Curation Information

Publication
Identification of novel HrpXo regulons preceded by two cis-acting elements, a plant-inducible promoter box and a -10 box-like sequence, from the genome database of Xanthomonas oryzae pv. oryzae.;Furutani A, Nakayama T, Ochiai H, Kaku H, Kubo Y, Tsuge S;FEMS microbiology letters 2006 Jun; 259(1):133-41 [16684113]
TF
HrpX [Q9ZIP8, view regulon]
Reported TF sp.
Xanthomonas oryzae pv. oryzae T7174R
Reported site sp.
Xanthomonas oryzae pv. oryzae T7174R
Created by
Dinara Sagitova
Curation notes
-

Experimental Process

15 ORFs preceded by a PIP box like sequence were identified by searching the X. oryzae genome with the PIP consensus. GUS reporter assays confirmed HrpX-dependent regulation under hrp-inducing conditions in nine of these genes. GUS reporter assays in conjunction with site-directed mutagenesis verified the importance of the putative PIP boxes in three representative HrpX-regulated genes.

Transcription Factor Binding Sites


TTCGCTTGCCCGTTAAGTGTTTCGT
TTCGTTTACGGAATCGCTTGTTCGT
TTCGCAAGTTCTGCAGCTTTTTCGG
TTCGCTTTGCGTCGCTTTACTTCGT
TTCGCCAGGAGACGCGTAACTGCGG
TTCGGACTGCGCGACGCCGGTTCGC
TTCGTCGCCGCACACAGGAATTCAC
TTCGCCATTGATGACAGAATTTCAC
TTCGCTTGCCCGTTAAGTGTTTCGT
TTCGTTTACGGAATCGCTTGTTCGT
TTCGCAAGTTCTGCAGCTTTTTCGG
TTCGCTTTGCGTCGCTTTACTTCGT
TTCGCCAGGAGACGCGTAACTGCGG
TTCGGACTGCGCGACGCCGGTTCGC
TTCGTCGCCGCACACAGGAATTCAC
TTCGCCATTGATGACAGAATTTCAC

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 Gene diagram Experimental techniques TF function TF type
TTCGCTTGCCCGTTAAGTGTTTCGT XOO_0080,
... ... XOO_0080 XOO_0081
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details GUS reporter gene assay (ECO:0005641) - activator monomer
TTCGTTTACGGAATCGCTTGTTCGT XOO_1669,
... ... XOO_1669 XOO_1668 XOO_1667
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details GUS reporter gene assay (ECO:0005641) - activator monomer
TTCGCAAGTTCTGCAGCTTTTTCGG XOO_2877
... ... XOO_2877
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details GUS reporter gene assay (ECO:0005641) - activator monomer
TTCGCTTTGCGTCGCTTTACTTCGT XOO_2967,
... ... XOO_2967 XOO_2966
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details GUS reporter gene assay (ECO:0005641) - activator monomer
TTCGCCAGGAGACGCGTAACTGCGG XOO_3844
... ... XOO_3844
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details GUS reporter gene assay (ECO:0005641) - Experimental technique details Site directed mutagenesis (ECO:0005667) - activator monomer
TTCGGACTGCGCGACGCCGGTTCGC XOO_4134
... ... XOO_4134
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details GUS reporter gene assay (ECO:0005641) - activator monomer
TTCGTCGCCGCACACAGGAATTCAC XOO_4208,
... ... XOO_4208 XOO_4209
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details GUS reporter gene assay (ECO:0005641) - Experimental technique details Site directed mutagenesis (ECO:0005667) - activator monomer
TTCGCCATTGATGACAGAATTTCAC XOO_4259,
... ... XOO_4259 XOO_4258
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details GUS reporter gene assay (ECO:0005641) - activator monomer