RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: feaR
Gene(s): feaR   Genome Browser M3D Gene expression COLOMBOS
Note(s): ArcA could be a negative regulator of feaR expression Zeng J,2013.
The expression of feaR is regulated by carbon or nitrogen limitation Zeng J,2013.
It is probable that the activities of both feaRp2 and feaRp1 are inhibited by binding of QseB to its downstream binding site Pasupuleti S,2018 If the affinity of QseB-P for the upstream site is higher than the affinity for the downstream site, feaR transcription would be maximally induced by intermediate levels of QseB-P and repressed by higher levels of QseB-P Pasupuleti S,2018
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Yamashita M., et al., 1996
Promoter
Name: feaRp2
+1: 1447309
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 26
Sequence: tatttcctatagtcaggctcattagcttcgtttattgcaacacaaatgcaacaataaaaaTacatttcacagagcgaaaac
                                        -35            -10  +1                   
Evidence: [COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Zeng J., et al., 2013
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
remote CRP-cyclic-AMP activator feaRp2 1447410 1447431 -111.5 tcgctttgtcAGCTGTGACAAGCTCCGCAAATcgtgacaata nd [COMP-HINF-SIMILAR-TO-CONSENSUS] nd [1]
[Nac,+] 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 Nac activator feaRp2 1447334 1447348 -32.5 gtcaggctcaTTAGCTTCGTTTATTgcaacacaaa nd [COMP-HINF] nd [2]
[NsrR,-] 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 NsrR repressor feaRp2 1447303 1447314 2.0 atgcaacaatAAAAATACATTTcacagagcga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [5]
[PhoB,-] 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 PhoB-phosphorylated repressor feaRp2 1447317 1447335 -17.0 gcttcgtttaTTGCAACACAAATGCAACAataaaaatac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
[QseB,-] 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 QseB-Phosphorylated repressor feaRp2 1447306 1447318 -3.0 acaaatgcaaCAATAAAAATACAtttcacagag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4]


Transcription unit          
Name: feaR
Gene(s): feaR   Genome Browser M3D Gene expression COLOMBOS
Note(s): The position of the putative GlrR-binding sites suggests that the feaRp1 promoter is the most likely candidate for induction of feaRp1 transcription; this promoter also has the closest match to the σ70 -35 and -10 consensus sequences Pasupuleti S,2018
Based on sequence analysis, it is possible that GlrR regulates feaR expression together with QseB, since the GACA bases that overlap the -10 region of the feaRp3 promoter and the ACA bases that overlap the -35 region of the feaRp2 promoter are the last four and three bases, respectively, of the reported GlrR (QseF) consensus binding site Pasupuleti S,2018
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Yamashita M., et al., 1996
Promoter
Name: feaRp1
+1: 1447349
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 66
Sequence: cgtgacaataaccgcttatgtctctatgcctgacaagacttatttcctatagtcaggctcAttagcttcgtttattgcaac
                                   -35               -10    +1                   
Evidence: [COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Zeng J., et al., 2013
TF binding sites (TFBSs)
[QseB,+] 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 QseB-Phosphorylated activator feaRp1 1447392 1447404 -49.0 caaatcgtgaCAATAACCGCTTAtgtctctatg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4]


Transcription unit       
Name: feaR
Synonym(s): maoB
Gene(s): feaR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Yamashita M., et al., 1996
Promoter
Name: feaRp
+1: 1447367
Distance from start of the gene: 84
Sequence: gtgacaagctccgcaaatcgtgacaataaccgcttatgtctctatgcctgacaagacttaTttcctatagtcaggctcatt
Evidence: [COMP-HINF-POSITIONAL-IDENTIFICATION]
Reference(s): [6] Ferrandez A., et al., 1997


Transcription unit       
Name: feaR
Gene(s): feaR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Yamashita M., et al., 1996
Promoter
Name: feaRp3
+1: 1447394
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 111
Sequence: ttcgctgtgacattcgctttgtcagctgtgacaagctccgcaaatcgtgacaataaccgcTtatgtctctatgcctgacaa
                                 -35                  -10   +1                   
Evidence: [COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Zeng J., et al., 2013


Evidence    

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

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

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

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

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

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

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


Reference(s)    

 [1] Yamashita M., Azakami H., Yokoro N., Roh JH., Suzuki H., Kumagai H., Murooka Y., 1996, maoB, a gene that encodes a positive regulator of the monoamine oxidase gene (maoA) in Escherichia coli., J Bacteriol 178(10):2941-7

 [2] Zeng J., Spiro S., 2013, Finely tuned regulation of the aromatic amine degradation pathway in Escherichia coli., J Bacteriol 195(22):5141-50

 [3] Yang C., Huang TW., Wen SY., Chang CY., Tsai SF., Wu WF., Chang CH., 2012, Genome-wide PhoB binding and gene expression profiles reveal the hierarchical gene regulatory network of phosphate starvation in Escherichia coli., PLoS One 7(10):e47314

 [4] Pasupuleti S., Sule N., Manson MD., Jayaraman A., 2018, Conversion of Norepinephrine to 3,4-Dihdroxymandelic Acid in Escherichia coli Requires the QseBC Quorum-Sensing System and the FeaR Transcription Factor., J Bacteriol 200(1)

 [5] Partridge JD., Bodenmiller DM., Humphrys MS., Spiro S., 2009, NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility., Mol Microbiol 73(4):680-94

 [6] Ferrandez A., Prieto MA., Garcia JL., Diaz E., 1997, Molecular characterization of PadA, a phenylacetaldehyde dehydrogenase from Escherichia coli., FEBS Lett 406(1-2):23-7

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