Curation Information

Publication
The CcpA regulon of Streptococcus suis reveals novel insights into the regulation of the streptococcal central carbon metabolism by binding of CcpA to two distinct binding motifs.;Willenborg J, de Greeff A, Jarek M, Valentin-Weigand P, Goethe R;Molecular microbiology 2014 Apr; 92(1):61-83 [24673665]
TF
CcpA [G5L2G2, view regulon]
Reported TF sp.
Streptococcus suis strain 10
Reported site sp.
Streptococcus suis strain 10
Created by
Dinara Sagitova
Curation notes
-

Experimental Process

Comparison of the transcriptome of the S.?suis wild-type strain 10 and strain 10?ccpA by DNA microarray revealed that 389 genes were differentially expressed. CcpA binding sites in the glgC and arcA promoters were identified by the Virtual Footprint software with the B.subtilis cre consensus sequence. EMSA demonstrated that CcpA binds specifically to the promoter regions of the genes containing a putative CcpA binding site. Site-directed mutagenesis showed that this binding was abolished when two nucleotide substitutions were introduced into the binding sites. GFP promoter fusion assays in the wild type S.suis and the ccpA mutant strains with wild-type and mutated CcpA binding sites showed that carbon catabolite repression of the glgC gene but not of the arcA was directly attributed to CcpA. CcpA regulon in vivo was identified by ChIP-Seq analysis. MEME software was used to identify CcpA consensus sequence in 115 ChIP-positive DNA regions.

ChIP assay conditions
For ChIP analysis the wild-type strain 10, strain 10ΔccpA and strain c10ΔccpA were grown in THB media to early exp and early stat growth phase. The in vivo cross-linking of the cultures was done with 0.15 mM EGS [ethylene glycol bis(succinic acid N-hydroxysuccinimide ester)] for 30 min followed by 1% (v/v) formaldehyde for 8 min, and afterwards quenched by addition of glycine in a final concentration of 0.125 molar at room temperature.
ChIP notes
ChIP and ChIP-qPCR was performed as described in Supplementary methods. ChIP-Sequencing libraries were prepared from 10 ng of immunoprecipitated DNA with the Illumina ChIP-Seq DNA Sample Prep Kit according to the Illumina instructions. Briefly, DNA was fragmented using the Covaris S2 system, the overhangs resulting from fragmentation were converted into blunt ends, an A-base was added to the 3′ end of the blunt phosphorylated DNA fragments, and adapters were ligated to the ends of the DNA fragments. The Illumina Cluster Station hybridized the fragments onto the flow cell and amplified them for sequencing on the Genome Analyzer IIx. The Genome Analyzer sequenced clustered template DNA using a robust four-colour DNA Sequencing-By-Synthesis (SBS) technology. Fragments were sequenced by 36 bp single end. The fluorescent images were processed to sequences using the Illumina Genome Analyzer Pipeline Analysis software 1.8. The sequence output (36 single end short reads) of the Genome Analyzer IIx was transformed to FastQ format, mapped against the genome sequence of reference strain Streptococcus_suis_P1/7 (NC_012925) with BWA

Transcription Factor Binding Sites


AAGGAAACGCTTTCAT
ATGTGAGCGTTTTCAA
TTGAAAACACTTTCTA
GTTTTTCATTTATTTTCAAGT
ATGGAAGCGTTTTCTT
ATGGAAGCGTTTTCAA
ATGTAAACATTTTCAA
ATTGAACCGTTTTCTT
GGTTTTCACAAAAATTTCTGT
CTTTTTCTATCCTTTTTTCAC
CTTTTTCAAATCCTTTCCCTT
TTATTTCAAAGATTTTCCAAT
TTGAAAACTTTTTCTA
GTTTTTCTGAAATTTTCATAC
ATTTTTCAGAAAATTTCCATT
AATTTTCAGAAAATTTCTTGA
TTTTTTCATAAATTTTCAGTT
CTTTTTCTTTAATTTTATCTA
CTTTTTCATAAATTTTGCCTT
TCTTTTCATAAAAATTCCAAT
TGTTTTCCGAAATATTTTCAT
GATTTTCAGTACATTTTTCAC
GAGTAAACGTTTTCTT
TTGTAATCGTTTTCTT
TATTAAACGCTTTCAT
AAGGAAACGCTTTCAT
TATTTTCATTTTTCTTTTCAA
CTCTTTCAAGCTATTTTCAAC
GAGATAGCGCTTACAT
TTGTAAACGTTTTCTT
TTTTTTCTTGAAAAATCCCTT
TATTCTCAAGCATTTTTTCAA
TTGTAAGCCTTTTCTT
TTTTTTCAAGAAATTTATCAA
AAGAAAACGTTTGCAA
ATAAAAACGCTTGCAA
ATTAAAACGCTTTCTT
ATGAAAACCCTTTCTT
TTGCAACCGTTTTCTT
TTGCAAGCATTTTCTA
TTGTTTCATGACATTTTTGGC
CATTTTCATAACCTTTCTGTA
GCGTAACCGTTTTCTT
GCTTTTCCGTAATATTTTAAA
TCGAAAACGATTTCAA
GCTTTTCAATTTGTTTTCAGT
CAGAAAACGGTTACAA
TTGAAACCACTTTCAA
TCTTTTCTGAAAATATTTTGT
GTGCAAACGTTTTCTT
AAGATAACGTTTTCCA
TTTTTTCCAAATTTTTCTCAC
TATTTTCAAGTTCATTTTCAT
CTTTTTCATAACTTTTCCTCC
CATTTTCTTTCCAATTTTCAA
CCTTTTCTGACATTTTTCTCT
ATAGAAGCGTTTTCAT
ACTTTTCTTTCAATTTTCCAA
TTTTTTCATTTCATTTTTTCC
CTTTTTCAATAAGTTTTCATC
AAGGAAAATCTTACAC
GATTTTCCTTCATTCTTTCAT
TTTTTTCAATAATTTTACTGT
CCCTTTCTTTCATTTTTTCAA
GAGAGAACGGTTTCTA
TTTTTTCAATGATTTTCTGAT
GATTTTCTGGATATTTTCACC
ATGATAACGCTTTCTT
CATTTTCCTAACCATTTTCAC
ATTTTTCAAGCCTATTTCAGT
GATTTTCAGAAAGATGTTCAA
TCTTTTCATGCACCTTTTCAT
TCTTTTCAAAATTATTTCTCT
GTTTTTCCTGAAAATTCCGTA
GTTTTTCCAACAATTTCCGGA
TTTTTTCAAGAAAATTTACAA
AAGGAAACGCTTTCAT
ATGTGAGCGTTTTCAA
TTGAAAACACTTTCTA
GTTTTTCATTTATTTTCAAGT
ATGGAAGCGTTTTCTT
ATGGAAGCGTTTTCAA
ATGTAAACATTTTCAA
ATTGAACCGTTTTCTT
GGTTTTCACAAAAATTTCTGT
CTTTTTCTATCCTTTTTTCAC
CTTTTTCAAATCCTTTCCCTT
TTATTTCAAAGATTTTCCAAT
TTGAAAACTTTTTCTA
GTTTTTCTGAAATTTTCATAC
ATTTTTCAGAAAATTTCCATT
AATTTTCAGAAAATTTCTTGA
TTTTTTCATAAATTTTCAGTT
CTTTTTCTTTAATTTTATCTA
CTTTTTCATAAATTTTGCCTT
TCTTTTCATAAAAATTCCAAT
TGTTTTCCGAAATATTTTCAT
GATTTTCAGTACATTTTTCAC
GAGTAAACGTTTTCTT
TTGTAATCGTTTTCTT
TATTAAACGCTTTCAT
AAGGAAACGCTTTCAT
TATTTTCATTTTTCTTTTCAA
CTCTTTCAAGCTATTTTCAAC
GAGATAGCGCTTACAT
TTGTAAACGTTTTCTT
TTTTTTCTTGAAAAATCCCTT
TATTCTCAAGCATTTTTTCAA
TTGTAAGCCTTTTCTT
TTTTTTCAAGAAATTTATCAA
AAGAAAACGTTTGCAA
ATAAAAACGCTTGCAA
ATTAAAACGCTTTCTT
ATGAAAACCCTTTCTT
TTGCAACCGTTTTCTT
TTGCAAGCATTTTCTA
TTGTTTCATGACATTTTTGGC
CATTTTCATAACCTTTCTGTA
GCGTAACCGTTTTCTT
GCTTTTCCGTAATATTTTAAA
TCGAAAACGATTTCAA
GCTTTTCAATTTGTTTTCAGT
CAGAAAACGGTTACAA
TTGAAACCACTTTCAA
TCTTTTCTGAAAATATTTTGT
GTGCAAACGTTTTCTT
AAGATAACGTTTTCCA
TTTTTTCCAAATTTTTCTCAC
TATTTTCAAGTTCATTTTCAT
CTTTTTCATAACTTTTCCTCC
CATTTTCTTTCCAATTTTCAA
CCTTTTCTGACATTTTTCTCT
ATAGAAGCGTTTTCAT
ACTTTTCTTTCAATTTTCCAA
TTTTTTCATTTCATTTTTTCC
CTTTTTCAATAAGTTTTCATC
AAGGAAAATCTTACAC
GATTTTCCTTCATTCTTTCAT
TTTTTTCAATAATTTTACTGT
CCCTTTCTTTCATTTTTTCAA
GAGAGAACGGTTTCTA
TTTTTTCAATGATTTTCTGAT
GATTTTCTGGATATTTTCACC
ATGATAACGCTTTCTT
CATTTTCCTAACCATTTTCAC
ATTTTTCAAGCCTATTTCAGT
GATTTTCAGAAAGATGTTCAA
TCTTTTCATGCACCTTTTCAT
TCTTTTCAAAATTATTTCTCT
GTTTTTCCTGAAAATTCCGTA
GTTTTTCCAACAATTTCCGGA
TTTTTTCAAGAAAATTTACAA
TTGAAAACACTTTCTA None
GTTTTTCATTTATTTTCAAGT None
ATGGAAGCGTTTTCTT None
ATGGAAGCGTTTTCAA None
ATGTAAACATTTTCAA None
ATTGAACCGTTTTCTT None
GGTTTTCACAAAAATTTCTGT None
CTTTTTCTATCCTTTTTTCAC None
CTTTTTCAAATCCTTTCCCTT None
TTATTTCAAAGATTTTCCAAT None
TTGAAAACTTTTTCTA None
GTTTTTCTGAAATTTTCATAC None
ATTTTTCAGAAAATTTCCATT None
AATTTTCAGAAAATTTCTTGA None
TTTTTTCATAAATTTTCAGTT None
CTTTTTCTTTAATTTTATCTA None
CTTTTTCATAAATTTTGCCTT None
TCTTTTCATAAAAATTCCAAT None
TGTTTTCCGAAATATTTTCAT None
GATTTTCAGTACATTTTTCAC None
GAGTAAACGTTTTCTT None
TTGTAATCGTTTTCTT None
TATTAAACGCTTTCAT None
AAGGAAACGCTTTCAT None
TATTTTCATTTTTCTTTTCAA None
CTCTTTCAAGCTATTTTCAAC None
GAGATAGCGCTTACAT None
TTGTAAACGTTTTCTT None
TTTTTTCTTGAAAAATCCCTT None
TATTCTCAAGCATTTTTTCAA None
TTGTAAGCCTTTTCTT None
TTTTTTCAAGAAATTTATCAA None
AAGAAAACGTTTGCAA None
ATAAAAACGCTTGCAA None
ATTAAAACGCTTTCTT None
ATGAAAACCCTTTCTT None
TTGCAACCGTTTTCTT None
TTGCAAGCATTTTCTA None
TTGTTTCATGACATTTTTGGC None
CATTTTCATAACCTTTCTGTA None
GCGTAACCGTTTTCTT None
GCTTTTCCGTAATATTTTAAA None
TCGAAAACGATTTCAA None
GCTTTTCAATTTGTTTTCAGT None
CAGAAAACGGTTACAA None
TTGAAACCACTTTCAA None
TCTTTTCTGAAAATATTTTGT None
GTGCAAACGTTTTCTT None
AAGATAACGTTTTCCA None
TTTTTTCCAAATTTTTCTCAC None
TATTTTCAAGTTCATTTTCAT None
CTTTTTCATAACTTTTCCTCC None
CATTTTCTTTCCAATTTTCAA None
CCTTTTCTGACATTTTTCTCT None
ATAGAAGCGTTTTCAT None
ACTTTTCTTTCAATTTTCCAA None
TTTTTTCATTTCATTTTTTCC None
CTTTTTCAATAAGTTTTCATC None
AAGGAAAATCTTACAC None
GATTTTCCTTCATTCTTTCAT None
TTTTTTCAATAATTTTACTGT None
CCCTTTCTTTCATTTTTTCAA None
GAGAGAACGGTTTCTA None
TTTTTTCAATGATTTTCTGAT None
GATTTTCTGGATATTTTCACC None
ATGATAACGCTTTCTT None
CATTTTCCTAACCATTTTCAC None
ATTTTTCAAGCCTATTTCAGT None
GATTTTCAGAAAGATGTTCAA None
TCTTTTCATGCACCTTTTCAT None
TCTTTTCAAAATTATTTCTCT None
GTTTTTCCTGAAAATTCCGTA None
GTTTTTCCAACAATTTCCGGA None
TTTTTTCAAGAAAATTTACAA None

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
AAGGAAACGCTTTCAT glgC,
... ... glgC glgC glgA glgB
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details GFP Promoter Fusion (ECO:0005636) - Experimental technique details Site directed mutagenesis (ECO:0005667) - repressor not specified
ATGTGAGCGTTTTCAA arcA,
... ... arcA SSU0581 arcB arcC
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details GFP Promoter Fusion (ECO:0005636) - Experimental technique details Site directed mutagenesis (ECO:0005667) - activator not specified
TTGAAAACACTTTCTA pfl,
... ... pfl dinB SSU0193
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - activator not specified
GTTTTTCATTTATTTTCAAGT pfl,
... ... pfl dinB SSU0193
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - activator not specified
ATGGAAGCGTTTTCTT adhE,
... ... adhE adhP
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - repressor not specified
ATGGAAGCGTTTTCAA glpK,
... ... glpK glpO glpF1 SSU0678 SSU0679
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - repressor not specified
ATGTAAACATTTTCAA ldh,
... ... ldh gyrA srtA radC
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - activator not specified
ATTGAACCGTTTTCTT pdhA,
... ... pdhA SSU1638
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - repressor not specified
GGTTTTCACAAAAATTTCTGT pdhA,
... ... pdhA SSU1638
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - repressor not specified
CTTTTTCTATCCTTTTTTCAC
... ... SSU0009 SSU0010 SSU0011 SSU0012 SSU0013 hpt ftsH
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
CTTTTTCAAATCCTTTCCCTT
... ... SSU0229 SSU0230 SSU0231 SSU0232 SSU0233
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
TTATTTCAAAGATTTTCCAAT
... ... SSU1194 SSU1195
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
TTGAAAACTTTTTCTA SSU1611,
... ... SSU1611 SSU1610
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GTTTTTCTGAAATTTTCATAC SSU1611,
... ... SSU1611 SSU1610
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
ATTTTTCAGAAAATTTCCATT leuA,
... ... leuA leuB leuC leuD SSU1737
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
AATTTTCAGAAAATTTCTTGA alsS,
... ... alsS ilvH ilvC SSU1683 SSU1684 SSU1685
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
TTTTTTCATAAATTTTCAGTT
... ... asnB SSU0316
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
CTTTTTCTTTAATTTTATCTA
... ... SSU0875
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
CTTTTTCATAAATTTTGCCTT SSU0680,
... ... SSU0680 SSU0681
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - repressor not specified
TCTTTTCATAAAAATTCCAAT pyrR,
... ... pyrR SSU0734 pyrB
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
TGTTTTCCGAAATATTTTCAT
... ... deoA deoC cdd SSU0934
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - repressor not specified
GATTTTCAGTACATTTTTCAC purA,
... ... purA SSU1757 uppS SSU1755 eep gshA
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GAGTAAACGTTTTCTT gla,
... ... gla SSU0248 SSU0250 SSU0251 SSU0252
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - activator not specified
TTGTAATCGTTTTCTT galK,
... ... galK galR galT SSU0331 SSU0332
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
TATTAAACGCTTTCAT pgmA
... ... pgmA
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - repressor not specified
AAGGAAACGCTTTCAT glgC,
... ... glgC glgC glgA glgB
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - repressor not specified
TATTTTCATTTTTCTTTTCAA glgC,
... ... glgC glgC glgA glgB
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - activator not specified
CTCTTTCAAGCTATTTTCAAC
... ... lacE lacG lacX
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - repressor not specified
GAGATAGCGCTTACAT SSU1230,
... ... SSU1230 SSU1229
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - repressor not specified
TTGTAAACGTTTTCTT glgP
... ... glgP
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - repressor not specified
TTTTTTCTTGAAAAATCCCTT eno,
... ... eno SSU1321
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - activator not specified
TATTCTCAAGCATTTTTTCAA
... ... upp clpP SSU1365 SSU1364
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
TTGTAAGCCTTTTCTT gtfA,
... ... gtfA dexB upp clpP SSU1365 SSU1364
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
TTTTTTCAAGAAATTTATCAA pgi,
... ... pgi SSU1835 SSU1834
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - repressor not specified
AAGAAAACGTTTGCAA SSU1849
... ... SSU1849
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
ATAAAAACGCTTGCAA malX,
... ... malX malQ malX
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - repressor not specified
ATTAAAACGCTTTCTT SSU1927,
... ... SSU1927 SSU1926 SSU1925 SSU1924 aspS SSU1922 nrdI
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
ATGAAAACCCTTTCTT SSU1929,
... ... SSU1929 SSU1928 SSU1930 SSU1931
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - activator not specified
TTGCAACCGTTTTCTT SSU0395,
... ... SSU0395 comFC
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - repressor not specified
TTGCAAGCATTTTCTA tufA
... ... tufA
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
TTGTTTCATGACATTTTTGGC
... ... prfC SSU1180
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
CATTTTCATAACCTTTCTGTA
... ... SSU0226 SSU0227 SSU0228 SSU0229
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GCGTAACCGTTTTCTT SSU0355,
... ... SSU0355 SSU0356 SSU0357
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GCTTTTCCGTAATATTTTAAA SSU0355,
... ... SSU0355 SSU0356 SSU0357
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
TCGAAAACGATTTCAA SSU0613,
... ... SSU0613 SSU0614 SSU0615
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - repressor not specified
GCTTTTCAATTTGTTTTCAGT
... ... SSU0908
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - activator not specified
CAGAAAACGGTTACAA SSU1172,
... ... SSU1172 SSU1171 SSU1170 SSU1169 SSU1168 SSU1167
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
TTGAAACCACTTTCAA ccpA,
... ... ccpA pepQ
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - activator not specified
TCTTTTCTGAAAATATTTTGT SSU1826,
... ... SSU1826 SSU1825 SSU1824 dut SSU1822 sms SSU1820 gpsA hasC
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GTGCAAACGTTTTCTT SSU1850
... ... SSU1850
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
AAGATAACGTTTTCCA wzg
... ... wzg
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - activator not specified
TTTTTTCCAAATTTTTCTCAC SSU1665,
... ... SSU1665 oppA
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
TATTTTCAAGTTCATTTTCAT
... ... SSU1889 SSU1888 SSU1887 SSU1886 SSU1885
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
CTTTTTCATAACTTTTCCTCC prtS,
... ... prtS SSU0756
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
CATTTTCTTTCCAATTTTCAA
... ... SSU0806 SSU0805 SSU0804
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
CCTTTTCTGACATTTTTCTCT
... ... SSU0806 SSU0805 SSU0804
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
ATAGAAGCGTTTTCAT pflC
... ... pflC
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - repressor not specified
ACTTTTCTTTCAATTTTCCAA htrA,
... ... htrA SSU1967 SSU1966 SSU1969
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - activator not specified
TTTTTTCATTTCATTTTTTCC pstS,
... ... pstS pstC SSU0951 pstB2 pstB1 phoU
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
CTTTTTCAATAAGTTTTCATC
... ... 1000000 SSU0984
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
AAGGAAAATCTTACAC
... ... SSU0886 SSU0885
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GATTTTCCTTCATTCTTTCAT
... ... SSU0886 SSU0885
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
TTTTTTCAATAATTTTACTGT
... ... SSU1350 SSU1349 rpmE2 SSU1351 rpsN SSU1353 SSU1354
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
CCCTTTCTTTCATTTTTTCAA SSU1578,
... ... SSU1578 SSU1577 metE metF
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - repressor not specified
GAGAGAACGGTTTCTA
... ... ssnA hslO SSU1762
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - activator not specified
TTTTTTCAATGATTTTCTGAT
... ... rpmH SSU1802 SSU1801 SSU1800 SSU1799 SSU1798 mutX SSU1796 SSU1795 SSU1794 ksgA
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GATTTTCTGGATATTTTCACC
... ... SSU0600
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
ATGATAACGCTTTCTT SSU0688,
... ... SSU0688 SSU0689 SSU0690 SSU0691 SSU0692 SSU0693
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - repressor not specified
CATTTTCCTAACCATTTTCAC
... ... SSU0911 SSU0910
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
ATTTTTCAAGCCTATTTCAGT
... ... SSU0556 aroA aroK pheA SSU0560 SSU0561
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GATTTTCAGAAAGATGTTCAA
... ... SSU0718 SSU0719 SSU0720 tRNA-Tyr
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
TCTTTTCATGCACCTTTTCAT
... ... SSU0821 SSU0822
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
TCTTTTCAAAATTATTTCTCT
... ... SSU0889
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GTTTTTCCTGAAAATTCCGTA
... ... SSU1024 zwf
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GTTTTTCCAACAATTTCCGGA sly
... ... sly
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
TTTTTTCAAGAAAATTTACAA
... ... SSU1302 SSU1301 SSU1300 SSU1299 SSU1298 SSU1297
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified