RegulonDB RegulonDB 11.1: Operon Form
   

nrdAB-yfaE operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: nrdAB-yfaE
Synonym(s): OP00063, nrd, nrdA
Gene(s): nrdA, nrdB, yfaE   Genome Browser M3D Gene expression COLOMBOS
Note(s): Based on ChIP-chip and consensus sequences (Virtual Footprint), a site of NsrR negatively controlling the nrdB gene has been identified Partridge JD,2009 The consensus sequence found for this gene is AAAATGCCTTAT, which lies in the intergenic region nrdA-nrdB.
DnaA acts both as an activator and a repressor on the nrdAB-yfaE operon, depending on the changing concentration of DnaA-ATP during the cell cycle Olliver A,2010 DnaA-ATP binds cooperatively to two high-affinity sites upstream of -35 (-48 and -36.5) and to a lower-affinity site overlapping the nrdAB promoter region (-14) Olliver A,2010
Based on the DNase I protection pattern, it was shown that DnaA-ADP binds to the sites upstream of -35 (-48 and -36.5) with lower affinity than DnaA-ATP, although at high DnaA-ADP/DnaA-ATP ratios Olliver A,2010
It has been shown that nrdA is not regulated in vivo by ArgP Marbaniang CN,2011 However, ArgP slightly binds to the regulatory regions of nrdA in vitro, as it exhibits low-affinity binding to ArgP Marbaniang CN,2011
Gel shift assay Han JS,1998. Marbaniang CN,2011 and DNase I protection assay results Han JS,1998 showed that ArgP binds in tandem upstream of the transcription start site of the gene nrd. Despite strong experimental evidence, those authors did not identify the center positions of the binding sites. The curator identified the consensus sequence of ArgP and assigned the possible central position of these binding sites, based on similarity to consensus sequences. According to this evidence, the curator assigned six possible binding sites of 20 bp for ArgP, located at bp -163.5, -190.5, -218.5, -244.5, -281.5, and -334.5 relative to the transcription start site of nrd. Based on DNase I protection assay results Han JS,1998, the curator suggested that ArgP binds with higher affinity to the binding sites located at a -244.5, -218.5, and -190.5.
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
A second region under control of H-NS was identified 127 bp downstream of the nrdA transcriptional start site within the nrdA structural gene. This region is rich in AT content (58.6%), but it does not contain either of the two H-NS consensus sequences Cendra Mdel M,2013
Evidence: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Jordan A., et al., 1996
[2] Martin JE., et al., 2011
Promoter
Name: nrdAp
+1: 2344755
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 110
Sequence: ttcctgagttatccacaaagttatgcacttgcaagagggtcattttcacactatcttgcaGtgaatcccaaacataccccc
                             -35                    -10     +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Huerta AM., et al., 2003
[4] Tuggle CK., et al., 1986
TF binding sites (TFBSs)
[ArgP,+] 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 ArgP activator nrdAp 2344411 2344430 -334.5 atggcttagcATTTAACAATAACCGAATAGaaaacaacca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] W [6], [7]
remote ArgP activator nrdAp 2344464 2344483 -281.5 aatctcttacATTCGCTTATATATTGACCAcaactgatac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] W [6], [9]
remote ArgP activator nrdAp 2344501 2344520 -244.5 tacatcagatTATGTGATGACTCGTGCTTAgatcaatttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] W [6], [9]
remote ArgP activator nrdAp 2344527 2344546 -218.5 cttagatcaaTTTTTGCAATCATTAGCAAAaagattaata nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] W [6], [9]
remote ArgP activator nrdAp 2344555 2344574 -190.5 aaaagattaaTAAGCCATCTATATCAATTTatctaaccta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] W [6], [9]
remote ArgP activator nrdAp 2344582 2344601 -163.5 tttatctaacCTATTATGCCGTTCAAGAAAtcgccgaaca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] W [6], [9]
[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 nrdAp 2344608 2344629 -136.5 gaaatcgccgAACAGTTATTTTTAACAAATTTttctcttccc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [10]
[DnaA,+] 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 DnaA-ATP activator nrdAp 2344703 2344711 -48.0 ccttcctgagTTATCCACAaagttatgca nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [8], [9]
proximal DnaA-ATP activator nrdAp 2344714 2344722 -36.5 tatccacaaaGTTATGCACttgcaagagg nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [8], [9]
[DnaA,-] 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 DnaA-ATP repressor nrdAp 2344737 2344745 -14.0 aagagggtcaTTTTCACACtatcttgcag nd [COMP-HINF-SIMILAR-TO-CONSENSUS] nd [11]
[Fis,+] 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 Fis activator nrdAp 2344425 2344439 -323.0 aacaataaccGAATAGAAAACAACCatttcgccat nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [8]
remote Fis activator nrdAp 2344479 2344493 -269.0 cttatatattGACCACAACTGATACatcagattat nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [8]
remote Fis activator nrdAp 2344549 2344563 -199.0 ttagcaaaaaGATTAATAAGCCATCtatatcaatt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [8]
remote Fis activator nrdAp 2344592 2344606 -156.0 ctattatgccGTTCAAGAAATCGCCgaacagttat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [8]
remote Fis activator nrdAp 2344620 2344634 -128.0 cagttattttTAACAAATTTTTCTCttcccattga nd [COMP-HINF-SIMILAR-TO-CONSENSUS] nd nd
[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
remote H-NS repressor nrdAp 2344309 2344323 -439.0 gtgcgtcataATTCAAGTTAATAACcttcagggat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [5]
remote H-NS repressor nrdAp 2344333 2344347 -415.0 ccttcagggaTATCAGTTATATTTAaactaaatta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [5]
[NrdR,-] 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 NrdR-Zn2+ repressor nrdAp 2344740 2344755 -7.5 agggtcatttTCACACTATCTTGCAGtgaatcccaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [12]
proximal NrdR-Zn2+ repressor nrdAp 2344772 2344787 25.5 ccaaacatacCCCCTATATATAGTGTtctaagcagc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [12]


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


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -6.8 2344673 2344693 tgacctaaggTGCGCGAAAGCCACTTTTTCcttcctgagt
  anti-terminator -8.8 2344646 2344682 cccattgactTTCCCGGACACCTTGTCTGACCTAAGGTGCGCGAAAgccacttttt
  anti-anti-terminator -4.3 2344651 2344665 tgactttcccGGACACCTTGTCTGacctaaggtg
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

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

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

 [IC] Inferred by curator

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Jordan A., Aragall E., Gibert I., Barbe J., 1996, Promoter identification and expression analysis of Salmonella typhimurium and Escherichia coli nrdEF operons encoding one of two class I ribonucleotide reductases present in both bacteria., Mol Microbiol 19(4):777-90

 [2] Martin JE., Imlay JA., 2011, The alternative aerobic ribonucleotide reductase of Escherichia coli, NrdEF, is a manganese-dependent enzyme that enables cell replication during periods of iron starvation., Mol Microbiol 80(2):319-34

 [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] Tuggle CK., Fuchs JA., 1986, Regulation of the operon encoding ribonucleotide reductase in Escherichia coli: evidence for both positive and negative control., EMBO J 5(5):1077-85

 [5] 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

 [6] Marbaniang CN., Gowrishankar J., 2011, Role of ArgP (IciA) in Lysine-Mediated Repression in Escherichia coli., J Bacteriol 193(21):5985-96

 [7] Ohtsubo T., Matsuda O., Iba K., Terashima I., Sekiguchi M., Nakabeppu Y., 1998, Molecular cloning of AtMMH, an Arabidopsis thaliana ortholog of the Escherichia coli mutM gene, and analysis of functional domains of its product., Mol Gen Genet 259(6):577-90

 [8] Augustin LB., Jacobson BA., Fuchs JA., 1994, Escherichia coli Fis and DnaA proteins bind specifically to the nrd promoter region and affect expression of an nrd-lac fusion., J Bacteriol 176(2):378-87

 [9] Han JS., Kwon HS., Yim JB., Hwang DS., 1998, Effect of IciA protein on the expression of the nrd gene encoding ribonucleoside diphosphate reductase in E. coli., Mol Gen Genet 259(6):610-4

 [10] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [11] Olliver A., Saggioro C., Herrick J., Sclavi B., 2010, DnaA-ATP acts as a molecular switch to control levels of ribonucleotide reductase expression in Escherichia coli., Mol Microbiol 76(6):1555-71

 [12] 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

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