Curation Information

Publication
Identification of novel hrp-regulated genes through functional genomic analysis of the Pseudomonas syringae pv. tomato DC3000 genome.;Zwiesler-Vollick J, Plovanich-Jones AE, Nomura K, Bandyopadhyay S, Joardar V, Kunkel BN, He SY;Molecular microbiology 2002 Sep; 45(5):1207-18 [12207690]
TF
HrpL [G3XDC4, view regulon]
Reported TF sp.
Pseudomonas syringae pv. tomato str. DC3000
Reported site sp.
Pseudomonas syringae pv. tomato str. DC3000
Created by
Erill Lab
Curation notes
-

Experimental Process

Computational search of HrpL binding sites was validated by DNA array analysis or Northern blot analysis using DC3000 (WT) and hrpL (L–) mutants in hrp-inducing medium.

Transcription Factor Binding Sites


TGGAACCAACTTGCACCTTCAACCACACA
TGGAACTGAAATCGATGCTCGACCACTTA
TGGAACCCGCTGGCATTGCATGCCACTCA
GGGAACCGGTCGCTGCGCTTTGCCACTCA
TGGAACCAACTTGCACCTTCAACCACACA
TGGAACTGAAATCGATGCTCGACCACTTA
TGGAACCCGCTGGCATTGCATGCCACTCA
GGGAACCGGTCGCTGCGCTTTGCCACTCA

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
TGGAACCAACTTGCACCTTCAACCACACA hrpK1,
... ... hrpK1 hopB1
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Northern blot (ECO:0005653) - activator not specified
TGGAACTGAAATCGATGCTCGACCACTTA hrpP, hrcU,
... ... hrpP hrcU hrpO hrcQa hrcQb hrcR hrcS hrcT
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Northern blot (ECO:0005653) - activator not specified
TGGAACCCGCTGGCATTGCATGCCACTCA avrE1,
... ... avrE1 hrpH
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Northern blot (ECO:0005653) - activator not specified
GGGAACCGGTCGCTGCGCTTTGCCACTCA hrpW1,
... ... hrpW1 shcM hopM1 shcE
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Northern blot (ECO:0005653) - activator not specified