Curation Information

Publication
Definition of the mycobacterial SOS box and use to identify LexA-regulated genes in Mycobacterium tuberculosis.;Davis EO, Dullaghan EM, Rand L;Journal of bacteriology 2002 Jun; 184(12):3287-95 [12029045]
TF
LexA [I6Y1J7, view regulon]
Reported TF sp.
Mycobacterium tuberculosis H37Rv
Reported site sp.
Mycobacterium tuberculosis H37Rv
Created by
Erill Lab
Curation notes
-

Experimental Process

SOS box is extended by 2bp on both ends to TCGAAC(N)4GTTCGA. This work was done on M. smegmatis, by replacing each base with every other on LexA site on upstream region of recA, measuring the effect on induction followed by DNA damage. New consensus was used to search M. tuberculosis genome, allowing up to 1 mismatch. Microarray analysis was performed on potentially regulated genes that have putative binding sites on upstream region.

Transcription Factor Binding Sites


TCGAACACATGTTCGA
TCGAACACATGTTCGA
TCGAACAATTGTTCGA
TCGAACGTATGTTCGA
TCGAAAGTATGTTCGA
TCGAAAGTATGTTCGA
TCGAACGAATGTGCGA
TCGAACATGTATTCGA
TCGCACACATGTTCGA
TAGAACGGTTGTTCGA
TCGAACAACCGTTCTA
TCGAACGATTGTTCGG
TCGAACACATGTTTGA
TCGAACAGGTGTTCGG
TCGAACATATTTTCGA
TCGAACACATGTTCGA
TCGAACACATGTTCGA
TCGAACAATTGTTCGA
TCGAACGTATGTTCGA
TCGAAAGTATGTTCGA
TCGAAAGTATGTTCGA
TCGAACGAATGTGCGA
TCGAACATGTATTCGA
TCGCACACATGTTCGA
TAGAACGGTTGTTCGA
TCGAACAACCGTTCTA
TCGAACGATTGTTCGG
TCGAACACATGTTTGA
TCGAACAGGTGTTCGG
TCGAACATATTTTCGA

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
TCGAACACATGTTCGA Rv1378c,
... ... Rv1378c Rv1377c Rv1376 Rv1375 pyrR pyrB pyrC Rv1382 carA carB pyrF
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - repressor dimer
TCGAACACATGTTCGA Rv3074,
... ... Rv3074 Rv3073c Rv3072c Rv3075c
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - repressor dimer
TCGAACAATTGTTCGA dnaE2,
... ... dnaE2 Rv3371 otsB2
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - repressor dimer
TCGAACGTATGTTCGA Rv3776,
... ... Rv3776 lipE echA21 Rv3773c hisC2 serU Rv3777 Rv3778c
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - repressor dimer
TCGAAAGTATGTTCGA Rv0336,
... ... Rv0336 PE6 rmlA Rv0333 Rv0332
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - repressor dimer
TCGAAAGTATGTTCGA Rv0515,
... ... Rv0515 Rv0514 Rv0513 hemB Rv0516c
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - repressor dimer
TCGAACGAATGTGCGA Rv1000c,
... ... Rv1000c Rv0999 Rv0998 Rv0997 arcA Rv1002c
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - repressor dimer
TCGAACATGTATTCGA Rv1702c,
... ... Rv1702c Rv1701 Rv1700 pyrG Rv1703c
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - repressor dimer
TCGCACACATGTTCGA Rv2100,
... ... Rv2100 PE21 PE_PGRS36 helZ
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - repressor dimer
TAGAACGGTTGTTCGA Rv2578c,
... ... Rv2578c Rv2577 dhaA
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - repressor dimer
TCGAACAACCGTTCTA dhaA,
... ... dhaA Rv2578c Rv2577
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - repressor dimer
TCGAACGATTGTTCGG ruvC,
... ... ruvC ruvA ruvB PE_PGRS44 vapB40 vapC40
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - repressor dimer
TCGAACACATGTTTGA lexA,
... ... lexA Rv2719c Rv2721c Rv2722 Rv2723 fadE20
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - repressor dimer
TCGAACAGGTGTTCGG recA,
... ... recA recX Rv2735c Rv2734 Rv2737A Rv2738c Rv2739c ephG
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - repressor dimer
TCGAACATATTTTCGA Rv3395c,
... ... Rv3395c Rv3394c Rv3395A
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - repressor dimer