RegulonDB RegulonDB 10.8: Operon Form
   

chiPQ operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: chiPQ
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: chiP-ybfN
Synonym(s): ybfMN
Gene(s): chiP, chiQ   Genome Browser M3D Gene expression COLOMBOS
Note(s): Rasmussen et. al., (2009) identified a ybfM-specific RNA species; however, it may be generated by premature termination in the ybfM-N intergenvic region or by degradation of the full-length transcript Rasmussen AA,2009
Regions protected by GalR and GalS upstream of the chiPp promoter were identified by DNase I footprinting Plumbridge J,2014 A binding site for both regulators was identified, 167.5 bp upstream of the chiPp promoter. In addition, two other weak binding sites for GalS nearer to the chiPp promoter were also identified Plumbridge J,2014 However, mutation in neither galR nor galS had any effect on chiP-lacZ expression Plumbridge J,2014
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Rasmussen AA., et al., 2009
Promoter
Name: chiPp
+1: 708236
Distance from start of the gene: 98
Sequence: cttacattctggttacagaaagagattgataattcgcgtcgcgaaaaatagtctgttcctGtagtcagcgagacttttctc
Evidence: [TIM]
Reference(s): [1] Rasmussen AA., et al., 2009
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP activator chiPp 708158 708174 -70.5 catcaaaataTGTGCGGTTGCTCATGTtcttacattc nd [APIORCISFBSCS] [2]
[NagC,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote NagC repressor chiPp 707980 708004 -244.0 cggcgtttttTCTGCTTTTCTTCGCGAATTAATTCcgcttcgcaa nd [BPP], [GEA] [2]
proximal NagC2 repressor chiPp 708203 708225 -22.0 gaaagagattGATAATTCGCGTCGCGAAAAATAgtctgttcct nd [AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [2], [3]
Note(s): 2This binding site was determined from a computational prediction based on different statistical methods Oberto J.,2010 The function of the binding site was assigned according to the distance from the transcription start, with NagC as the transcriptional repressor.3This binding site was determined from a computational prediction based on different statistical methods Oberto J.,2010 The function of the binding site was assigned according to the distance from the transcription start, with NagC as the transcriptional repressor.


Transcription unit       
Gene(s): chiQ   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight


Evidence    

 [TIM] Transcription initiation mapping

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [CV(GEA)] cross validation(GEA)


Reference(s)    

 [1] Rasmussen AA., Johansen J., Nielsen JS., Overgaard M., Kallipolitis B., Valentin-Hansen P., 2009, A conserved small RNA promotes silencing of the outer membrane protein YbfM., Mol Microbiol 72(3):566-77

 [2] Plumbridge J., Bossi L., Oberto J., Wade JT., Figueroa-Bossi N., 2014, Interplay of transcriptional and small RNA-dependent control mechanisms regulates chitosugar uptake in Escherichia coli and Salmonella., Mol Microbiol 92(4):648-58

 [3] Oberto J., 2010, FITBAR: a web tool for the robust prediction of prokaryotic regulons., BMC Bioinformatics 11:554

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