Curation Information

Publication
Molecular mechanisms of master regulator VqsM mediating quorum-sensing and antibiotic resistance in Pseudomonas aeruginosa.;Liang H, Deng X, Li X, Ye Y, Wu M;Nucleic acids research 2014 Jul 17; (): [25034696]
TF
VqsM [Q9I1P2, view regulon]
Reported TF sp.
Pseudomonas aeruginosa PAO1
Reported site sp.
Pseudomonas aeruginosa PAO1
Created by
Dinara Sagitova
Curation notes
-
External databases
NCBI GEO (GSE57284) http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57284.

Experimental Process

EMSA confirmed that VqsM directly regulates lasI expression. lux reporter assays verified VqsM-dependent regulation of lasI in vivo. DNase I footprinting localized VqsM binding region in the lasI promoter. EMSA performed with a truncated lasI probe in which the putative binding site was deleted showed that binding by VqsM was abolished. Furthermore, EMSAs with lasI promoter containing VqsM binding site in which point mutations were introduced showed that VqsM bound with much lower affinity than to the wild type promoter. ChIP-Seq analysis identified VqsM-binding regions in the P. aeruginosa PAO1. MEME motif discovery tool identified a 15-bp VqsM consensus sequence (GG[A/T][T/C/G][C/G][T/A/G][C/A/G][C/T/A][T/C]CGGCCA). EMSAs with the promoter regions of PA2227/PA2228, PA2588, PA5324, PA3106, and PA3342 validated ChIP-Seq results. qRT-PCR confirmed VqsM-dependent regulation of PA2227/PA2228, PA2588, PA5324, PA3106, and PA3342. Consensus search identified a putative VqsM binding motif in the promoter regions of exsA, nfxB, PA2227, and PA2588 genes. EMSA confirmed that exsA was directly regulated by VqsM. exsA-lux reporter assays in the WT and vqsM mutant strains confirmed VqsM-mediated activation of exsA expression. In a similar manner, nfxB expression was shown to be directly regulated by VqsM.

ChIP assay conditions
Wild type P. aeruginosa MPAO1 containing empty pAK1900 or pAK1900-VqsM-VSV was cultured in LB medium supplemented with ampicillin until the mid-log phase (Optical Density; OD = 0.6), before it was treated with 1% formaldehyde for 10 min at 37°C. Cross-linking was stopped by addition of 125 mM glycine. Bacterial pellets were washed twice with a Tris buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl), and then re-suspended in 500 μl IP buffer (50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, mini-protease inhibitor cocktail (Roche) and the DNA was sonicated to 100–300 bp. Insoluble cellular debris was removed by centrifugation and the supernatant used as input sample in IP experiments. Both control and IP samples were washed by protein A beads (General Electric), and then incubated with 50 μl agarose-conjugated anti-VSV (vesicular stomatitis virus) antibodies (Sigma) in IP buffer. Washing, crosslink reversal, and purification of the ChIP DNA were conducted by following previously published protocols
ChIP notes
DNA fragments (150–250 bp) were selected for library construction and sequencing libraries prepared using the NEXTflex™ ChIP-Seq Kit (Bioo Scientific). The libraries were sequenced using the HiSeq 2000 system (Illumina). ChIP-seq reads were mapped to the P. aeruginosa genomes, using TopHat (version 2.0.0) with two mismatches allowed. Only the uniquely mapped reads were kept for the subsequent analyses. The enriched peaks were identified using MACS software (version 2.0.0), which was followed by MEME analyses to generate the VqsM-binding motif. The ChIP-Seq data files have been deposited in NCBI's (National Center of Biotechnology Information) Gene Expression Omnibus (GEO) and can be accessed through GEO Series accession number GSE57284.

Transcription Factor Binding Sites


GGTGCTGATCGGCCA
GGATCAGCTCGGCCA
TCTCCACCTCGGCCA
TGATCTTTTGACAGC
GGATATTTTCGGACA
TGATCTTTTCGGACG
TGATTTTCAAAGCCA
GGTGAGCGCCGGCCA
CGAGGTCTTCGGCGA
GGTTCAGCTCGGCCT
GGATCGCGTCGGCCA
GGTGAGTTTCGGCCT
CGATCTTCTTGTACA
TGATAGGATTGGCGT
GGATATTTTCGGACA
CGATCTCCTCGGCCA
GGTTTTCCTTGGCCA
TGATCTTCCCGGCCA
CGAGCACCTCGGCCA
GGATCGCCACGGCCA
GGACAAAATCGGCCA
CGTCGAGTTCGGTCA
GGATGCGATCGGACA
TGTCCACGTCCGCCA
GGATCGATTCGGCCA
GGACTTCTTCGGCCA
GGATGGTTATGGCCA
TGACGATATCGGACA
GGACTTCGCCGGCCA
GGATCATTTCCGCCT
GGTGAATTTCGGACA
GGATCTTCTCGGCCA
GGTGGATACCGGCCT
GGATGCCGTCGGCCA
GGACCTGATCGGCCA
GGATCGTTTCGGCCA
GGATCGCCCCGGACA
CGACCACCTCGGCCA
TGATGTATTCGGCCA
GGTGCTGATCGGTCA
GGTGCTGATCGGCCA
GGATCAGCTCGGCCA
TCTCCACCTCGGCCA
TGATCTTTTGACAGC
GGATATTTTCGGACA
TGATCTTTTCGGACG
TGATTTTCAAAGCCA
GGTGAGCGCCGGCCA
CGAGGTCTTCGGCGA
GGTTCAGCTCGGCCT
GGATCGCGTCGGCCA
GGTGAGTTTCGGCCT
CGATCTTCTTGTACA
TGATAGGATTGGCGT
GGATATTTTCGGACA
CGATCTCCTCGGCCA
GGTTTTCCTTGGCCA
TGATCTTCCCGGCCA
CGAGCACCTCGGCCA
GGATCGCCACGGCCA
GGACAAAATCGGCCA
CGTCGAGTTCGGTCA
GGATGCGATCGGACA
TGTCCACGTCCGCCA
GGATCGATTCGGCCA
GGACTTCTTCGGCCA
GGATGGTTATGGCCA
TGACGATATCGGACA
GGACTTCGCCGGCCA
GGATCATTTCCGCCT
GGTGAATTTCGGACA
GGATCTTCTCGGCCA
GGTGGATACCGGCCT
GGATGCCGTCGGCCA
GGACCTGATCGGCCA
GGATCGTTTCGGCCA
GGATCGCCCCGGACA
CGACCACCTCGGCCA
TGATGTATTCGGCCA
GGTGCTGATCGGTCA

Quantitative data format: Fold enrichment

GGTGCTGATCGGCCA 2.26815
GGATCAGCTCGGCCA 3.00595
TCTCCACCTCGGCCA 2.25879
TGATCTTTTGACAGC None
GGATATTTTCGGACA None
TGATCTTTTCGGACG None
TGATTTTCAAAGCCA None
GGTGAGCGCCGGCCA 2.38928
CGAGGTCTTCGGCGA 2.07034
GGTTCAGCTCGGCCT 2.82713
GGATCGCGTCGGCCA 3.56756
GGTGAGTTTCGGCCT 2.1929
CGATCTTCTTGTACA 2.60392
TGATAGGATTGGCGT 3.04852
GGATATTTTCGGACA 5.74304
CGATCTCCTCGGCCA 2.25836
GGTTTTCCTTGGCCA 6.64417
TGATCTTCCCGGCCA 3.14207
CGAGCACCTCGGCCA 4.96073
GGATCGCCACGGCCA 2.70936
GGACAAAATCGGCCA 3.43664
CGTCGAGTTCGGTCA 2.26895
GGATGCGATCGGACA 2.71658
TGTCCACGTCCGCCA 2.17581
GGATCGATTCGGCCA 2.71658
GGACTTCTTCGGCCA 2.36891
GGATGGTTATGGCCA 2.55659
TGACGATATCGGACA 2.82127
GGACTTCGCCGGCCA 2.11403
GGATCATTTCCGCCT 2.20556
GGTGAATTTCGGACA 2.83009
GGATCTTCTCGGCCA 3.14439
GGTGGATACCGGCCT 1.77062
GGATGCCGTCGGCCA 2.51423
GGACCTGATCGGCCA 2.23562
GGATCGTTTCGGCCA 2.79861
GGATCGCCCCGGACA 2.18791
CGACCACCTCGGCCA 5.55462
TGATGTATTCGGCCA 2.56405
GGTGCTGATCGGTCA 2.18398
GTGCAGACCGGCGTGATGGAGGGCGCGCGGATGCCGTTCGGCCAGCCGCTGAAGGCGACCGACGGAGCCTTCGATGTACTCGCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGATCCTCGGTGAGAAGCACGATGCCAAGGCGGCGGCGGTCAAGCCGGAAAGCGTGATGACCGACGAAACCCGGCAACTGCTGACCGCCTTCCAGAAGCCGGTGCGTACCCAGGCCGACCCCTACCCCTACGAGTCGCGGGTCCTGCAGGGGATCTGGGCAGCGGCGCCGTACCTGCACAACGGCTCGGTGCCGACCCTGGAAGAGTTGCTGAAGCCGGCCGCGGAGCGGGTGGAATCCTTCCCGGTGGGCTCGGCCTACGACGTGGACAAGGTCGGCCTCGCCGCCCAGCAGACCCAATTCGGCAGCTATGTGCT None
CCGGAGTGGGTCACCGGCGTCCACGACAGCGTCGCCGTGCGGGTCACCGACCATCCCCTGGTACAGGAACTGTGCCATCTCACCGGTCCGCTGATCTCCACCTCGGCCAATCCGGCCGGGCGCCCGGCGGCGCGCACGCGGCTGCGGGTGGAGCAATACTTCCACGACGA None
CACCAGTTCCGACAGTTGCTCGCCGCCGAAGCCGCGGGTCAGCGCGCCGATGGGGTAGACCTTGGCGTTGCCGGCCTCGCGGGCGCGGTCGAGGATCAGCTCGGCCACCGCCGGGGTGTCCAGCACCGGCCGGGTGTAGGGCGGGCAGCACAGGCTGGTGGTGCCGCCGGCCGCGGCGGCGCGGGTCTCGCTTTCGA None
CCGACCACGGCGATGCGCTTGCCGGTGGCCGGCGAGCGCTTGAACGGATGTTCGTCGAAGCCGGCGTGGTCGAGGGCGTAGCGTTGCAACTGGCCGATCAGCACCGGTGCGCATTCCTGGGCGTTGTTGCGTACGCAGGCCCGCTGGCAGAGGAT None
GATGGCCTTCGCCGTCGAGCTGGAGGAATGGGTCGGCGCCCACTGGCACCGCTTCATCACCCGCCATGCCAGCGGCGAGTTCGAGGCGGCGCGGGTGACCCTGGAGAGCATGCGGCGTCCGCTCGGCATGCTCTTCCGGGCGCTCGGCGGCGCACCGGGGGTAGCCCTCGAGGCGACCCCGGCGCGCCGCCTGCTGCTACGCCGCACCTGGTTGCAGCGGGTCGCCGGGACCTGCGAGCAGGCCCCGGTGTCCTGGTTCAACGGCGACAGCCTGCGCCTGCCGGAATCCCTCGCGGTCTATCCGCAGGCCGAGCTGAACCGCGAACTGTATCGCTGGCTGGCGCTGCTGGCGGCCAGCGCCGGGCCGCTGCGGCACTGGGCCCAGGACAACCAGCGCTGGGCGCGGCAGTTGCTCGATGCCTATCCGGCGCTGCGCCCGCGCTACGCCCGGCTGGTCGCCGCGCATCTGCGCCAGCGCCCGTCGCTGGACGATTGCCCGGCGGCAGACGCCGAACTGGAAATCGCCCTGCGCCGCGCGCTTGCCGAGCCGGGCAGCGTCGAGCGCTTCCCGCGAGTCGAGCGGGCGCCCTGGCCGGTGCCGCTGTGGCTGTATCCCGGCGAGCGCTGGACGCCTTCCGCCAGTGCGGAGGACGGCGAGGAAGCGGCCGCCGGCGCCGGCAAGCGCCAGGTCGCCCGCAGCGGAGCGCGCAAGCGCGCCGAGCGCATTGAGGAACGCAACAGCGAACGCAACCTGCTGCTGTTCCGCCTGGAAAGCCTGCTCA None
GGCGCGCGCGTCGCCGAAGACCTCGACTACCTGTCGCTGTCGCGCCAGCGCACGCAGAAGGGCGGCGGCCTGCGCCTGGATCTCGACCTGCCGGCCGCCGACTACGATGACCTGCCGCTCGGCCCCGGGCTGAAGCTGCCCGAGTGGGACTATCGGCAGCAGCGCCTGCTGAGCGACCACGTGCTGCTGCAACCGATGCGGCCGCGCGGCGCGACCAGCGCCAGCCTGCCGGCGCACCTGGAGAAGACCGCGCTGCATCTGCGCCGCCAGTTCGCCTGCCTGCGCGACGGCCGCCAACGCCTGCGCCAGCAGCCGCAAGGCGACGAGATCGACCTCGATGCCTGGCT None
TGGAGTCGAGGGGGGCGTAGCGGACAGGAAGGGGGTGAGCGCCGGCCATCCTGCATGGACGGCAAGGCAGGCGGGTAAAAAAAGGCCGCCTGCGTGGGGAGGCACCGGCGGCCAGTCGGTTCGGCAGCGTCGAGCCGGTCTGCAAGGGCTGGCGCAGGTCTCGGCTGCGGCCTGCGCCGACGCTCCCGAGGGCATTCG None
CCGCCCTTGAGCGAACCGGTGAAGCCGACCGCGCGGATGGCCGGATGGCGCACCAGCGCCTCGCCGACGCCGCTGCCGTAGACCATGTTGAATACCCCGTCCGGCATGCCGCTGTCGGCCGCCGCCTGGAGGATCGCGTCGGCCACGCATTCGGCTGTGGCCATGTGTCCGCCGTGGGCCTTGACCACCACCGGACAGCCGGCGGCCAGGGCGGCGGCGCTGTCGCCGCCGGCGGTGGAAAAGGCCAGCGGGAAGTTGCTGGCACCGAACACCG None
GCCTCGGCCAGGCCATCGCCGAGCACCTGCCGGCGCGCAGCCTGCCGTGGGTGCTGGGGGTGAGTTTCGGCCTGGCCCTGGCGTTCGGCCTGGCCGGCCTGCTGGCGTTGCTGGTGACGCTGATGCTCTTCGCCTGGCTGCGCAGCCGTT None
AGGGGAGCGTGGGGAATAGCGTTGTCTCAAAATGGAGACGTAATCGAGCGAAAGTTCAGTGGCTATGCAGGTCTCAGTTCGTCTCTATTTCGAGACGAGTCCCGCTATCGAGACGCATGCCCAGCGCCACGATCTTCTTGTACAGGGTCGAGCGACCCAGGCCCAGGCGTTTCGCCGCTTCCACCACATTGCCGGCACTCTGCGCCAGGGCCCGTCCGA None
CCCAATCTCAAACTAGATAGATCAGTGGAAACTGTTTCTGAATTCTGTAGTAGACTGCCCGGTCCAACGTCTGAATGCATGTCTAAAACTCGCTGTTTCCGAGTACCCCAGAATATCGCTAATACGATCAACTGGTATCGATGAATTCAGTAGCAGTGCAATTGCTCGTTCTTTGCGGGCCTTATCTACAATCTGGCGATAAGTGCAGCCCTCGTCCGCCAAGCGACGTCTTACCGTCCGCTCATTCATGCGTAAATACTTTGCGGTAGTCACCAAGCTAGGGTATTGATCTGGTATGGAATCAAGGAATAACTCGATTCGCTGACGGAGCCCTCCCATCTCTACTTCCAACAGAGCATTGAAACTCTCACCTGCCATAGTCAGGGCCGACTGAAATACCGCCGGATTGGCAGTCGCCAGTGTTCTATTCAACTGATGAGCTGGAAAGCTAAATATTATGTCATTTCCTTCATGCTTCACAGGCAAAGAAAAGAAACCTTCATATATTGTTTTATCTGCGCCGTGCACAGGCACTGTCAATGCAGAGATGGGAAAGTCATTACCTAACAGATCCATAATGAGCTTGTAGGTTGCAGAGGCTATAACATTTACATGAAACTGACGGGATGCGTCATTCCACTCTGGCTTAAAGTTAACTGAAATATGGATTTCTACTTCGTAATTCTCCCTAGGCTTGACGCCAACATTAGCTATATCACGATTGAACAACTTGACATAGGCCCTGATGACTTTCAAAATATCACCTACGTTCTCGGCGCATAGCAACGCCAATCCTATCACGCCATAATCAGATATATGGTAATAAGTTCCAAGATTCAGTCCTTCTTTTCCTGAATACCCCTTGCTGACTATCCAGTTGTAAAGTGCGTCACTTCTTGACTCTTGTTCTGCCGCAAAGGGTGGTATTGCGATATCACGATCACGAAGATAGTTCTGCAGAGGGCGCCATTCAAAATCAAATATGTGTTCGGTCACCATGTCTATATTCACCTCACCCCTACTGTTCTTGATATAGCCCTGAACGCTGCAAGTGCCTCATGCTCCATACGGATGCCGTCAACGTTGTAGTCGACATACGCGGAGGTCTTTGCAATCACCACACGCCTAA None
TCGATCTCTCAGTTTGTGCTAGCTCGTCTCGACCCAGCTAACAGCCAGTGACTATCCGGTAGTGGAGCAAGGTTAAGTCCTTAAGGACTTTTCTCTTAAAGGTGAAGATCAAGGCATTTCACCATCTACTGATATTTAATTTTAACTCGCTTAACACTACTCCGCACGCATGCCATGCACTACTATTATCTGAGTCGCGAAGGTATCCGCCTCCCTTGGACTATGCTTTCAATTTAGCAACACGAAACACTGCAGCATGATCGATATCGCCCTTGGATGAATCGGCAGACTCATCAATAGGCGCCCGCAATAAACAAGACCCAACATCACCGCATATCCCGGAGGATCAGCAACAGGATAGATTCAGTCTTTTTCATTATTTCCATCCGCCGCCTCATGCGTACTACTAGCCCGAAAGCTGATAAAACCAGCATGAAGCATCTTTTTGCTAGAGTATCTTCGGACAAATGCCGGATATTTTCGGACACCCTCTTCGGCAGGTCCTTAGCGGCACCATGTCTTATCTGCGCTTTTATTTCATTAAACACCCCATAGAGAGTACTAATGACTTGTCGTCCAGATTGTAACTATCGTAGATGAGTCGACTAGAGGTATTCGCTACAATTTATAGATTC None
GACGACTTGCCCTCGCTGCCGAAATAGCGCGCCCGCTCGCCGCGCGCGGTGACGATCTCCTCGGCCAGCAGGCAGGCGTTGTCGCGCGCGTAGGCGTAGCCGATGCCATAGCCCAGGCCGCGCTCATCCTTGGCCCGGATGTGCGGCACGCCATAGGCGGTC None
ATGCCTGCCTTGGTGAATTCGCGCGCCAGCGCCAGGCCGGCGATCCCGGCCCCCTGGATAAGAACGGTCATCCGTTGCTCCTTAGCAGCGGCATCCGTCGCGACTTCGCGCGGTCGCGACAGGCCTGCCCGAGACGATGAAAATGTCCATCCTAGCCGCCCCGGACAGCCCACCGACCCTATCAGAAGATCGAGTTGACCCTGCTCGCCGACACCTCGCCGCTCGCTTTTCCTGTCCTCCAGGCCACCGGGAGTCCGGCGCGCCGGGAAGGCAAGCGTGGCCCGGGCACGGCACGCGTGGCCGGAAATCCCCGCTAGCCGCCGCCCGCCGCGGCGCTACGGTTTTCCTTGGCCAGCGGCCTCCCGAGCGCCGGCAAGCGGCGATGGCGCCTGAAGCTCAGGGCGACCGGCCCGCGCCACCACCGCCCACGACGATCATCCAGGCGCAGCCACCCCGGCGAGAGTGGCCGGGACGGCAGTGCTCAGCCGGGCCACGGCAAGCATGCACGACCGATCGGCACGGCGTCG None
AGCTTGGCCCGGATCAGCCGCGCCAGCACGGGCGCATCGCCGCCGCTGGAGACCGCCACCACCAGCGGCGAACGGTCGACGATGGCCGGGAAGATCACGCTGCACAGGGCCGGCGCGTCCACCACGTTGACCGGTATCCCGCGCGCATTGGCCGCTCGCGACACCTCGGCGTTCAGCGGTTCGTCGTCGGTGGCGGCGATGATCAGGGCGCAGCCGGGCTGGTCGCCGTCCTGGTAGTCGCGTTCGAGCAGCTCGCCGCCGCCCTGCTCCACCAGATGCCGCAGTTCGATGTGGATCTGCGGCGCGACCACGCGCAGGCGCGC None
CATTGACACGGATATCCGGGCCCAGGCTGGCGGCCAGGGCATGGGTCAGCGCCAGCAACCCGCCCTTGCTCGCGGCGTAGGCCTCGGAGTCAGGCTCCGACTGGTGGGCACGAGTCGAGGCGATGTTGACGATGGCGCCATTGTGCGCGCGCAGATAAGGCGTGCAGTACTTGGCCAGCAGCATCGGACCGGTCAGGTTGACCGCCAGGGTCCGGGTCCACTCGCCGAGACTCAGCGCCTCCAGCGGCGTATTGCGCGGATTGGCGATGGCGGCGTTGCAGACCAGGCCGTCGAGGCGGCCGAACTGACCGAGCACCTCGGCCACGCTCATCGCCACCTGGCCCTCCTGGGCCACGTCCATGGCCACGAACCAGGCGTGC None
CACCGCCACCGGCTCCACCGTGCTCAGCGGGCTGGACGACATGTCCCCGGGCATCCTCATCTGGCGCTCTCTGCTGCACTGGCTGGGCGGCATCGGCTTCATCGCCATGGCCGTGGCGATCCTGCCGATGCTGCGGATCGGCGGCATGCGCCTGTTCCAGACCGAATCCTCGGACCGCTCGGAAAAGGTCCTGCC None
AGCTCTGCGAAGAGCGGCTGTGCCTGGCATTTTTTCCTGTCGAACCTAGCATTCGCCGCCTCGTCCCGCAGTCACCGGCGGCGCCAGCCACAGGGACAAAATCGGCCATGGACTCAGGCCACCACCTGGTTACGGCCGAACGCCTTGGCTTCGTAAAGCGCGCGATCGGCATGCTCGTAGAGATCGTAGAGACGCTTCAGGTCGTTGCCCGGGGTCGGCCACAGGCAGGACACGCCGACCGACAGGGTCACTTCGCGCGCCGTGTCCGACGCCTCGTGCTCCATGCGCAGCGCCTGGACCTGTGCGCGCAGCGCTTCCGCGCGCAGCCTCGCCTCGTGCTCGTTGGCGCCGTACAGCAACAGGGCGAACTCTTC None
CAACTTCGTCATCGACCGGCCGCTGCACCTACGCTGCGAGGCCGGCGCCGAACTGGACGGCGGCGGCCACGGCAGTCTGCTGACCCTGACCAGCCCCGGGATCACCGTCGAGGGCTGCCGGCTGCGCAACTGGGGGCGCAACCTGACCGAACTCGACGCCGCGATCTTCGTCGGCAAGGCCGCC None
TGTCGCGCAGCGGCAGGCCGACCTCGATCTCCTCGACGATGGTGCCCGGCCGCGCGCTCATCACCAGGATGCGATCGGACATGGCGATCGCCTCGACCAGGTCGTGGGTAATGAACAGCGCGGTCTTGCGTTGCTCGCAGAGCATCCGCGCCAGGTCCTGCTG None
CAGGCGTTCGTGCAAGCGCGCGGCGCTGTCCACGTCCGCCAGCTCGATGGCCAGGCTCGCCGCCCGGTTCAGTTCCTCGTCCATGGAGCCTCCGCCAGCAATGCGTCGCAACGCTCGCGCACGAACGCGCGCAAGAGGGTCACCGGACGGGTCAACTGGGCGCGGTGGGTACACAAGAGGTTCATCGGCGTCGCT None
CCAGCAACTCACCCATTTCCAGGCCCTGGAGCATCTTCAGTTGCGCCAGCAGTTCGCCACGGATCGATTCGGCCATGCTCGCCGGATCGCGATGGGCGCCGCCCAGCGGTTCGTCGATGACCTTGTCGACGATGCCCAGGCCTTTCAGGCGCTCGGCGGTGATGCCCATGGCCTCGGCGGCTTCCGGCGCCTTCTCGGCGGTCTTCCAGAGGATGGAGGCGCAGCCTTCCGGCGAGATCACCGAATAGGTGGAGTATTGCAGCATGTTCAACTGGTCGCAGACACCGATGGCCAGCGCGCCGCCGGAACCGC None
AACCGGCCGCGGGAGCGCACGCTGATCAGCGCGTCGGTGCCCGACAGGTTGTCCAGCGCGTTGACCACCAGCGCGCCGTTGTCGGCCCAGGGCTGCGGCACGCGCTGGCCGAAGAAGTCCTGCACCTGGACCCACATGCGATCGCTGAGCAGGTCGGTATCGGCCACGACGATGACATTGATGTTGCGCGCCTCCTTCAGGCCTTCGCGATGCCCCTCGATGCCCTCCGCGAAGGCACTCTTCGCCGGCCCCTGGATACGGGCGG None
CTGCCCGCCCGGCCCCGATGCCGACGGTACCAGCCGGCGCACGGCGCGCAGCCCCATCCTCCCTGCGCGACCGATCTCGTCCGCCCCACCCGGGCGCCGCGCCGCCGCATCGGCGCACTGGCCATAACCATCCGGCCGCACGGAAGCACTCCGTCGTGCCCCGACTGCCAGGGACCTTCCCACCATGACCGCCGCCACCCTCGCCGCCGACGCCGCTCCGGAA None
GTTCCATGTCCGATATCGTCATCGTCGCCGGCGCCCGTACTCCCATGGGCGGCTTCCAGGGCAGCCTGGCCGGCGTTTCCGCGGTCGACCTGGGTGCCGTCGCGATCCGCGAAGCGGTGCAGCGCGCCGGCATCGCCGCCGAGGACGTACAGGAAGTGATCATGGGTTGCGTCCTGCCCGCCGGCCTGA None
CTCGACGAGGAAGGCGACGAACGCCCGGTCCAGCGCCCGTAGCCAGCCGCGCGCCACCCACAGGTCGAGCTGGCGCAGCAGGTCGTGGCGTGCCGCCAGCGGTTGCGCTACCTGGTCGTCGCGGCCATCGCGGACTTCGCCGGCCAGTTGCTTGAGGGTCGGATTCATCGCTCGGCTCCCGGCTGGCCGCTGAACAG None
CGGGTTGCGGAACAGGCCCTGCATCGCCACCCCGGACAGCGCCAGCACCGCGCCCACGGCCAGGCCGAGCAGGGTCCGCGGCAGGCGGATCTGGCCGAGGATCATTTCCGCCTGGGCCAGGCCCGTTCCATCGAGCGGCAGCCCGGCCAGGCGCAGCGCGG None
GAGCGGGCGACTCCCCAAGCATAGCCGGCGGGACGGCGGCATCCGCCACGGCGGCGCGCTGCGCCCGTCGACCGGGGCCAGGGTTCGGCAGAAAAAACGCTCAGCGCAGCCTGACGCCACTTGAAGACTTTTCTTACAAAACCTTGGCCAGCGGCCAGGAAAAGAGTGGGCATTGTCCGAAATTCACCTCTATCC None
CCTGGCCGAGGCCGCCGCGCTGGACGGCAAGGTGTTCCACGCCGGCACCGCGCTGAAGGATGGCCAGGTGGTCACCTCCGGCGGCCGCGTGCTCTGTGCCACCGCCATCGGCGAGAGCGTGTCCGCCGCCCAGCAACAGGCCTATCGCCTGGCCGAGAAGATCCGCTGGAACGGCTGCTTCTACCGCAAGGACATCGGCTACCGTGCCATCGCCCGCGAGCGCGGCGAGTCCTGACCGGGCCCGAAGCCGCGGGCGCCGCACGGCGCTT None
GCGTCGGCACGTCCAGCGCCGCCGCCAGGTGACCGAGGCCGGTATCCACCGCCACGCAGGCGCGCGCGCCGGCAAGCACCTTGGCCATGCCGGCCAGGGATAATCTGGGGAGTACCGCGGCATTTTCCAACCCCGCCGCCAGGCGCCCGGCCCGCTCCCGCTCGGCGGCGCTGCCCCAGGGCAGGCGCACCGACCAGCCGCGCTCGCACATGCGCTCGGCCAGTTCGCGCCAGTAGGCTTCCGGCCAATGCTTGGTGACCCAGGTAGTACCGTGCAGGAACACC None
CATCTCGGTCTCGCTGTGGTGGGCGTTGAACACCGGATGCTGCAGGTAGGCCGAAGTGCGTTGCAGGACCGCCGGGATGCCGTCGGCCACCGCCCCGCCATCCAGGTGCGCGACATCCAGCCCGTGGCCGGCGCCGAGGAAGATCTCGAACAGGGTCGCCAGGGTCGCCGCGTCACAGGTTTCGTCGAGGCTCAGGGCCAGCCGCCGGTCGTCGA None
CGCGGATAGCGCGGGTCGGCGCCAGGCGCACGGCGAAGGCCAGCAGCAGGGCCACGGCGACCGTCGCCAGCGCGGCGATGCCGCCCAGCGTCAGGGTATGGCCGATCAGGTCCCAGTAGCGCTCGTCGAGGTCGAAACGGCCCTGGCGCCAGAACCAGACAACCAGTTGCGCCACGGGAATCACGAAGGCGCAGAGGAACACCAGCCCGCACCAGGCGCTCGCCGCCAGCGCCCTGGCGCCGCGCAGGCGATACAGCGGCGCGCCGCGCGGAC None
CTGCAACTGGGAGAGCTCGCGATGAATGTACAGGCTGCTGTCATCCACGCTGGGAACCACCGCAGGTGGCGTTTCCACCGGGATCGTTTCGGCCATCTTCACTTCTGCTTCGCTTTCCACGTTCGCCACTACGGTTTCGTCGGCGGCGATACGTTCGATCTCATCAAGTCCT None
GCGGCCCGCCGGGCACCGGCAAGACCCTCCTGGCCAGCCGCCTGCCCGGCCTGCTGCCGGCGCTCGACGAGGACGAAGCCCTGGAGGTCGCGGCGATCCATTCGGTGGCCAGCCACGTCCCCCTCAGGCACTGGCCGCAGCGACCGTTCCGCCAGCCGCACCACTCCGCCTCCGCGC None
TGGATCATGCTCACGGCCTGGCGGTAGGAGATGCGCTGGGTAGGGTCCTGCAGGTCTTCGACGGTGAAGCCCAGGCCCCGGCACAGCCGCGCGGGATCGACACCATGGCCTTCGACCACCTCGGCCAGCGTCTGCAGCAGGAAGGTGGATACCTGGGCGAGTTCGTAGCGCGCATCGGCGGCATTGTTGTGCATGGGCGAAATCCTGAGCCGGTCTCGGCTTCGTTCTTGTTCTGGCGGTGGATCGCGACATGGGATGAGCGTCCCATCATATAGCGTTCCGCACAGATGTAACAAAGCATTGCGCAGTGTCCGCAAATCCCCCCCTCGCTGACCGTCAATGCCCTGCCTCGGCCTGCCGTTAGGGCTTATTCCTATGCCGTGCCCCGAGCCACGCCAACAATAATAAGAGCCCGCCCATGAACCCGATCCGCCCCCACAGGCCCCTGCGCCTGGCCGCCTGCGTCACCCTCGCCGTCAGCTGCTGCACCCACGCCAGCGAAGGCGGCGTGGACAACATTGG None
ACGTGGATGCAGGCGCCCGGATAGGGCACCAGGAAGAATTCGGTGACGCGGCCCTTGGCGTCGTTCTCCAGCGGCACCGGGTAGCCGCCGAGGCGGATCGCCTTGCCATCCAGGCTGGCGACGGTCTTGGCCGAATACATCACCGCCGGCATCTTCCGGTCCGACTGCTTCAGGCCCCCCTTGCTGGTGAAGGTGCCGGCGGCCTCCGGGGTGTCGTGGACGATGTCGGGCATTTCTTCCAGCGCCTTGCGGTCGGCCGGCGGCATCAGTTCCAGCCAGTCGGTCTCGGGCAGTTCGGCGTGGACCAGGGGTGA None
TCGCGCTTGTCCACCACTACCACGAAGGGCGTCCCGGCGGTGCGCAGGCGAGCGCTGACCAACCCGCCAACCCGGCCATGACCGATCAGCACCGCATGCTCGCGCTCCAGGATCGGCGGCGGCAGGTCCTGCGCCGGCATCTCGCGGACCCCGCCAGCGGCCTCCGCCAGGCGCTGCTCCTTGCGTTGCTGCAGGCGATCGATGGCGATGAACAGCAGCGGATTGACCAGGATCGACAGGATCGCC 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
GGTGCTGATCGGCCA
... ... PA0439 PA0440
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GGATCAGCTCGGCCA
... ... PA0401
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
TCTCCACCTCGGCCA
... ... PA0022
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
TGATCTTTTGACAGC nfxB,
... ... nfxB oprJ mexD mexC
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Luciferase reporter assay (ECO:0005648) - activator not specified
GGATATTTTCGGACA
... ... PA2230 PA2229 PA2225 PA2226 vqsM PA2228
Experimental technique details Consensus search (ECO:0005624) - not specified not specified
TGATCTTTTCGGACG lasI,
... ... lasI rsaL
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Site directed mutagenesis (ECO:0005667) - activator not specified
TGATTTTCAAAGCCA exsA,
... ... exsA pscL pscK pscJ pscI pscH pscG pscF pscE pscD pscC pscB exsD
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Luciferase reporter assay (ECO:0005648) - activator not specified
GGTGAGCGCCGGCCA
... ... PA0845
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
CGAGGTCTTCGGCGA
... ... PA0525
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GGTTCAGCTCGGCCT
... ... PA0525
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GGATCGCGTCGGCCA
... ... PA1253
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GGTGAGTTTCGGCCT
... ... cobV
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
CGATCTTCTTGTACA
... ... bdhA PA2004 PA2005
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
TGATAGGATTGGCGT
... ... PA2225 PA2226 vqsM
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GGATATTTTCGGACA
... ... PA2230 PA2229 PA2225 PA2226 vqsM PA2228
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - not specified not specified
CGATCTCCTCGGCCA
... ... lldA PA2383 PA2384 pvdQ
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GGTTTTCCTTGGCCA
... ... PA2588 pqsH
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - not specified not specified
TGATCTTCCCGGCCA
... ... cysG
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
CGAGCACCTCGGCCA
... ... PA3106
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - not specified not specified
GGATCGCCACGGCCA
... ... PA3214 PA3213 PA3212 PA3211 PA3208 PA3209 trkH
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GGACAAAATCGGCCA
... ... PA3341 PA3342
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - not specified not specified
CGTCGAGTTCGGTCA
... ... nosF nosD nosL nosY
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GGATGCGATCGGACA
... ... PA3509 PA3510 PA3511 PA3512 PA3513 PA3514 PA3504 PA3505 PA3506 PA3507 PA3508
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
TGTCCACGTCCGCCA
... ... PA3565
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GGATCGATTCGGCCA
... ... PA3638 accA
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GGACTTCTTCGGCCA
... ... PA3669 PA3670
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GGATGGTTATGGCCA
... ... PA3749
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
TGACGATATCGGACA
... ... PA3925 PA3924
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GGACTTCGCCGGCCA
... ... recD
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GGATCATTTCCGCCT
... ... PA4707 PA4706 PA4705
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GGTGAATTTCGGACA
... ... PA4767 PA4766 smpB
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GGATCTTCTCGGCCA
... ... purD retS
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GGTGGATACCGGCCT
... ... waaC waaG waaP PA5008 PA5007 PA5006 PA5005 PA5004 PA5003 PA5002 PA5001
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GGATGCCGTCGGCCA
... ... gcvP1
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GGACCTGATCGGCCA
... ... PA5216 gcvT1 gcvH1
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GGATCGTTTCGGCCA
... ... ppk
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GGATCGCCCCGGACA
... ... PA5290 PA5291
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
CGACCACCTCGGCCA
... ... PA5324 PA5325
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - not specified not specified
TGATGTATTCGGCCA
... ... PA5423
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified
GGTGCTGATCGGTCA
... ... PA5518 PA5517
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - not specified not specified