Curation Information

Publication
Regulatory targets of quorum sensing in Vibrio cholerae: evidence for two distinct HapR-binding motifs.;Tsou AM, Cai T, Liu Z, Zhu J, Kulkarni RV;Nucleic acids research 2009 May; 37(8):2747-56 [19276207]
TF
HapR [A0A0H3Q915, view regulon]
Reported TF sp.
Vibrio cholerae C6706
Reported site sp.
Vibrio cholerae C6706
Created by
Erill Lab
Curation notes
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Experimental Process

Multiple sequence alignment of aphA, hapR VCA0865, VC0900, VC2370 and VCA0080 orthologs identify two distinct types of sites on different groups of genes: one with variable spacer and another with fixed dimensions. Using PSSM coupled with ad-hoc rules for the variable spacers, putative sites were predicted genome-wide and verified by EMSA. These verified sites were used to build a new PSSM and predict more sites, which were also verified. Lux reporter assays were used to show that bound HapR targets actually repressed/activated downstream genes. For vca0880 type 2 (fixed) motif, site directed mutagenesis and EMSA were carried out and validated the profile obtained through multiple site alignment.

Transcription Factor Binding Sites


TTATTGATATTAGTGTTTATAT
TTATTGAGCGTTTTGTGGGTAA
TTATTGAGAATAATGTCAGTTT
TTATTGATTTTTATGTGCCACA
CTATTGATTATTATGTGAGAAA
TTATTGGTTTTATTGTGGCTTT
TTACTGAGTAGTTTGTGACACG
TAATTGATTATTGTGTAACTAT
CTATTGATAAAGATGTAGTCTT
CTAATGATTATTTTGTTATTTG
TTATTGATATTAGTGTTTATAT
TTATTGAGCGTTTTGTGGGTAA
TTATTGAGAATAATGTCAGTTT
TTATTGATTTTTATGTGCCACA
CTATTGATTATTATGTGAGAAA
TTATTGGTTTTATTGTGGCTTT
TTACTGAGTAGTTTGTGACACG
TAATTGATTATTGTGTAACTAT
CTATTGATAAAGATGTAGTCTT
CTAATGATTATTTTGTTATTTG

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
TTATTGATATTAGTGTTTATAT VCD_000453,
... ... VCD_000453 VCD_000452 VCD_000451 VCD_000450 VCD_000449
Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TTATTGAGCGTTTTGTGGGTAA VCD_000641,
... ... VCD_000641 VCD_000642 VCD_000640 VCD_000639 fbpC
Experimental technique details EMSA (ECO:0001807) - Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TTATTGAGAATAATGTCAGTTT VCD_001716
... ... VCD_001716
Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TTATTGATTTTTATGTGCCACA VCD_003131,
... ... VCD_003131 uvrC VCD_003129 VCD_003132
Experimental technique details EMSA (ECO:0001807) - Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
CTATTGATTATTATGTGAGAAA VCD_002332
... ... VCD_002332
Experimental technique details EMSA (ECO:0001807) - Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TTATTGGTTTTATTGTGGCTTT VCD_001556
... ... VCD_001556
Experimental technique details EMSA (ECO:0001807) - Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TTACTGAGTAGTTTGTGACACG VCD_000466
... ... VCD_000466
Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TAATTGATTATTGTGTAACTAT VCD_000099,
... ... VCD_000099 VCD_000098 VCD_000097 VCD_000096
Experimental technique details EMSA (ECO:0001807) - Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
CTATTGATAAAGATGTAGTCTT VCD_003401,
... ... VCD_003401 VCD_003400 VCD_003399 VCD_003398 VCD_003397 VCD_003396 VCD_003402
Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
CTAATGATTATTTTGTTATTTG
... ... VCD_001024 VCD_001025
Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified