RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit       
Name: nhaAR
Gene(s): nhaA, nhaR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
[IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Dover N., et al., 2001
[2] Pannuri A., et al., 2012
Promoter
Name: nhaAp2
+1: 17317
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 172
Sequence: tacttttcctaattaatccctcaggaatcctcaccttaagctatgattatctaggcttagGgtcactcgtgagcgcttaca
                              -35              -10          +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Dover N., et al., 2001
[3] Huerta AM., et al., 2003


Transcription unit          
Name: nhaAR
Synonym(s): OP00281
Gene(s): nhaA, nhaR   Genome Browser M3D Gene expression COLOMBOS
Note(s): The nhaAR operon is induced by the presence of monovalent cations, high pH, low temperature, and stationary phase Padan E,1999. White-Ziegler CA, Um S, Pérez NM, Berns AL, Malhowski AJ, Young S,2008
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
[IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Dover N., et al., 2001
[2] Pannuri A., et al., 2012
[4] Rahav-Manor O., et al., 1992
Promoter
Name: nhaAp1
+1: 17458
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 31
Sequence: aattattcctacactataatctgattttaacgatgattcgtgcggggtaaaatagtaaaaAcgatctattcacctgaaaga
                           -35                  -10         +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Dover N., et al., 2001
[3] Huerta AM., et al., 2003
[5] Karpel R., et al., 1991
TF binding sites (TFBSs)
[H-NS,-] 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 H-NS repressor nhaAp1 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [8]
[NhaR,+] 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 NhaR-Na+ activator nhaAp1 17384 17400 -66.0 ttcttcaataGCTCGTAAAAAACGAATtattcctaca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [4], [6], [7], [8]
proximal NhaR-Na+ activator nhaAp1 17406 17422 -44.0 cgaattattcCTACACTATAATCTGATtttaacgatg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [4], [6], [7], [8]
proximal NhaR-Na+ activator nhaAp1 17416 17432 -34.0 ctacactataATCTGATTTTAACGATGattcgtgcgg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [4], [6], [7]
proximal NhaR-Na+ activator nhaAp1 17447 17464 -3.0 gtgcggggtaAAATAGTAAAAACGATCTattcacctga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [4], [6], [7], [8]


Transcription unit       
Name: nhaR
Gene(s): nhaR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-HINF] Inferred by a human based on computational evidence


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts

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


Reference(s)    

 [1] Dover N., Padan E., 2001, Transcription of nhaA, the main Na(+)/H(+) antiporter of Escherichia coli, is regulated by Na(+) and growth phase., J Bacteriol 183(2):644-53

 [2] Pannuri A., Yakhnin H., Vakulskas CA., Edwards AN., Babitzke P., Romeo T., 2012, Translational repression of NhaR, a novel pathway for multi-tier regulation of biofilm circuitry by CsrA., J Bacteriol 194(1):79-89

 [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] Rahav-Manor O., Carmel O., Karpel R., Taglicht D., Glaser G., Schuldiner S., Padan E., 1992, NhaR, a protein homologous to a family of bacterial regulatory proteins (LysR), regulates nhaA, the sodium proton antiporter gene in Escherichia coli., J Biol Chem 267(15):10433-8

 [5] Karpel R., Alon T., Glaser G., Schuldiner S., Padan E., 1991, Expression of a sodium proton antiporter (NhaA) in Escherichia coli is induced by Na+ and Li+ ions., J Biol Chem 266(32):21753-9

 [6] Carmel O., Dover N., Rahav-Manor O., Dibrov P., Kirsch D., Karpel R., Schuldiner S., Padan E., 1994, A single amino acid substitution (Glu134-->Ala) in NhaR1 increases the inducibility by Na+ of the product of nhaA, a Na+/H+ antiporter gene in Escherichia coli., EMBO J 13(8):1981-9

 [7] Carmel O., Rahav-Manor O., Dover N., Shaanan B., Padan E., 1997, The Na+-specific interaction between the LysR-type regulator, NhaR, and the nhaA gene encoding the Na+/H+ antiporter of Escherichia coli., EMBO J 16(19):5922-9

 [8] Dover N., Higgins CF., Carmel O., Rimon A., Pinner E., Padan E., 1996, Na+-induced transcription of nhaA, which encodes an Na+/H+ antiporter in Escherichia coli, is positively regulated by nhaR and affected by hns., J Bacteriol 178(22):6508-17

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