RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: nrdDG
Gene(s): nrdG, nrdD   Genome Browser M3D Gene expression COLOMBOS
Note(s): FNR is responsible for anaerobic activation of the nrdDG operon. Both sites of FNR (-64.5 and -33.5) have an additive effect in coordinating nrdDG operon expression in response to shifting oxygen concentrations Roca I,2008
The nrdD gene is upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides 32385082.

H-NS represses expression of the class Ia (nrdAB operon) and class III (nrdDG operon) ribonucleotide reductases (RNRs) both in aerobically and in anaerobically growing cells. Under aerobic conditions, repression occurs during the exponential phase of growth as well as at the transition from the exponential to the stationary phase, a period when no dNTPs are needed. Under anoxic conditions, repression occurs mainly in exponentially growing cells Cendra Mdel M,2013
Evidence: [ITCR] Inferred through co-regulation
Reference(s): [1] Garriga X., et al., 1996
Promoter
Name: nrdDp
+1: 4462838
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 178
Sequence: caaaaaaagctcaaacatccttgatgcaaagcactatatatagactttaaaatgcgtcccAacccaatatgttgtattaat
                     -35                        -10         +1                   
Note(s):

Evidence: [ICWHO]
[TIM]
Reference(s): [2] Boston T., et al., 2003
[3] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR1 activator nrdDp 4462865 4462878 -33.5 ctcaaacatcCTTGATGCAAAGCACtatatataga nd [APIORCISFBSCS], [BPP], [GEA], [SM] [2], [4]
proximal FNR2 activator nrdDp 4462896 4462909 -64.5 tgctttttacTTTGAGCTACATCAAaaaaagctca nd [APIORCISFBSCS], [BPP], [GEA], [SM] [2], [4]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS repressor nrdDp nd nd nd nd nd [BPP], [GEA], [IGI] [6]
[NrdR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NrdR-Zn2+ repressor nrdDp 4462822 4462837 9.5 aatgcgtcccAACCCAATATGTTGTATtaatcgacta nd [APIORCISFBSCS], [BPP], [GEA] [5]
proximal NrdR-Zn2+ repressor nrdDp 4462853 4462868 -22.5 cttgatgcaaAGCACTATATATAGACTttaaaatgcg nd [APIORCISFBSCS], [BPP], [GEA] [5]
Note(s): 1The operon nrdDG is induced under anaerobiosis in the stationary phase, and this induction is FNR dependent.
2The operon nrdDG is induced under anaerobiosis in the stationary phase, and this induction is FNR dependent.1The operon nrdDG is induced under anaerobiosis in the stationary phase, and this induction is FNR dependent.
2The operon nrdDG is induced under anaerobiosis in the stationary phase, and this induction is FNR dependent.


Transcription unit       
Name: nrdG
Gene(s): nrdG   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [7] Zaslaver A., et al., 2006
Promoter
Name: nrdGp
+1: Unknown
Evidence: [IEP]
Reference(s): [7] Zaslaver A., et al., 2006


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [SM] Site mutation

 [IGI] Inferred from genetic interaction

 [IEP] Inferred from expression pattern


Reference(s)    

 [1] Garriga X., Eliasson R., Torrents E., Jordan A., Barbe J., Gibert I., Reichard P., 1996, nrdD and nrdG genes are essential for strict anaerobic growth of Escherichia coli., Biochem Biophys Res Commun 229(1):189-92

 [2] Boston T., Atlung T., 2003, FNR-mediated oxygen-responsive regulation of the nrdDG operon of Escherichia coli., J Bacteriol 185(17):5310-3

 [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] Roca I., Ballana E., Panosa A., Torrents E., Gibert I., 2008, Fumarate and nitrate reduction (FNR) dependent activation of the Escherichia coli anaerobic ribonucleotide reductase nrdDG promoter., Int Microbiol 11(1):49-56

 [5] Torrents E., Grinberg I., Gorovitz-Harris B., Lundstrom H., Borovok I., Aharonowitz Y., Sjoberg BM., Cohen G., 2007, NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes., J Bacteriol 189(14):5012-21

 [6] Cendra Mdel M., Juarez A., Madrid C., Torrents E., 2013, H-NS is a novel transcriptional modulator of the ribonucleotide reductase genes in Escherichia coli., J Bacteriol 195(18):4255-63

 [7] Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette MG., Alon U., 2006, A comprehensive library of fluorescent transcriptional reporters for Escherichia coli., Nat Methods 3(8):623-8

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