RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: zinT
Synonym(s): yodA
Gene(s): zinT   Genome Browser M3D Gene expression COLOMBOS
Note(s): yodA expression is induced by cadmiun and hydrogen peroxide Puskarova A,2002
Based on a double relA spoT mutation, it was shown that loss of these genes stringently abolished the induction of zinT during cadmium exposure. However, ppGpp is not sufficient for yodA induction since its expression is not elevated during stationary phase Puskarova A,2002
The zinT gene is upregulated when E. coli is exposed to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Puskarova A., et al., 2002
Promoter
Name: zinTp
+1: 2041346
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 29
Sequence: tgctctcgtttcctaagagttgttgcattttgctatatgttacaatataacattacacatCatatacattaactctggagg
                       -35                    -10           +1                   
Note(s): The activity of this promoter is induced by cadmium Puskarova A,2002
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[1] Puskarova A., et al., 2002
TF binding sites (TFBSs)
[Fur,+] 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 Fur-Fe2+ activator zinTp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [1]
[OxyR,+] 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 OxyR activator zinTp 2041358 2041374 21.5 tatacattaaCTCTGGAGGAAACTGTTttggcgattc nd [EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL] S [4]
[SoxS,+] 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 SoxS activator zinTp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [1]
[Zur,-] 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 Zur-Zn2+ repressor zinTp 2041319 2041341 -16.0 tgcattttgcTATATGTTACAATATAACATTACacatcatata nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [3]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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

 [EXP-IEP-RNA-SEQ] high throughput RNA-seq evidence

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

 [EXP-CHIP-EXO-MANUAL] ChIP-exo evidence used in manual assertion

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


Reference(s)    

 [1] Puskarova A., Ferianc P., Kormanec J., Homerova D., Farewell A., Nystrom T., 2002, Regulation of yodA encoding a novel cadmium-induced protein in Escherichia coli., Microbiology 148(Pt 12):3801-11

 [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] Panina EM., Mironov AA., Gelfand MS., 2003, Comparative genomics of bacterial zinc regulons: enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins., Proc Natl Acad Sci U S A 100(17):9912-7

 [4] Seo SW., Kim D., Szubin R., Palsson BO., 2015, Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655., Cell Rep 12(8):1289-99

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