RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: zwf
Synonym(s): OP00294
Gene(s): zwf   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expresion of zwf gene is induced under oxidative stress Lu C,2003 and under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013
MarA, SoxS, and Rob activate zwf trancription in vitro; all three depend on the same zwf sequences for activation. However, only SoxS and MarA induce glucose 6-phosphate dehydrogense activity (zwf product) in vivo.
The expression of the zwf gene was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants of two transcriptional regulators, Fnr and Fur Kumar R,2011
The transcription of the gene zwf is enhanced under high oxygen saturation (300%) Baez A,2013
Reference(s): [1] Ariza RR., et al., 1995
Promoter
Name: zwfp
+1: 1936376
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 62
Sequence: tcgcacgggtggataagcgtttacagttttcgcaagctcgtaaaagcagtacagtgcaccGtaagaaaattacaagtatac
                                  -35                  -10  +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[3] Lisser S., et al., 1993
[4] Rowley DL., et al., 1991
TF binding sites (TFBSs)
[Cra,-] 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 Cra repressor zwfp 1936403 1936420 -35.5 gggtggataaGCGTTTACAGTTTTCGCAagctcgtaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [13]
[FNR,-] 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 FNR repressor zwfp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [14]
[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+ repressor zwfp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [14]
[MarA,+] 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 MarA activator zwfp 1936420 1936439 -54.0 gcttttcccgTAATCGCACGGGTGGATAAGcgtttacagt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5], [6], [7], [8]
[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
proximal Rob activator zwfp 1936420 1936439 -54.0 gcttttcccgTAATCGCACGGGTGGATAAGcgtttacagt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [7]
[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
proximal SoxS activator zwfp 1936418 1936437 -51.5 ttttcccgtaATCGCACGGGTGGATAAGCGtttacagttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [8], [9], [10], [11], [12]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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

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

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

 [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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Ariza RR., Li Z., Ringstad N., Demple B., 1995, Activation of multiple antibiotic resistance and binding of stress-inducible promoters by Escherichia coli Rob protein., J Bacteriol 177(7):1655-61

 [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] Lisser S., Margalit H., 1993, Compilation of E. coli mRNA promoter sequences., Nucleic Acids Res 21(7):1507-16

 [4] Rowley DL., Wolf RE., 1991, Molecular characterization of the Escherichia coli K-12 zwf gene encoding glucose 6-phosphate dehydrogenase., J Bacteriol 173(3):968-77

 [5] Gillette WK., Martin RG., Rosner JL., 2000, Probing the Escherichia coli transcriptional activator MarA using alanine-scanning mutagenesis: residues important for DNA binding and activation., J Mol Biol 299(5):1245-55

 [6] Jair KW., Martin RG., Rosner JL., Fujita N., Ishihama A., Wolf RE., 1995, Purification and regulatory properties of MarA protein, a transcriptional activator of Escherichia coli multiple antibiotic and superoxide resistance promoters., J Bacteriol 177(24):7100-4

 [7] Jair KW., Yu X., Skarstad K., Thony B., Fujita N., Ishihama A., Wolf RE., 1996, Transcriptional activation of promoters of the superoxide and multiple antibiotic resistance regulons by Rob, a binding protein of the Escherichia coli origin of chromosomal replication., J Bacteriol 178(9):2507-13

 [8] Martin RG., Gillette WK., Rhee S., Rosner JL., 1999, Structural requirements for marbox function in transcriptional activation of mar/sox/rob regulon promoters in Escherichia coli: sequence, orientation and spatial relationship to the core promoter., Mol Microbiol 34(3):431-41

 [9] Fawcett WP., Wolf RE., 1995, Genetic definition of the Escherichia coli zwf "soxbox," the DNA binding site for SoxS-mediated induction of glucose 6-phosphate dehydrogenase in response to superoxide., J Bacteriol 177(7):1742-50

 [10] Jair KW., Fawcett WP., Fujita N., Ishihama A., Wolf RE., 1996, Ambidextrous transcriptional activation by SoxS: requirement for the C-terminal domain of the RNA polymerase alpha subunit in a subset of Escherichia coli superoxide-inducible genes., Mol Microbiol 19(2):307-17

 [11] Pomposiello PJ., Bennik MH., Demple B., 2001, Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate., J Bacteriol 183(13):3890-902

 [12] 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

 [13] Shimada T., Yamamoto K., Ishihama A., 2011, Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli., J Bacteriol 193(3):649-59

 [14] Kumar R., Shimizu K., 2011, Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures., Microb Cell Fact 10:3

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