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| Operon |  |
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| Name: | icd |
| This page displays every known transcription unit of this operon and their known regulation. | |
| Name: | icd |
| Gene(s): | icd Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | Under nitrogen-rich growth conditions, the expression of the icdA gene increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, gene expression was decreased in the cyoA and cydB and Fnr mutants. It is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the two promoters that transcribe the gene could be regulated by the regulators Kumar R,2011 The expression of the gene icdA is decreased under acidic growth conditions in microaerobiosis but not in aerobiosis Marzan LW,2013 |
| Evidence: | [ITCR] Inferred through co-regulation |
| Reference(s): | [1] Prost JF., et al., 1999 |
| Promoter | |
| Name: | icdAp2 |
| +1: | 1194961 |
| Sigma Factor: | Sigma70 Sigmulon |
| Distance from start of the gene: | 162 |
| Sequence: |
tctaaaagaagttttttgcatggtattttcagagattatgaattgccgcattatagcctaAtaacgcgcatctttcatgac -35 -10 +1 |
| Evidence: |
[ICWHO] [TIM] |
| Reference(s): |
[2] Huerta AM., et al., 2003 [1] Prost JF., et al., 1999 |
| Name: | icd | |||||||||
| Synonym(s): | OP00148 | |||||||||
| Gene(s): | icd Genome Browser M3D Gene expression COLOMBOS | |||||||||
| Note(s): | icdA gene expression is repressed under anaerobiosis by nitrate and glycerol and by the transcription factors ArcA, FNR, and IHF. It is not known which of two promoters is regulating FNR and IHF. Under aerobiosis, icdA expression appears to still be partially repressed by arcA and LB medium or minimal glucose medium and it is induced by acetate Chao G,1997. Under nitrogen-rich growth conditions, the expression of the icdA gene increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, gene expression was decreased in the cyoA and cydB and Fnr mutants. It is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the two promoters that transcribe the gene could be regulated by the regulators Kumar R,2011 The expression of the gene icdA is decreased under acidic growth conditions in microaerobiosis but not in aerobiosis Marzan LW,2013 Three direct repeats (DRs) of ArcA-P are involved in the repression of the icdAp1 promoter Park DM,2014 Mutating the two sites with the highest information (DR1 and DR2) eliminated ArcA binding to all three DRs and ArcA repression of the icdA gene. Furthermore, when DR3 (the site with the lowest information content) was mutated, both eliminated DNA binding to DR3 and significantly weakened icdA repression were observed, despite the fact that binding to DR1 and DR2 was intact. A four-DR engineered element was added, and it enhanced the ArcA-binding site in icdA Park DM,2014 All three DR elements are important for full cooperative anaerobic repression of the icdA gene, and the degeneracy in these DR elements is important for preserving O2-dependent regulation Park DM,2014 Binding of ArcA in the promoter region of icdAp1 showed plasticity in the binding site architectures, which could be a common regulatory strategy for regulators that acts as a repressor at multiple targets Park DM,2014 |
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| Reference(s): |
[3] Herold C., et al., 1990 [1] Prost JF., et al., 1999 |
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| Promoter | ||||||||||
| Name: | icdAp1 | |||||||||
| +1: | 1195008 | |||||||||
| Sigma Factor: | Sigma70 Sigmulon | |||||||||
| Distance from start of the gene: | 115 | |||||||||
| Sequence: |
gcattatagcctaataacgcgcatctttcatgacggcaaacaatagggtagtattgacaaGccaattacaaatcattaaca -35 -10 +1 |
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| Evidence: |
[HIPP] [ICWHO] [IHBCE] [RS-EPT-CBR] [TIM] |
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| Reference(s): |
[4] Chao G., et al., 1997 [2] Huerta AM., et al., 2003 [1] Prost JF., et al., 1999 [5] Salgado H, et al., 2012 |
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| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| proximal | ArcA-phosphorylated | repressor | icdAp1 | 1194998 | 1195013 | -3.0 | caatagggtaGTATTGACAAGCCAATtacaaatcat | nd | [GEA], [APIORCISFBSCS], [BPP] | [4], [6], [7], [8] |
| proximal | ArcA-phosphorylated | repressor | icdAp1 | 1195016 | 1195031 | 16.0 | aagccaattaCAAATCATTAACAAAAaattgctcta | nd | [EME], [GEA], [AIBSPD], [APIORCISFBSCS], [BPP], [CCE] | [4], [6], [7], [8], [9] |
| Reference(s) |
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|---|---|
[ICWHO] Inferred computationally without human oversight