Curation Information

Publication
CcpA ensures optimal metabolic fitness of Streptococcus pneumoniae.;Carvalho SM, Kloosterman TG, Kuipers OP, Neves AR;PloS one 2011; 6(10):e26707 [22039538]
TF
CcpA [A0A0H2ZQ65, view regulon]
Reported TF sp.
Streptococcus pneumoniae D39
Reported site sp.
Streptococcus pneumoniae D39
Created by
Elliot White
Curation notes
-

Experimental Process

Researchers used a consensus search of the CRE box (CcpA binding site) in the pneumoniae genome to compile a list of genes with CRE boxes in the promoter. They then cross-referenced that list with the results (trimmed to only significant results) of a DNA-array that compared wt to a CcpA deletion.

Transcription Factor Binding Sites


ATGAAAGCGCAAACTT
ACAAAAACGCTTACAT
TGGAAAAGGCTTTCTT
ATGAAATCGGTATCTT
TTGACAACGGTTTCAT
AAGCAAACGCTTACTT
ACGAAAACGTTTGCAC
AAGTAATCGCTTTCTT
CAGAAAACGCTTCCTA
TATAAAGCGTTTTCAT
ATGAAATCGCATACAA
ATGAAACCGTTTCCTT
GTGTAATCGTTTTCTT
TATAAAACGTTTTCAA
ATGAAACTGTTTACAA
TAGAAAGCGTTTTCTT
AAGAAAGCGCTTTATT
ATGAAAGCGCAAACTT
ACAAAAACGCTTACAT
TGGAAAAGGCTTTCTT
ATGAAATCGGTATCTT
TTGACAACGGTTTCAT
AAGCAAACGCTTACTT
ACGAAAACGTTTGCAC
AAGTAATCGCTTTCTT
CAGAAAACGCTTCCTA
TATAAAGCGTTTTCAT
ATGAAATCGCATACAA
ATGAAACCGTTTCCTT
GTGTAATCGTTTTCTT
TATAAAACGTTTTCAA
ATGAAACTGTTTACAA
TAGAAAGCGTTTTCTT
AAGAAAGCGCTTTATT

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
ATGAAAGCGCAAACTT bgaC,
... ... bgaC SPD_0064 SPD_0069 SPD_0068 SPD_0067 SPD_0066
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator dimer
ACAAAAACGCTTACAT SPD_0093,
... ... SPD_0093 SPD_0094 SPD_0096 SPD_0095
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator dimer
TGGAAAAGGCTTTCTT SPD_0265,
... ... SPD_0265 SPD_0266
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator dimer
ATGAAATCGGTATCTT ilvB,
... ... ilvB SPD_0403 SPD_0402 ilvH
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator dimer
TTGACAACGGTTTCAT SPD_0559,
... ... SPD_0559 SPD_0561 SPD_0560 prtA
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator dimer
AAGCAAACGCTTACTT lctO,
... ... lctO lysS
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator dimer
ACGAAAACGTTTGCAC exp5,
... ... exp5 ftsX prfB ftsE
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator dimer
AAGTAATCGCTTTCTT SPD_1010,
... ... SPD_1010 SPD_1011 serB eno
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator dimer
CAGAAAACGCTTCCTA SPD_1075,
... ... SPD_1075 srtA gyrA
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator dimer
TATAAAGCGTTTTCAT SPD_1409,
... ... SPD_1409 SPD_1410
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator dimer
ATGAAATCGCATACAA SPD_1496,
... ... SPD_1496 SPD_1495 nanE-1
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator dimer
ATGAAACCGTTTCCTT SPD_1610,
... ... SPD_1610 SPD_1609 SPD_1611 galE-2 galT-1 SPD_1614
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator dimer
GTGTAATCGTTTTCTT galK,
... ... galK galT-2 galR SPD_1636 SPD_1637
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator dimer
TATAAAACGTTTTCAA pflA,
... ... pflA lysA
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator dimer
ATGAAACTGTTTACAA SPD_1834,
... ... SPD_1834 SPD_1835 SPD_1836 SPD_1837 yajC
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator dimer
TAGAAAGCGTTTTCTT SPD_1978,
... ... SPD_1978 arcC SPD_1979
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator dimer
AAGAAAGCGCTTTATT glpK,
... ... glpK glpO SPD_2014
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator dimer