Curation Information

Publication
Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus.;Rodionov DA, Novichkov PS, Stavrovskaya ED, Rodionova IA, Li X, Kazanov MD, Ravcheev DA, Gerasimova AV, Kazakov AE, Kovaleva GY, Permina EA, Laikova ON, Overbeek R, Romine MF, Fredrickson JK, Arkin AP, Dubchak I, Osterman AL, Gelfand MS;BMC genomics 2011 Jun 15; 12 Suppl 1( ):S3 [21810205]
TF
NagR [Q8EBJ8, view regulon]
Reported TF sp.
Shewanella oneidensis MR-1
Reported site sp.
Shewanella oneidensis MR-1
Created by
Sefa Kilic
Curation notes
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Experimental Process

Identification of target genes by comparative genomics analysis. EMSA to show binding. To confirm the regulation, targeted mutagenesis on NagR and qRT-PCR to measure relative transcript levels.

Transcription Factor Binding Sites


AATGACAGCGTTGTCTTT
AATGACAACGCTGTCATT
AATGACAACGCTGTCATC
CATGACAGCGTTGTCATT
TTTGACAACGTTGTCTTT
AATGACAGCGTTGTCTTT
AATGACAACGCTGTCATT
AATGACAACGCTGTCATC
CATGACAGCGTTGTCATT
TTTGACAACGTTGTCTTT

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
AATGACAGCGTTGTCTTT nagP
... ... nagP
Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Site directed mutagenesis (ECO:0005667) - repressor not specified
AATGACAACGCTGTCATT nagK,
... ... nagK nagB nagA nagX
Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Site directed mutagenesis (ECO:0005667) - repressor not specified
AATGACAACGCTGTCATC SO_3510,
... ... SO_3510 hexB SO_4804
Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Site directed mutagenesis (ECO:0005667) - repressor not specified
CATGACAGCGTTGTCATT SO_3514,
... ... SO_3514 SO_3513 SO_3512 nagR
Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Site directed mutagenesis (ECO:0005667) - repressor not specified
TTTGACAACGTTGTCTTT SO_1071,
... ... SO_1071 gbpA
Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Site directed mutagenesis (ECO:0005667) - repressor not specified