RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: hicAB
Gene(s): hicA, hicB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
[IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Jorgensen MG., et al., 2009
Promoter
Name: hicAp1
+1: 1509221
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 65
Sequence: cttccttcctgattttgcattgcattctgccgttgcggcgatttagtgctattttcgagcAaattacacacggaggtaaac
                           -35                    -10       +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[1] Jorgensen MG., et al., 2009
TF binding sites (TFBSs)
[CRP,+] 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
proximal CRP-cyclic-AMP activator hicAp1 1509152 1509174 -58.5 cgcaaagaaaTTCTGGAATCTTCCTTCCTGATTttgcattgca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [3]


Transcription unit          
Name: hicAB
Gene(s): hicA, hicB   Genome Browser M3D Gene expression COLOMBOS
Note(s): When hicAB mRNA is produced from hicAp2, only the hicB cistron is translated; that is, this mRNA produces only HicB but not the HicA protein. This happens because this transcript starts just 1 base upstream of the SD sequence of hicA Turnbull KJ,2017.
The hicAB operon is induced in response to amino acid and carbon starvation Jorgensen MG,2009
Evidence: [COMP-AINF] Inferred computationally without human oversight
[IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Promoter
Name: hicAp2
+1: 1509275
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 11
Sequence: tcgagcaaattacacacggaggtaaacactaatgtttactttgttgatatactcagcggcAgggaggcgatgtgaaacaaa
                       -35                      -10         +1                   
Note(s): The activation of the promoter hicAp2 is not affected by the Sxy protein, whereas the hicAp1 promoter is Turnbull KJ,2017.
Evidence: [COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Turnbull KJ., et al., 2017
TF binding sites (TFBSs)
[HicB,-] 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
proximal HicB repressor hicAp2 1509234 1509255 -30.5 ttacacacggAGGTAAACACTAATGTTTACTTtgttgatata nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF] Inferred by a human based on computational evidence

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

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

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Jorgensen MG., Pandey DP., Jaskolska M., Gerdes K., 2009, HicA of Escherichia coli defines a novel family of translation-independent mRNA interferases in bacteria and archaea., J Bacteriol 191(4):1191-9

 [2] 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

 [3] Turnbull KJ., Gerdes K., 2017, HicA toxin of Escherichia coli derepresses hicAB transcription to selectively produce HicB antitoxin., Mol Microbiol 104(5):781-792

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