RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: norVW
Gene(s): norV, norW   Genome Browser M3D Gene expression COLOMBOS
Note(s): Although the NorR regulator protein can bind independently to each of the three binding sites in the norV promoter region controlling the flavorubredoxin gene expression, the presence of these three sites is required for in vivo induction of the norVW operon. Using protein cross-linking experiments it was demonstrated that NorR binds to the promoter of the flavorubredoxin gene as a trimer Justino MC,2005.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
[EXP-IEP] Inferred from expression pattern
[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Gardner AM., et al., 2003
[2] Hutchings MI., et al., 2002
[3] da Costa PN., et al., 2003
Promoter
Name: norVp
+1: 2832439
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 37
Sequence: ttatttatagagtaaaaacaatcagataaaaaactggcacgcaatctgcaattagcaagaCatctttttagaacacgctga
                                   -24         -12          +1                   
Note(s): This promoter was identified by microarray assays with a mutant σ54 strain and a σ54-overexpressing strain, and by σ54-related promoter element identification Zhao K,2010
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.
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-AINF-SIMILAR-TO-CONSENSUS]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [4] Huerta AM., et al., 2003
[5] Reitzer L., et al., 2001
[6] Tucker NP., et al., 2004
[7] Zhao K., et al., 2010
TF binding sites (TFBSs)
[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
remote FNR repressor norVp 2832292 2832305 -140.5 aaactcatctTTGCCTCACTGTCAatttgactat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [3]
[IHF,+] 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 IHF activator norVp 2832385 2832397 -48.0 aattttatttATAGAGTAAAAACaatcagataa nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [6]
[IHF,-] 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 IHF repressor norVp 2832449 2832461 17.0 catctttttaGAACACGCTGAATaaattgaggt nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [6]
[NarL,-] 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 NarL-phosphorylated repressor norVp 2832358 2832364 -78.0 tcattttgacTACTCATtaatgggcat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [3]
proximal NarL-phosphorylated repressor norVp 2832367 2832373 -69.0 ctactcattaATGGGCAtaattttatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [3]
[NarP,-] 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 NarP-phosphorylated repressor norVp 2832353 2832368 -78.0 gatagtcattTTGACTACTCATTAATgggcataatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [3]
proximal NarP-phosphorylated repressor norVp 2832362 2832377 -69.0 tttgactactCATTAATGGGCATAATtttatttata nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [3]
[NorR,+] 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
remote NorR activator norVp 2832301 2832313 -132.0 tttgcctcacTGTCAATTTGACTatagatattg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [2], [6], [8], [9], [10]
remote NorR activator norVp 2832322 2832334 -111.0 ctatagatatTGTCATATCGACCatttgattga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [2], [6], [8], [9], [10]
proximal NorR activator norVp 2832346 2832358 -87.0 tttgattgatAGTCATTTTGACTactcattaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [2], [6], [8], [9], [10], [11]


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

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

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

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

 [EXP-IEP] Inferred from expression pattern

 [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.

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

 [EXP-GSELEX] high throughput Genomic SELEX-chip evidence


Reference(s)    

 [1] Gardner AM., Gessner CR., Gardner PR., 2003, Regulation of the nitric oxide reduction operon (norRVW) in Escherichia coli. Role of NorR and sigma54 in the nitric oxide stress response., J Biol Chem 278(12):10081-6

 [2] Hutchings MI., Mandhana N., Spiro S., 2002, The NorR protein of Escherichia coli activates expression of the flavorubredoxin gene norV in response to reactive nitrogen species., J Bacteriol 184(16):4640-3

 [3] da Costa PN., Teixeira M., Saraiva LM., 2003, Regulation of the flavorubredoxin nitric oxide reductase gene in Escherichia coli: nitrate repression, nitrite induction, and possible post-transcription control., FEMS Microbiol Lett 218(2):385-93

 [4] 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

 [5] 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

 [6] Tucker NP., D'Autr?aux B., Studholme DJ., Spiro S., Dixon R., 2004, DNA binding activity of the Escherichia coli nitric oxide sensor NorR suggests a conserved target sequence in diverse proteobacteria., J Bacteriol 186(19):6656-60

 [7] Zhao K., Liu M., Burgess RR., 2010, Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis., Nucleic Acids Res 38(4):1273-83

 [8] Gardner AM., Helmick RA., Gardner PR., 2002, Flavorubredoxin, an inducible catalyst for nitric oxide reduction and detoxification in Escherichia coli., J Biol Chem 277(10):8172-7

 [9] Justino MC., Goncalves VM., Saraiva LM., 2005, Binding of NorR to three DNA sites is essential for promoter activation of the flavorubredoxin gene, the nitric oxide reductase of Escherichia coli., Biochem Biophys Res Commun 328(2):540-4

 [10] Tucker NP., D'autreaux B., Spiro S., Dixon R., 2006, Mechanism of transcriptional regulation by the Escherichia coli nitric oxide sensor NorR., Biochem Soc Trans 34(Pt 1):191-4

 [11] Tucker N., D'autreaux B., Spiro S., Dixon R., 2005, DNA binding properties of the Escherichia coli nitric oxide sensor NorR: towards an understanding of the regulation of flavorubredoxin expression., Biochem Soc Trans 33(Pt 1):181-3

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