RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: fpr
Synonym(s): OP00261
Gene(s): fpr   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [1] Bianchi V., et al., 1993
[2] Jair KW., et al., 1995
Promoter
Name: fprp
+1: 4114499
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 27
Sequence: tcgattgagccttccagtccttcgggactggaatttttttgttcggagaacgaagataagGcaagtcaatcaaaacaggag
                                 -35                        +10                  
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
Reference(s): [3] Huerta AM., et al., 2003
[4] Martin RG., et al., 1999
TF binding sites (TFBSs)
[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 fprp 4114548 4114567 -58.5 atcctctgatTGATTTGATCGATTGAGCCTtccagtcctt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5]
[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 fprp 4114546 4114565 -56.5 cctctgattgATTTGATCGATTGAGCCTTCcagtccttcg 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] C [2], [4], [6], [7], [8]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -17.4 4114517 4114548 cgattgagccTTCCAGTCCTTCGGGACTGGAATTTTTTTGTtcggagaacg
  anti-terminator -6.53 4114539 4114585 ccggaaatgcAGGTGCACATCCTCTGATTGATTTGATCGATTGAGCCTTCCAGTCCttcgggactg
  anti-anti-terminator -9.6 4114562 4114608 tccactatctGGATCGCAAAGACCCGGAAATGCAGGTGCACATCCTCTGATTGATTtgatcgattg
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [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


Reference(s)    

 [1] Bianchi V., Reichard P., Eliasson R., Pontis E., Krook M., Jornvall H., Haggard-Ljungquist E., 1993, Escherichia coli ferredoxin NADP+ reductase: activation of E. coli anaerobic ribonucleotide reduction, cloning of the gene (fpr), and overexpression of the protein., J Bacteriol 175(6):1590-5

 [2] 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

 [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] 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

 [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] Martin RG., Rosner JL., 2011, Promoter discrimination at class I MarA regulon promoters mediated by glutamic acid 89 of the MarA transcriptional activator of Escherichia coli., J Bacteriol 193(2):506-15

 [7] 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

 [8] 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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