAAC
GTAGACAACGTTGTCAGC
GCTGACAACGTTATCAGC
ATTGACAGCGTTGTCATC

Quantitative data format: PSSM score

GTTGACAACGCTGTCAAC 19.32
GTAGACAACGTTGTCAGC 19.26
GCTGACAACGTTATCAGC 18.72
ATTGACAGCGTTGTCATC 18.27

Gene Regulation

Regulated genes for each binding site are displayed below. Gene regulation diagrams show binding sites, positively-regulated genes, negatively-regulated genes, both positively and negatively regulated genes, genes with unspecified type of regulation. For each indvidual site, experimental techniques used to determine the site are also given.

Site sequence	Regulated genes	Experimental techniques	TF function	TF type
GTTGACAACGCTGTCAAC	glk, iroN	Experimental technique details GUS reporter gene assay (ECO:0005641) GUS reporter gene assay - ECO:0005641 This is a reporter assay technique, used typically to measure expression of a target gene. A promoter of interest is investigated by fusioning it with the reporter gene, which is then monitored. In GUS, the reporter is the β-glucuronidase enzyme from Escherichia coli, capable of transforming non-fluorescent substates into fluorescent, thereby allowing detection. - Experimental technique details Visual sequence inspection (nan) Visual sequence inspection - nan Visual inspection of promoter region to identify putative binding sites based on previous knowledge -	repressor	not specified
GTAGACAACGTTGTCAGC	glk, iroN	Experimental technique details GUS reporter gene assay (ECO:0005641) GUS reporter gene assay - ECO:0005641 This is a reporter assay technique, used typically to measure expression of a target gene. A promoter of interest is investigated by fusioning it with the reporter gene, which is then monitored. In GUS, the reporter is the β-glucuronidase enzyme from Escherichia coli, capable of transforming non-fluorescent substates into fluorescent, thereby allowing detection. - Experimental technique details Visual sequence inspection (nan) Visual sequence inspection - nan Visual inspection of promoter region to identify putative binding sites based on previous knowledge -	repressor	not specified
GCTGACAACGTTATCAGC	fyuA	Experimental technique details GUS reporter gene assay (ECO:0005641) GUS reporter gene assay - ECO:0005641 This is a reporter assay technique, used typically to measure expression of a target gene. A promoter of interest is investigated by fusioning it with the reporter gene, which is then monitored. In GUS, the reporter is the β-glucuronidase enzyme from Escherichia coli, capable of transforming non-fluorescent substates into fluorescent, thereby allowing detection. - Experimental technique details Visual sequence inspection (nan) Visual sequence inspection - nan Visual inspection of promoter region to identify putative binding sites based on previous knowledge -	repressor	not specified
ATTGACAGCGTTGTCATC	glk,	Experimental technique details GUS reporter gene assay (ECO:0005641) GUS reporter gene assay - ECO:0005641 This is a reporter assay technique, used typically to measure expression of a target gene. A promoter of interest is investigated by fusioning it with the reporter gene, which is then monitored. In GUS, the reporter is the β-glucuronidase enzyme from Escherichia coli, capable of transforming non-fluorescent substates into fluorescent, thereby allowing detection. - Experimental technique details Visual sequence inspection (nan) Visual sequence inspection - nan Visual inspection of promoter region to identify putative binding sites based on previous knowledge -	repressor	not specified