Curation Information

Publication
Detailed analysis of Helicobacter pylori Fur-regulated promoters reveals a Fur box core sequence and novel Fur-regulated genes.;Pich OQ, Carpenter BM, Gilbreath JJ, Merrell DS;Molecular microbiology 2012 Jun; 84(5):921-41 [22507395]
TF
Fur [B5Z6G7, view regulon]
Reported TF sp.
Helicobacter pylori G27
Reported site sp.
Helicobacter pylori G27
Created by
Dinara Sagitova
Curation notes
-

Experimental Process

Putative Fur binding sites were identified by genome-wide search using Genamics Expression Software. Specific binding of Fur and the Fur boxes was shown via EMSA. Fur-regulated expression was confirmed by using cat reporter system. Additionally, introduction of a Fur box in the promoter region of a gene otherwise non-Fur-regulated cause this gene to exhibit Fur-dependent regulation.

Transcription Factor Binding Sites


TAAAAAGCATTATTA
TAATAATGCTTTTTA
TAAAAATGATTATTC
TAATCATAATAATTA
TAATTATTATTTTTA
TAATAATGGTTATTA
TAATAATTATTTTTA
TAATTATAATGATTA
TAATAATAATTATCA
TAATAACGATTATTG
CAAAAATCATTATTA
TAAAAAGCATTATTA
TAATAATGCTTTTTA
TAAAAATGATTATTC
TAATCATAATAATTA
TAATTATTATTTTTA
TAATAATGGTTATTA
TAATAATTATTTTTA
TAATTATAATGATTA
TAATAATAATTATCA
TAATAACGATTATTG
CAAAAATCATTATTA

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
TAAAAAGCATTATTA
... ... HPG27_51 putP HPG27_49 HPG27_48 HPG27_52
Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Site directed mutagenesis (ECO:0005667) - repressor dimer
TAATAATGCTTTTTA
... ... HPG27_51 putP HPG27_49 HPG27_48 HPG27_52
Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Site directed mutagenesis (ECO:0005667) - repressor dimer
TAAAAATGATTATTC
... ... HPG27_199 HPG27_200 HPG27_201 HPG27_202
Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Site directed mutagenesis (ECO:0005667) - repressor dimer
TAATCATAATAATTA
... ... HPG27_272 HPG27_271 HPG27_270 HPG27_269 HPG27_268 amiE
Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Site directed mutagenesis (ECO:0005667) - repressor dimer
TAATTATTATTTTTA
... ... HPG27_444 hofC
Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Site directed mutagenesis (ECO:0005667) - repressor dimer
TAATAATGGTTATTA fecA,
... ... fecA fliP glmU feoB
Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Site directed mutagenesis (ECO:0005667) - repressor dimer
TAATAATTATTTTTA HPG27_763,
... ... HPG27_763 HPG27_762 acpS fliL HPG27_766 HPG27_767
Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Site directed mutagenesis (ECO:0005667) - repressor dimer
TAATTATAATGATTA
... ... HPG27_825 HPG27_826
Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Site directed mutagenesis (ECO:0005667) - repressor dimer
TAATAATAATTATCA HPG27_830,
... ... HPG27_830 HPG27_829 ruvC
Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Site directed mutagenesis (ECO:0005667) - repressor dimer
TAATAACGATTATTG
... ... HPG27_1063 HPG27_1062 flgK HPG27_1065
Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Site directed mutagenesis (ECO:0005667) - repressor dimer
CAAAAATCATTATTA
... ... HPG27_1518 HPG27_1517 HPG27_1516 HPG27_1515 HPG27_1514 metN HPG27_1512 HPG27_1511 HPG27_1519 pdxA
Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Site directed mutagenesis (ECO:0005667) - repressor dimer