RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
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: [EXP-IEP-COREGULATION] 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: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[1] Prost JF., et al., 1999
TF binding sites (TFBSs)
[Cra,+] 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 Cra activator icdAp2 1194876 1194893 -76.5 gaacgttgcgAGCTGAATCGCTTAACCTggtgatttct nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [1]


Transcription unit          
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
Reference(s): [3] Herold C., et al., 1990
[1] Prost JF., et al., 1999
Promoter
Name: icdAp1
+1: 1195008
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 115
Sequence: gcattatagcctaataacgcgcatctttcatgacggcaaacaatagggtagtattgacaaGccaattacaaatcattaaca
                          -35                    -10        +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
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
TF binding sites (TFBSs)
[ArcA,-] 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 ArcA-phosphorylated repressor icdAp1 1194998 1195013 -3.0 caatagggtaGTATTGACAAGCCAATtacaaatcat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4], [6], [7], [8]
proximal ArcA-phosphorylated repressor icdAp1 1195016 1195031 16.0 aagccaattaCAAATCATTAACAAAAaattgctcta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-CHIP], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [4], [6], [7], [8], [9]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [COMP-HINF] Inferred by a human based on computational evidence

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

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

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

 [EXP-IEP-MICROARRAY] Expression microarray evidence

 [COMP-AINF-PATTERN-DISCOVERY] Automated inference based on sequence pattern discovery

 [EXP-CHIP-CHIP] ChIP-chip evidence


Reference(s)    

 [1] Prost JF., Negre D., Oudot C., Murakami K., Ishihama A., Cozzone AJ., Cortay JC., 1999, Cra-dependent transcriptional activation of the icd gene of Escherichia coli., J Bacteriol 181(3):893-8

 [2] 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

 [3] Herold C., Birge EA., 1990, Location of icdA and fadR on the physical map of Escherichia coli., J Bacteriol 172(12):6618

 [4] Chao G., Shen J., Tseng CP., Park SJ., Gunsalus RP., 1997, Aerobic regulation of isocitrate dehydrogenase gene (icd) expression in Escherichia coli by the arcA and fnr gene products., J Bacteriol 179(13):4299-304

 [5] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [6] Park DM., Kiley PJ., 2014, The influence of repressor DNA binding site architecture on transcriptional control., MBio 5(5)

 [7] Salmon KA., Hung SP., Steffen NR., Krupp R., Baldi P., Hatfield GW., Gunsalus RP., 2005, Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA., J Biol Chem 280(15):15084-96

 [8] Shalel-Levanon S., San KY., Bennett GN., 2005, Effect of oxygen, and ArcA and FNR regulators on the expression of genes related to the electron transfer chain and the TCA cycle in Escherichia coli., Metab Eng 7(5-6):364-74

 [9] Federowicz S., Kim D., Ebrahim A., Lerman J., Nagarajan H., Cho BK., Zengler K., Palsson B., 2014, Determining the control circuitry of redox metabolism at the genome-scale., PLoS Genet 10(4):e1004264

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