Curation Information

Publication
Novel regulatory cascades controlling expression of nitrogen-fixation genes in Geobacter sulfurreducens.;Ueki T, Lovley DR;Nucleic acids research 2010 Nov; 38(21):7485-99 [20660485]
TF
GnfM [Q74EF9, view regulon]
Reported TF sp.
Geobacter sulfurreducens DL1
Reported site sp.
Geobacter sulfurreducens DL1
Created by
Erill Lab
Curation notes
-

Experimental Process

Homologs of the NtrC family were cloned and used in EMSA against known nitrogen fixation gene RpoN-dependent promoters. This identified GnfM. The specific binding site for GnfM was identified by DNAse footprinting. Functionality was validated by site-directed mutagenesis in conjunction with beta-gal assays under inducing conditions (NH4Cl).

Transcription Factor Binding Sites


TGCTGAAATATTGGGCA
TGATTGAAAAAGCGGCA
TGCCGATAAATCAGGCA
TGCCCACCTCAACATCA
TGCACAGTTTTGGTGCA
TGCATAAAATGCAGGCA
TGCTGAAATATTGGGCA
TGATTGAAAAAGCGGCA
TGCCGATAAATCAGGCA
TGCCCACCTCAACATCA
TGCACAGTTTTGGTGCA
TGCATAAAATGCAGGCA

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
TGCTGAAATATTGGGCA gnfK,
... ... gnfK amtB glnK GSU0938 hisN GSU0943
Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) - activator monomer
TGATTGAAAAAGCGGCA gnfK,
... ... gnfK amtB glnK GSU0938 hisN GSU0943
Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) - activator monomer
TGCCGATAAATCAGGCA gdhA,
... ... gdhA GSU1306 ftn GSU1308
Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) - activator monomer
TGCCCACCTCAACATCA gdhA,
... ... gdhA GSU1306 ftn GSU1308
Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) - activator monomer
TGCACAGTTTTGGTGCA gdhA,
... ... gdhA GSU1306 ftn GSU1308
Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) - activator monomer
TGCATAAAATGCAGGCA gdhA,
... ... gdhA GSU1306 ftn GSU1308
Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) - activator monomer