Curation Information

Publication
Inventory and functional analysis of the large Hrp regulon in Ralstonia solanacearum: identification of novel effector proteins translocated to plant host cells through the type III secretion system.;Cunnac S, Occhialini A, Barberis P, Boucher C, Genin S;Molecular microbiology 2004 Jul; 53(1):115-28 [15225308]
TF
HrpB [P31778, view regulon]
Reported TF sp.
Ralstonia solanacearum GMI1000
Reported site sp.
Ralstonia solanacearum GMI1000
Created by
Erill Lab
Curation notes
-

Experimental Process

hrpB-dependent gene expression of studied genes was determined by measuring the b-galactosidase activity generated by the gene reporter fusions in strains GMI1000 (wild type) and GMI1525 (hrpB mutant) in minimal medium inducing conditions. This analysis revealed that 48 new genes are regulated by hrpB. In several cases, the ratio of b-galactosidase activity in the parental strain versus the hrpB mutant was inferior to threefold, so the expression of the corresponding genes was monitored in the presence of the pAM5 plasmid, which carries a constitutively expressed hrpB gene. pAM5 significantly induced the expression of these transcriptional fusions, thus confirming that the corresponding genes are genuine brg genes. Several brg genes identified above appear to be organized in operons (brg 3–4, brg 26–27, brg 41–42). In order to confirm that some of these neighbouring brg genes were transcribed from a single promoter, RT-PCR analysis was performed, which showed that both the brg40–brg41 and the hrpY–brg3–brg4 genes are organized in operons driven by the brg40 and hrpY promoters. Consensus search for putative HrpB-binding sites had been performed in a previous paper (PMID: 15060033).

Transcription Factor Binding Sites


TTCGCTTTGAGGTCGGCAACTTCGC
TTCGTCCCGCGCACGGGACATTCGG
TTCGGCGGGGGCGCCGGCCCTTCGC
TTCGCTCGCCGGTCTAGTGCTTCGC
TTCGGGCCAAATGCGAAACCTTCGC
TTCGCAATCCCCAACATTGTTTCGC
TTCGCCGTTCAGGCCGCGGGTTCGC
TTCGTTTTCCAGCTCGAGTGTTCGG
TTCGCGAACGGAGACCACTTTTCGC
TTCGGGCCGGGCCCGATTTCTTCGC
TTCGCACCGGCGCGCACAACTTCGC
TTCGTTTTGTGATGTGCCGCTTCGG
TTCGCATCACCCTTCATTTCTTCGC
TTCGCAAGGCGGGCGAGGAGTTCGG
TTCGCACGGGGCCTCCCCAATTCGC
TTCGCTCGGCACAACAAGACTTCGC
TTCGCATCTTAACGCATAACTTCGC
TTCGGTTCGGGCACGACTGCTTCGC
TTCGCCGGCAGCGCGTCCGGTTCGA
TTCGCTGCCGGAGGCAGGGCTTCGT
TTCGCCTGTTGCCGTGTTTTTTCGT
TTCGTTTGCCGGCAGCTTCTTTCGT
TTCGTACCTGTCCTCAATGTTTCGC
TTCGCATACGCGCACATCCTTTCGC
TTCGTCCAAAGCGTTCGCGGTTCGG
TTCGCTTTTGGATGCGGCGCTTCGT
TTCGGTCGCCGCGCGGGCATTTCGC
TTCGCCCGAACGGCAGCGCGTTCGC
TTCGGGCGGCGAACCGATCATTCGT
TTCGTCACCGGGCCGCCACTTTCGC
TTCGCCCGCGGCCACCGGGCTTCGC
TTCGTTTATGCGAGCACATTTTCGG
TTCGCGGATGGACAACGCGCTTCGC
TTCGCTCGCCGGTCTAGTGCTTCGC
TTCGCGCGGGCCCGCAGATTTTCGT
TTCGCCCCCGGCCCCATCCATTCGC
TTCGCGGCGGGCGACACCGGTTCGT
TTCGCCAACGCAGCCAGTTTTTCGC
TTCGTGTTAGCTGTGAAAGCTTCGC
TTCGCTTTGAGGTCGGCAACTTCGC
TTCGTCCCGCGCACGGGACATTCGG
TTCGGCGGGGGCGCCGGCCCTTCGC
TTCGCTCGCCGGTCTAGTGCTTCGC
TTCGGGCCAAATGCGAAACCTTCGC
TTCGCAATCCCCAACATTGTTTCGC
TTCGCCGTTCAGGCCGCGGGTTCGC
TTCGTTTTCCAGCTCGAGTGTTCGG
TTCGCGAACGGAGACCACTTTTCGC
TTCGGGCCGGGCCCGATTTCTTCGC
TTCGCACCGGCGCGCACAACTTCGC
TTCGTTTTGTGATGTGCCGCTTCGG
TTCGCATCACCCTTCATTTCTTCGC
TTCGCAAGGCGGGCGAGGAGTTCGG
TTCGCACGGGGCCTCCCCAATTCGC
TTCGCTCGGCACAACAAGACTTCGC
TTCGCATCTTAACGCATAACTTCGC
TTCGGTTCGGGCACGACTGCTTCGC
TTCGCCGGCAGCGCGTCCGGTTCGA
TTCGCTGCCGGAGGCAGGGCTTCGT
TTCGCCTGTTGCCGTGTTTTTTCGT
TTCGTTTGCCGGCAGCTTCTTTCGT
TTCGTACCTGTCCTCAATGTTTCGC
TTCGCATACGCGCACATCCTTTCGC
TTCGTCCAAAGCGTTCGCGGTTCGG
TTCGCTTTTGGATGCGGCGCTTCGT
TTCGGTCGCCGCGCGGGCATTTCGC
TTCGCCCGAACGGCAGCGCGTTCGC
TTCGGGCGGCGAACCGATCATTCGT
TTCGTCACCGGGCCGCCACTTTCGC
TTCGCCCGCGGCCACCGGGCTTCGC
TTCGTTTATGCGAGCACATTTTCGG
TTCGCGGATGGACAACGCGCTTCGC
TTCGCTCGCCGGTCTAGTGCTTCGC
TTCGCGCGGGCCCGCAGATTTTCGT
TTCGCCCCCGGCCCCATCCATTCGC
TTCGCGGCGGGCGACACCGGTTCGT
TTCGCCAACGCAGCCAGTTTTTCGC
TTCGTGTTAGCTGTGAAAGCTTCGC

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
TTCGCTTTGAGGTCGGCAACTTCGC RS_RS21155
... ... RS_RS21155
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGTCCCGCGCACGGGACATTCGG RS_RS21185,
... ... RS_RS21185 RS_RS21190 RS_RS21195
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGGCGGGGGCGCCGGCCCTTCGC RS_RS21135
... ... RS_RS21135
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
TTCGCTCGCCGGTCTAGTGCTTCGC RS_RS07415, RS_RS07420
... ... RS_RS07415 RS_RS07420
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGGGCCAAATGCGAAACCTTCGC RS_RS04330,
... ... RS_RS04330 RS_RS25165
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGCAATCCCCAACATTGTTTCGC RS_RS18605
... ... RS_RS18605
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGCCGTTCAGGCCGCGGGTTCGC RS_RS16880
... ... RS_RS16880
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGTTTTCCAGCTCGAGTGTTCGG RS_RS16095, RS_RS16100,
... ... RS_RS16095 RS_RS16100 RS_RS16090 RS_RS16085
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGCGAACGGAGACCACTTTTCGC RS_RS18700,
... ... RS_RS18700 RS_RS18705 RS_RS18710 RS_RS18715 RS_RS18720
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGGGCCGGGCCCGATTTCTTCGC RS_RS16485,
... ... RS_RS16485 RS_RS16480 RS_RS16490
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGCACCGGCGCGCACAACTTCGC
... ... RS_RS19880
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
TTCGTTTTGTGATGTGCCGCTTCGG RS_RS23330
... ... RS_RS23330
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGCATCACCCTTCATTTCTTCGC RS_RS18175
... ... RS_RS18175
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGCAAGGCGGGCGAGGAGTTCGG RS_RS06765
... ... RS_RS06765
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGCACGGGGCCTCCCCAATTCGC RS_RS17905
... ... RS_RS17905
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGCTCGGCACAACAAGACTTCGC RS_RS01205
... ... RS_RS01205
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGCATCTTAACGCATAACTTCGC RS_RS18200,
... ... RS_RS18200 RS_RS18195
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGGTTCGGGCACGACTGCTTCGC RS_RS21155
... ... RS_RS21155
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGCCGGCAGCGCGTCCGGTTCGA RS_RS20340,
... ... RS_RS20340 RS_RS20345 RS_RS20350 RS_RS20355
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGCTGCCGGAGGCAGGGCTTCGT RS_RS09085
... ... RS_RS09085
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGCCTGTTGCCGTGTTTTTTCGT RS_RS06800
... ... RS_RS06800
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGTTTGCCGGCAGCTTCTTTCGT RS_RS06805
... ... RS_RS06805
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGTACCTGTCCTCAATGTTTCGC RS_RS22070,
... ... RS_RS22070 RS_RS22065
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGCATACGCGCACATCCTTTCGC RS_RS17625
... ... RS_RS17625
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGTCCAAAGCGTTCGCGGTTCGG RS_RS21180
... ... RS_RS21180
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGCTTTTGGATGCGGCGCTTCGT RS_RS21170
... ... RS_RS21170
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGGTCGCCGCGCGGGCATTTCGC RS_RS21340,
... ... RS_RS21340 RS_RS21335
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGCCCGAACGGCAGCGCGTTCGC RS_RS21370
... ... RS_RS21370
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGGGCGGCGAACCGATCATTCGT RS_RS11845
... ... RS_RS11845
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGTCACCGGGCCGCCACTTTCGC RS_RS22055,
... ... RS_RS22055 RS_RS22050
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGCCCGCGGCCACCGGGCTTCGC RS_RS22105
... ... RS_RS22105
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGTTTATGCGAGCACATTTTCGG RS_RS20625
... ... RS_RS20625
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGCGGATGGACAACGCGCTTCGC RS_RS16390,
... ... RS_RS16390 RS_RS16385
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGCTCGCCGGTCTAGTGCTTCGC RS_RS07415,
... ... RS_RS07415 RS_RS07420
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
TTCGCGCGGGCCCGCAGATTTTCGT RS_RS23800,
... ... RS_RS23800 RS_RS23805 RS_RS23810
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGCCCCCGGCCCCATCCATTCGC RS_RS22570,
... ... RS_RS22570 RS_RS22565 RS_RS22560 RS_RS22555
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGCGGCGGGCGACACCGGTTCGT RS_RS24155,
... ... RS_RS24155 RS_RS24160
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGCCAACGCAGCCAGTTTTTCGC RS_RS03050,
... ... RS_RS03050 RS_RS03045 RS_RS03040
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified
TTCGTGTTAGCTGTGAAAGCTTCGC RS_RS15945
... ... RS_RS15945
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - activator not specified