Curation Information

Publication
Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens.;Leang C, Krushkal J, Ueki T, Puljic M, Sun J, Juárez K, Núñez C, Reguera G, DiDonato R, Postier B, Adkins RM, Lovley DR;BMC genomics 2009 Jul 22; 10():331 [19624843]
TF
RpoN [Q74BZ1, view regulon]
Reported TF sp.
Geobacter sulfurreducens strain DL1
Reported site sp.
Geobacter sulfurreducens strain DL1
Created by
Erill Lab
Curation notes
-

Experimental Process

RpoN sites predicted with PromScan. DNA array with w-t and overexpressed RpoN (rpoN mutant was not viable). Further validation of expression with primer extension.

Transcription Factor Binding Sites


TGGCATTTCGGTTGCA
TGGTATCCCCCTTGCT
AGGCAGACTATTTGCT
TGGCACAATGCTTGCC
TGGCACGTGGGGTGCA
TGGCACATAACATGCT
TGGCATTTCGGTTGCA
TGGTATCCCCCTTGCT
AGGCAGACTATTTGCT
TGGCACAATGCTTGCC
TGGCACGTGGGGTGCA
TGGCACATAACATGCT

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
TGGCATTTCGGTTGCA fliL,
... ... fliL flgE fliM fliN fliO fliP fliQ fliR flhB GSU0427
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGTATCCCCCTTGCT dcuB,
... ... dcuB GSU2750 GSU2749 GSU2748 GSU2747 GSU2746 GSU2753
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
AGGCAGACTATTTGCT glnB,
... ... 2000000 glnB glnA GSU1834 trpS scpA scpB GSU1830 GSU1829 GSU1828 nadB GSU1837 hrpB GSU1839 GSU1840 GSU1841 GSU1842
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCACAATGCTTGCC fdnG, fdnI, fdnT,
... ... fdnG fdnI fdnT GSU0776 GSU0775 GSU0774 GSU0773 GSU0772 fdnH fdhD/mobA-2
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCACGTGGGGTGCA nifEN,
... ... nifEN nifX fdxN nifB draT GSU2801 draG ycbK
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCACATAACATGCT flgJ, flgM, flgN, flgK, flgL, csrA,
... ... flgJ flgM flgN flgK flgL csrA fliW flgI flgH flgA flgG flgF fliA flhG flhF flhA
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified