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| Operon |  |
|---|---|
| Name: | nuoABCEFGHIJKLMN |
| This page displays every known transcription unit of this operon and their known regulation. | |
| Name: | nuoABCEFGHIJKLMN | |||||||||
| Synonym(s): | nuo1-14 | |||||||||
| Gene(s): | nuoN, nuoM, nuoL, nuoK, nuoJ, nuoI, nuoH, nuoG, nuoF, nuoE, nuoC, nuoB, nuoA Genome Browser M3D Gene expression COLOMBOS | |||||||||
| Note(s): | Computer analysis revealed one inverted repeat upstream of nuoM that could form a stable stem-and-loop structure. It may serve as a signal of transcription regulation, causing RNA polymerase pausing. Each insertion used to construct a nuo mutant (nuoB-C, nuoF, nuoG, nuoH, nuoI, nuoM, and nuoN) exerted a polar effect upon dowstream transcription. With the exception of nuoB, this mutant synthesized detectable levels of the NuoCD subunit but did not synthesize any NuoG subunit. NuoG affects the promoter activity of this operon, although it is not known whether the effect of NuoG on the promoter is a direct one. The nuo operon is regulated by O2 and nitrate via ArcA, NarL, FNR, and IHF. The main effect is an anaerobic repression by ArcA and nitrate stimulation by NarL. Under nitrogen-rich growth conditions, the expression of the nuoA gene increased in a mutant for the transcriptional regulator Fnr. However, under nitrogen-limited growth conditions, the gene expression was decreased. Under both nitrogen-limited and nitrogen-rich growth conditions, the expression of nuoA increased in the mutants for cyoA and Fur. However, it is unknown if the effects of the transcriptional regulators act directly on the 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 nuoA is increased under acidic growth conditions in microaerobiosis Marzan LW,2013 nuoABC, among other genes involved in carbon source transport and metabolism, were downregulated in two MG1655 lysogens carrying closely related Stx2a phages O104 and PA8 1208335|. CpxR represses transcription of the nuo and cyo operons in enteropathogenic Escherichia coli (EPEC), and these complexes confer adaptation to stresses that compromise envelope integrity. CpxR does not repress nuo transcription through steric hindrance of RNA polymerase Guest RL, Wang J, Wong JL, Raivio TL,2017 On the other hand, overproduction of NlpE downregulated nuo transcription in a CpxRA-dependent manner Guest RL, Wang J, Wong JL, Raivio TL,2017 Two putative binding sites were found -104 bp upstream and 48 bp downstream of the nuoA transcription start site that were required for repression of nuo-lux expression upon activation of the Cpx response Guest RL, Wang J, Wong JL, Raivio TL,2017 Based on site mutation and gene expression analyses, the functionality of these sites was demonstrated in mid-log-phase cells respiring in terrific broth conditions Guest RL, Wang J, Wong JL, Raivio TL,2017 Further, it is possible that an interaction between CpxR proteins bound separately at the proximal and distal binding sites prevents nuo transcription initiation through a looping mechanism Browning DF, Busby SJ,2004 A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for nuoA and nuoB . This structure could regulate the expression of the genes, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020. |
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| Evidence: | [BTEI] Boundaries of transcription experimentally identified | |||||||||
| Reference(s): |
[1] Archer CD., et al., 1995 [2] Leif H., et al., 1995 |
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| Promoter | ||||||||||
| Name: | nuoAp2 | |||||||||
| +1: | 2405162 | |||||||||
| Sigma Factor: | Sigma70 Sigmulon | |||||||||
| Distance from start of the gene: | 90 | |||||||||
| Sequence: |
atagaaaggagtaaaaaaccacatcaattagctgtataaaagaatttctacagtgattgtAaggttttttttattcctccc -35 -10 +1 |
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| Evidence: |
[ICWHO] [TIM] |
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| Reference(s): |
[3] Bongaerts J., et al., 1995 [4] Huerta AM., et al., 2003 [5] Weidner U., et al., 1993 |
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| Terminator(s) | ||||||||||
| Type: | rho-independent | |||||||||
| Sequence: | ttcagaaaaaCCGCCGAGCATGTCGGCGGctttctgact | |||||||||
| Reference(s): | [5] Weidner U., et al., 1993 | |||||||||
| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| remote | ArcA-phosphorylated | repressor | nuoAp2 | 2405263 | 2405277 | -108.0 | tgctaatggtGTTGATATTATGTAAactaatgtga | nd | [GEA], [BCE], [SM] | [7], [8], [9] |
| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| proximal | IHF | repressor | nuoAp2 | 2405222 | 2405234 | -66.0 | ttgttaaagtTGACAAAAGGTTAtagaaaggag | nd | [GEA], [APIORCISFBSCS], [BPP] | [3], [10] |
| proximal | IHF | repressor | nuoAp2 | 2405230 | 2405242 | -74.0 | agaaacttttGTTAAAGTTGACAaaaggttata | nd | [GEA], [APIORCISFBSCS], [BPP] | [3], [10] |
| proximal | IHF | repressor | nuoAp2 | 2405239 | 2405251 | -83.0 | ctaatgtgaaGAAACTTTTGTTAaagttgacaa | nd | [GEA], [APIORCISFBSCS], [BPP], [SM] | [3], [10] |
| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| remote | NarL-phosphorylated | activator | nuoAp2 | 2405281 | 2405287 | -122.0 | gggcattaaaTGCTAATggtgttgata | nd | [GEA], [APIORCISFBSCS] | nd |
| Name: | nuoABCEFGHIJKLMN | |||||||||
| Synonym(s): | nuo1-14 | |||||||||
| Gene(s): | nuoN, nuoM, nuoL, nuoK, nuoJ, nuoI, nuoH, nuoG, nuoF, nuoE, nuoC, nuoB, nuoA Genome Browser M3D Gene expression COLOMBOS | |||||||||
| Note(s): | Computer analysis revealed one inverted repeat upstream of nuoM that could form a stable stem-and-loop structure. It may serve as a signal of transcription regulation, causing RNA polymerase pausing. Each insertion used to construct a nuo mutant (nuoB-C, nuoF, nuoG, nuoH, nuoI, nuoM, and nuoN) exerted a polar effect upon dowstream transcription. With the exception of nuoB, this mutant synthesized detectable levels of the NuoCD subunit but did not synthesize any NuoG subunit. NuoG affects the promoter activity of this operon, although it is not known whether the effect of NuoG on the promoter is a direct one. Under nitrogen-rich growth conditions, the expression of the nuoA gene increased in a mutant for the transcriptional regulator Fnr. However, under nitrogen-limited growth conditions, the gene expression was decreased. Under both nitrogen-limited and nitrogen-rich growth conditions, the expression of nuoA increased in the mutants for cyoA and Fur. However, it is unknown if the effects of the transcriptional regulators act directly on the 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 nuoA is increased under acidic growth conditions in microaerobiosis Marzan LW,2013 nuoABC, among other genes involved in carbon source transport and metabolism, were downregulated in two MG1655 lysogens carrying closely related Stx2a phages O104 and PA8 1208335|. A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for nuoA and nuoB. This structure could regulate the expression of the genes, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020. |
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| Evidence: | [BTEI] Boundaries of transcription experimentally identified | |||||||||
| Reference(s): |
[3] Bongaerts J., et al., 1995 [13] Falk-Krzesinski HJ., et al., 1998 [5] Weidner U., et al., 1993 |
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| Promoter | ||||||||||
| Name: | nuoAp1 | |||||||||
| +1: | 2405335 | |||||||||
| Distance from start of the gene: | 263 | |||||||||
| Sequence: |
tcctgtcaaaatagacccgtattttttccattgcttcacaacggacacgattcaacaacaTctaattatcctggagtcgtc |
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| Evidence: | [TIM] | |||||||||
| Reference(s): | [3] Bongaerts J., et al., 1995 | |||||||||
| Terminator(s) | ||||||||||
| Type: | rho-independent | |||||||||
| Sequence: | ttcagaaaaaCCGCCGAGCATGTCGGCGGctttctgact | |||||||||
| Reference(s): | [5] Weidner U., et al., 1993 | |||||||||
| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| remote | Fis | activator | nuoAp1 | 2405466 | 2405480 | -138.5 | acgtaaatttGTTGCTGCGTTTTTGttatggaatg | nd | [GEA], [APIORCISFBSCS], [BPP] | [10], [14] |
| remote | Fis | activator | nuoAp1 | 2405526 | 2405540 | -198.5 | gtcccgaacgCACAAATAATCGCCTgaaaaaaatc | nd | [GEA], [APIORCISFBSCS], [BPP] | [10], [14] |
| remote | Fis | activator | nuoAp1 | 2405563 | 2405577 | -235.5 | tacaaaactgTTCATTTTTCAACCAccagagattc | nd | [GEA], [APIORCISFBSCS], [BPP] | [10], [14] |
| Name: | nuoMN |
| Gene(s): | nuoN, nuoM Genome Browser M3D Gene expression COLOMBOS |
| Evidence: | [BTEI] Boundaries of transcription experimentally identified [PAGTSBP] Products of adjacent genes in the same biological process |
| Reference(s): | [15] Zaslaver A., et al., 2006 |
| Promoter | |
| Name: | nuoMp |
| +1: | Unknown |
| Note(s): | Zaslaver et al. demonstrated in 2006, by means of a library of fluorescent transcription fusions, that this promoter can be transcribed in vitro Zaslaver A,2006. Based on this, a putative promoter was suggested, but the +1 site of the transcription initiation has not been determined, although there exists promoter activity. |
| Evidence: | [IEP] |
| Reference(s): | [15] Zaslaver A., et al., 2006 |
| Terminator(s) | |
| Type: | rho-independent |
| Sequence: | ttcagaaaaaCCGCCGAGCATGTCGGCGGctttctgact |
| Reference(s): | [5] Weidner U., et al., 1993 |
| Reference(s) |
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|---|---|
[ICWHO] Inferred computationally without human oversight