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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 |
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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 |
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Promoter | |||||||||||
Name: | nrdAp | ||||||||||
+1: | 2344755 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 110 | ||||||||||
Sequence: |
ttcctgagttatccacaaagttatgcacttgcaagagggtcattttcacactatcttgcaGtgaatcccaaacataccccc -35 -10 +1 |
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Evidence: |
[COMP-AINF] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
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Reference(s): |
[3] Huerta AM., et al., 2003 [4] Tuggle CK., et al., 1986 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
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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] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
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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] |
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] |
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] |
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 |
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] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
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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] |
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 | ![]() |
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Regulation, transcriptional elongation | |
Attenuator type: | Transcriptional |
Strand: | forward |
Structure type | Energy | LeftPos | RightPos | Sequence (RNA-strand) | |
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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" |
Reference(s) |
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