Curation Information

Publication
Response to copper stress in Streptomyces lividans extends beyond genes under direct control of a copper-sensitive operon repressor protein (CsoR).;Dwarakanath S, Chaplin AK, Hough MA, Rigali S, Vijgenboom E, Worrall JA;The Journal of biological chemistry 2012 May 18; 287(21):17833-47 [22451651]
TF
CsoR [D6EK73, view regulon]
Reported TF sp.
Streptomyces coelicolor A3(2)
Reported site sp.
Streptomyces lividans 1326
Created by
Erill Lab
Curation notes
-
External databases
Protein Data Bank (4adz) .

Experimental Process

CsoR binding sites in the genome sequence of Streptomyces coelicolor A3(2) were predicted using a comparative genomics approach. Three target sequences were selected for in vitro analyses: AAATACCCCTGGTGGGTATAT, located -42 bp upstream TLS of csoR TTATACCCCCTAGGGGTAAGG, located -25 np upstream TLS of SCO2730 GGGTACCCCCTAGGGGTATAC, located -83 bp upstream TLS of SCO1045 Binding of S. lividans CsoR to these proteins was validated by EMSA using w-t and mutated protein. RNA-seq was performed and all three genes were shown to be induced under copper induction and on a csoR- background. Expression of csoR, not apparent in RNA-seq was confirmed to be CsoR/copper mediated by promoter probing with a undecylprodigiosin (redD) reporter assay.

Transcription Factor Binding Sites


AAATACCCCTGGTGGGTATAT
TTATACCCCCTAGGGGTAAGG
GGGTACCCCCTAGGGGTATAC
AAATACCCCTGGTGGGTATAT
TTATACCCCCTAGGGGTAAGG
GGGTACCCCCTAGGGGTATAC

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
AAATACCCCTGGTGGGTATAT SCO4136,
... ... SCO4136 SCO4137 SCO4138
Experimental technique details EMSA (ECO:0001807) - Experimental technique details RNA-Seq (ECO:0005664) - Experimental technique details undecylprodigiosin (redD) reporter assay - repressor tetramer
TTATACCCCCTAGGGGTAAGG SCO2730, SCO2731,
... ... SCO2730 SCO2731 SCO2729
Experimental technique details EMSA (ECO:0001807) - Experimental technique details RNA-Seq (ECO:0005664) - repressor tetramer
GGGTACCCCCTAGGGGTATAC SCO1045, SCO1046,
... ... SCO1045 SCO1046 SCO1044
Experimental technique details EMSA (ECO:0001807) - Experimental technique details RNA-Seq (ECO:0005664) - repressor tetramer