TABLE 1 

CRP binding peaks identified by ChIP-seq in the V. cholerae strain N16961 genome

Genome
component
Peak centeraSite centerbSite P valuecSequencedGene(s) close to
CRP binding sitese
CRP
regulatedf
Chromosome I5577155796.53.5E−03AGTGACTAAGCGTACA23Sa1ND
9987199790.58.3E−03TGTTACGAATATTACAglpE<(VC0103)Yes
134815134755.55.6E−03TTTGTTTTGGATCGATVC0142a<>VC0143Yes
150732150753.53.2E−07TGAGATTCAAATCACAVC0159<>16SbYes
177320177327.53.2E−03CATAATCTGTATCAAAVC0175Yes
242521242505.57.1E−03TAAGGTTTAAGCCATT(VC0237)No
249227249187.59.8E−03TTTGAAGGATGGCGTT(VC0242)No
264229264210.55.1E−03TTAAATATGTATCATAVC0258><VC0259No
274582NAgNANA(VC0269)No
294153294127.57.6E−03TGTAGGTGATATCTCAVC0284No
454607454517.53.4E−03TGTGTTGTTGCTCAATVC0423<>VC0424Yes
516492516436.51.7E−03TGACAGTAATATCACTVC0485<>VC0486No
522621522571.55.3E−03AGTCCATTTGCTCACAVC0489No
527963527988.51.1E−03AGTTATTTTTTTCACTVC0493<>VC0494No
569841569895.54.9E−04AACGATTTTCCTCATAVC0537<>VC0538Yes
657711657766.55.2E−05TGTGACTCCCTTCGCAVC0621No
676093676049.52.4E−03AATGATATAAATCCAAompU<>greAYes
707829707908.57.3E−03GCCGCTTGGCATCACAVC0661<>VC0662No
712256712206.51.6E−03TGCAATCTAAGTCATTVC0665No
713923714007.51.1E−03TTAGAATTTAATCGTAVC0666No
748263748338.54.1E−03GGCGAGATTACGCGTAVC0699<>VC0700No
756779756854.58.4E−07TGTGATAAAAGTCACTVC0706No
762509762522.51.8E−03TCTGACAATTATCTCGVC0713Yes
788515788501.56.9E−03TGTGAAATTTCACAAGVC0734No
815345815346.53.6E−07TGTGATATGATTCACAengAYes
818079818158.52.6E−03GGTTAATTAAGTCGCAVC0765Yes
819917819936.51.0E−02CGTCCGCAATATCAAAVC0766<>VC0767No
880295880357.55.3E−03TATGAGAAAGATAAAA(VC0821)No
888697888746.52.1E−03TGCAATTAAGTTCTCAtcpI<>tcpPYes
894874894817.57.9E−03TATTATTGGATTCATT(VC0833)No
904634NANANA(VC0842)Yes
906219NANANAacfA<>acfDNo
911066911128.53.1E−03TATGATGAAAAACATTVC0845><VC0846No
936058936026.51.5E−03AAAGAGCTAAATCGTT(VC0870)No
999018999093.59.6E−03CTTGGTTGTTTTCAATVC0932<>VC0934Yes
10118351011745.52.4E−03AGTGAGCTTGCCCAAG(VC0947)No
10375601037566.51.2E−03TTCGACGCATTTCAAAVC0972Yes
10540131054031.51.4E−05CGTGATTTTTGTCGCGtppB<>rfaHNo
10611591061198.51.5E−06GGTGATTAGGATCACAnagA<>VC0995No
10901451090112.55.6E−04TGTGATGTTTGGCATCVC1021No
11002041100264.54.0E−05TGTGATGCAAATCGATVC1034Yes
11394711139535.54.0E−03TCTGATTATTTTCAAGVC1073No
11749541174946.56.7E−06TGTGGTTTATGTCACAVC1104No
11987581198847.56.0E−05TGTGAGCTGTGGCACTVC1130<>VC1131No
12125391212568.54.7E−03AGAGGCGAAATTCATTVC1142<>clpSYes
12247861224787.54.2E−06TGTGATACTGGTCTCAVC1152<>tfoXNo
13829251382894.55.9E−03TGTGAGAATTGTTAATVC1301Yes
13967721396717.51.2E−03ATTGATGTCACTCAAAVC1313<>VC1314Yes
14089361408937.53.8E−03TTTTAACTGGTTCACAVC1323<>VC1325Yes
15490421549038.56.9E−03TGTGCAATTTGTCTGArtxB<>rtxHYes
15681641568072.55.5E−03TATGAAAATGATGATActxANo
16836521683636.52.0E−03AGTGATGGGGTTAACAVC1571<>VC1572No
17035841703620.56.4E−03TAATAAAAATGTCACAVC1592No
17416001741668.54.7E−05TGTGATACGCTTCTCGVC1620<>VC1621Yes
17766781776642.54.8E−03AGTGATTTATCACTAAVC1649<>VC1650No
17895101789532.51.9E−05TATGACCAGTATCGCAVC1656<>VC1658No
19034701903498.58.0E−04TTTGAGTTAATTCAAT(VC1736)Yes
19196511919579.56.2E−03TGTGCTAAATACAACG(VC1771)Yes
1922932NANANA(VC1773)No
19672951967278.52.1E−06CGAGATCTAAATCACAVC1825<>VC1826No
19847761984846.53.3E−04TGAGAACTTTGTCAAAVC1844Yes
19900741990055.54.4E−03GTCGAGACCACTCATAVC1851No
19940541994088.55.4E−03ATTAATAAAAATCAAAompT<>dinGYes
20048392004771.52.9E−03TTTTAACAAAGTCACAVC1864<>VC1865Yes
20553952055442.56.2E−03CATCAAATTTTTCACAVC1904<>VC1905Yes
20590772059085.59.7E−03TGCCACGCAACGCTCAcysB<>VC1909Yes
21683872168407.54.2E−03TTTGAGGAATTCCGCTVC2013Yes
21906662190734.55.0E−03TGTGCGAATGTTAACAVC2035No
21931102193078.51.1E−05AACGATATAAATCACAVC2036<>VC2037Yes
23744762374498.53.0E−05TGTGAGCTTTATCATGVC2219<>VC2220No
24337432433742.51.1E−06GGTGATTAAAATCACAVC2278<>VC2279No
24576082457631.51.3E−06AGCGATTAAGATCACAVC2303<>VC2305No
25373892537396.54.6E−03TGTGAATTCGGTGAAAgltBNo
25503522550386.58.7E−03TGTTACTGGTATAACA(VC2385)No
25513562551299.53.5E−03AGTGATAAAAGTGAAG(VC2386)No
25586082558615.53.7E−03GATGAATTTATTCATCVC2390Yes
26103822610307.59.8E−03GCTGATTCGCGTCTTGVC2435<>tolCNo
26538382653780.57.5E−04CGCGAGTCTCTTCAAAVC2473Yes
26673262667406.58.8E−03TAATATTCACGTCAAAVC2486No
26993902699329.51.5E−03GGTGATGGTCGCCACTpyrBNo
27433492743361.58.1E−04ATCGCGTCACATCACAVC2561<>cpdBNo
27879392787903.53.0E−04TGAGATAAACCCCACAVC2618Yes
28452462845280.55.7E−07TGTGATTTTCATCACGVC2677No
28647572864763.59.2E−04ATAGATAAAACTCTCAVC2698<>aspAYes
29334682933432.57.5E−04TTTGATTATCATCAAC16sgND
29368692936904.53.1E−04TTCGATACCAAGCACA23ShND
 
Chromosome II1206712085.55.4E−08TGTGATCCGAATCACTVCA0012<>VCA0013Yes
8636486274.55.8E−03GTCGAAATTCGCCACAVCA0076No
9901698927.52.0E−07TGTGATCTTTATCACTVCA0089No
114856114864.58.6E−03TTTAATAGATTTCTCAVCA0104<>VCA0105No
152867152849.57.4E−04TGTGATTGATGTGGCAVCA0138No
181749181688.52.5E−03TGAGAAAGCATTCAAAVCA0164<>VCA0165No
217815217798.56.0E−03TGTTATAAAAACCAAT(VCA0200)No
237015237049.56.6E−03TAAGAATTATTTTACAhlyB<>hlyANo
247246247185.57.5E−03TTGGCATAGCATCACAVCA0224<>VCA0225Yes
267292267253.53.7E−03TGATAGGTAGATCACCVCA0246<>VCA0247No
300413300391.58.4E−03TGCCCTATCTATCAAAVCA0281Yes
334916334914.54.3E−03ATTGACAGCTATCTAA(VCA0334)No
458259458254.53.8E−03CGTGATTAAAAACGTCVCA0523Yes
481906481918.52.0E−03TTTCATAAAAGTCACGVCA0544<>VCA0545Yes
492167492243.56.9E−07TGTGATTGGAATCACTVCA0554<>VCA0556No
564616NANANA(VCA0628)Yes
598381598370.54.9E−04GTTGACAACAGTCACA(VCA0662)<>VCA0663No
630430630499.51.5E−03AATGATAGATAACACAVCA0691Yes
687485687472.53.3E−03CGTGATCGACATTAAA(VCA0742)>VCA0743No
741821741822.57.8E−06TGTGCTTTACATCACTVCA0801Yes
784413784364.52.1E−05TGTGATGCCGCTCGCAVCA0840Yes
785337785352.55.1E−04TTTGAACTTAGTCATTVCA0843Yes
801056801043.51.7E−05TGTGAAATGGCTCGCAVCA0849Yes
832501832514.56.2E−03TGCGACCTTGATTAACVCA0880Yes
849892849906.53.0E−03GTTGACGCCTTTCTCAVCA0896Yes
870862870876.51.1E−03AATGATCAGGGGCAAAVCA0917<>VCA0919Yes
874452874411.54.1E−03TATAAATCAAATCATTVCA0923Yes
897315897352.54.8E−06AGCGAGCCAAATCACAVCA0945<>VCA0946Yes
902411902377.56.6E−03TGAAACACTTACCACTVCA0952Yes
930851NANANA(VCA0982)<>VCA0983No
963517963536.58.2E−04TGTTAAGCAAATCGCAVCA1013<>VCA1015No
994614994588.52.5E−05CATGACACAGGTCACAVCA1043<>(VCA1044)Yes
10159571015902.52.0E−05TTTGACCATTATCACAVCA1063No
  • a Center of peak for CRP binding in ChIP-seq assays.

  • b Center of binding site identified by FIMO (Find Individual Motif Occurrences) using DNA motif recovered from the ChIP-seq data by MEME (Multiple Em for Motif Elicitation).

  • c P value assigned to each site by FIMO describing the significance of the match to the motif generated by MEME.

  • d DNA sequence of site identified by FIMO.

  • e Parentheses indicate that the CRP site is located within that gene. Pairs of arrows represent divergent (<>) or convergent (><) genes. Single arrows indicate that gene pairs are in the same orientation on either the forward (>) or reverse (<) strand. Gene identification numbers are shown unless an alternative name for the gene is provided in the genome annotation or the wider literature. Genes regulated by ToxR or ToxT are underlined.

  • f CRP-regulated genes described by Fong and Yildiz (41). ND, not detected: genes encoding stable rRNA species were not included in the transcriptome analysis and so no change in transcription could be detected.

  • g NA, not applicable.