RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: chaC
Gene(s): chaC   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[IC] Inferred by curator
Reference(s): [1] Reitzer L., et al., 2001
[2] Zaslaver A., et al., 2006
Promoter
Name: chaCp
+1: 1272422
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 85
Sequence: agttaaagctattcgtgcggtgttgccttgcaagtggtccgtggattgcatattgtcccgTtagtggtttcaaaatgagca
                                   -24         -12          +1                   
Note(s): We assigned a putative transcription start site to this promoter based on the observation that the majority of the σ54-dependent promoters, whose transcription start sites were determined experimentally, present a distance of 11 nucleotides between the transcription start site and the -12 box Barrios H,1999.
Zaslaver et al. demonstrated in 2006, by means of a library of fluorescent transcription fusions, that this promoter can be transcribed in vitro Zaslaver A,2006. Based on this, a putative promoter was suggested, but the +1 site of the transcription initiation has not been determined, although there exists promoter activity.
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-AINF-SIMILAR-TO-CONSENSUS]
[EXP-IEP]
Reference(s): [3] Huerta AM., et al., 2003
[1] Reitzer L., et al., 2001
[2] Zaslaver A., et al., 2006
TF binding sites (TFBSs)
[Rob,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Rob activator chaCp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [4]


Transcription unit       
Name: chaBC
Gene(s): chaB, chaC   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [5] Ivey DM., et al., 1993


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [EXP-IEP] Inferred from expression pattern

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis


Reference(s)    

 [1] Reitzer L., Schneider BL., 2001, Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli., Microbiol Mol Biol Rev 65(3):422-44, table of contents

 [2] Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette MG., Alon U., 2006, A comprehensive library of fluorescent transcriptional reporters for Escherichia coli., Nat Methods 3(8):623-8

 [3] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [4] Wang Z., Xue T., Hu D., Ma Y., 2020, A Novel Butanol Tolerance-Promoting Function of the Transcription Factor Rob in Escherichia coli., Front Bioeng Biotechnol 8:524198

 [5] Ivey DM., Guffanti AA., Zemsky J., Pinner E., Karpel R., Padan E., Schuldiner S., Krulwich TA., 1993, Cloning and characterization of a putative Ca2+/H+ antiporter gene from Escherichia coli upon functional complementation of Na+/H+ antiporter-deficient strains by the overexpressed gene., J Biol Chem 268(15):11296-303

RegulonDB