RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: deoCABD
Synonym(s): OP00024
Gene(s): deoC, deoA, deoB, deoD   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Albrechtsen H., et al., 1980
[2] Svenningsen BA. 1975
Promoter
Name: deoCp1
+1: 4616679
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 644
Sequence: gaggtaacgccagaaacgttttattcgaacatcgatctcgtcttgtgttagaattctaacAtacggttgcaacaacgcatc
                        -35                      -10        +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Huerta AM., et al., 2003
[4] Valentin-Hansen P., et al., 1982
Terminator(s)
Type: rho-independent
Sequence: tgccttgtgaAGCCGGAGCGGGAGACTGCTCCGGCtttttagtat
Reference(s): [5] Larsen JE., et al., 1987
TF binding sites (TFBSs)
[DeoR,-] 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 DeoR repressor deoCp1 4616063 4616078 -608.0 cgcgcggcaaTCCCTTCTTTTTCACAcagcaagtta nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] nd nd
proximal DeoR repressor deoCp1 4616663 4616678 -8.0 atctcgtcttGTGTTAGAATTCTAACatacggttgc nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] nd nd
remote DeoR repressor deoCp1 4616939 4616954 269.0 gcaggaagctGTGGGTAAGGCAGATTgttttctgct nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] nd nd


Transcription unit          
Name: deoCABD
Synonym(s): OP00024, deo
Gene(s): deoC, deoA, deoB, deoD   Genome Browser M3D Gene expression COLOMBOS
Note(s): Gavigan et al. (1999) and Perini et al. (1996) showed that CytR binds in tandem in the regulated intergenic region Gavigan SA,1999. Perini LT,1996. On the other hand, in 1997, Pedersen and Valentin-Hanses showed that CytR binds to octamer repeats, GTTGCATT in either the direct or inverted orientation and preferably separated by 2 or 3 bp Pedersen H,1997. Jorgensen CI,1998. For this reason the length of the CytR DNA-binding site is variable.
However, footprinting analyses showed that the dimers of CytR are flanked or sandwiched by two dimers of CRP Chahla M,2003. Shin M,2001. Mollegaard NE,1993. Pedersen H,1991. Sogaard-Andersen L,1991. Sogaard-Andersen L,1993. Thus, the binding sites of CytR located in this region were assigned by the curator in agreement based on similarity to the consensus sequence and on the data from the footprinting assays and mutational evidence Perini LT,1996. Holst B,1992. Holt AK,2010. Pedersen H,1997. Sogaard-Andersen L,1990. Zolotukhina MA,2002.
The repressor CytR and the activator CRP, two dimeric proteins, interact to form a complex repressor nucleoprotein in the intergenic region. When only CRP is bound to this promoter, it functions as an activator, and then, when CytR binds to DNA and to CRP, the activation is repressed because CytR masks an activating region of CRP that otherwise would contact the RNA polymerase to activate transcription Mollegaard NE,1993. Sogaard-Andersen L,1991. Valentin-Hansen P, Søgaard-Andersen L, Pedersen H,1996. Meibom KL, Kallipolitis BH, Ebright RH, Valentin-Hansen P,2000. Sogaard-Andersen L,1993. The CytR protein cannot act alone; the synergistic DNA binding is increased by direct interaction with CRP Mollegaard NE,1993. Pedersen H,1991. Sogaard-Andersen L,1991. Sogaard-Andersen L,1993. Sogaard-Andersen L,1990. Sogaard-Andersen L,1990. Sogaard-Andersen L,1991. At times CytR also repositions CRP to alternative DNA-binding sites that are not functional for activation Valentin-Hansen P, Søgaard-Andersen L, Pedersen H,1996.
The deoCAB genes are upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Albrechtsen H., et al., 1980
[2] Svenningsen BA. 1975
Promoter
Name: deoCp2
+1: 4617278
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 45
Sequence: gatttccttaattgtgatgtgtatcgaagtgtgttgcggagtagatgttagaatactaacAaactcgcaaggtgaatttta
                       -35                       -10        +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Huerta AM., et al., 2003
[4] Valentin-Hansen P., et al., 1982
Terminator(s)
Type: rho-independent
Sequence: tgccttgtgaAGCCGGAGCGGGAGACTGCTCCGGCtttttagtat
Reference(s): [5] Larsen JE., et al., 1987
TF binding sites (TFBSs)
[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 deoCp2 4617174 4617195 -93.5 tgaaagtgaaTTATTTGAACCAGATCGCATTAcagtgatgca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17]
proximal CRP-cyclic-AMP activator deoCp2 4617227 4617248 -40.5 agatttccttAATTGTGATGTGTATCGAAGTGtgttgcggag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [7], [8], [9], [10], [12], [13], [14], [15], [16], [18]
[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 repressor deoCp2 4617174 4617195 -93.5 tgaaagtgaaTTATTTGAACCAGATCGCATTAcagtgatgca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17]
[CytR,-] 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 CytR repressor deoCp2 4617180 4617201 -87.5 tgaattatttGAACCAGATCGCATTACAGTGAtgcaaacttg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [7], [8], [9], [10], [11], [12], [13], [15], [16], [18]
proximal CytR repressor deoCp2 4617200 4617216 -70.5 gcattacagtGATGCAAACTTGTAAGTagatttcctt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [7], [8], [9], [10], [11], [12], [13], [15], [16], [18]
proximal CytR repressor deoCp2 4617208 4617227 -61.0 gtgatgcaaaCTTGTAAGTAGATTTCCTTAattgtgatgt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [7], [8], [9], [10], [11], [12], [13], [15], [16], [18]
[DeoR,-] 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 DeoR repressor deoCp2 4616383 4616398 -887.0 gtagccccctTTTGTGAAAATTTTATcatgcaccgg nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] nd nd
remote DeoR repressor deoCp2 4616962 4616977 -308.0 attgttttctGCTTCCAGTGCCAGAAaatggcgctt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] nd nd
proximal DeoR repressor deoCp2 4617262 4617277 -8.0 tgcggagtagATGTTAGAATACTAACaaactcgcaa nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IMP-SITE-MUTATION] nd nd
[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 deoCp2 4617169 4617183 -102.0 tcatttgaaaGTGAATTATTTGAACcagatcgcat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [6]
[ModE,-] 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 ModE-molybdate repressor deoCp2 4617231 4617254 -35.0 ttccttaattGTGATGTGTATCGAAGTGTGTTGCggagtagatg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [19]


Transcription unit       
Name: deoBD
Gene(s): deoB, deoD   Genome Browser M3D Gene expression COLOMBOS
Note(s): A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for deoB . This structure could regulate the expression of the gene, 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.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [20] Valentin-Hansen P., et al., 1984
Promoter
Name: deoBp
+1: 4619567
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 36
Sequence: gcaccggaaagcacaccaactgtctatcgccgtatcagcgaataacggtatactgatctgAtcatttaaatttgaagcact
                                                 -10        +1                   
Evidence: [COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [21] Salgado H, et al., 2012
[20] Valentin-Hansen P., et al., 1984
Terminator(s)
Type: rho-independent
Sequence: tgccttgtgaAGCCGGAGCGGGAGACTGCTCCGGCtttttagtat
Reference(s): [5] Larsen JE., et al., 1987


Transcription unit       
Name: deoABD
Gene(s): deoA, deoB, deoD   Genome Browser M3D Gene expression COLOMBOS
Note(s): It has been observed that the transcriptional regulator IHF binds near the start gene of deoA Kasho K,2021.
Evidence: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Promoter
Name: deoAp
+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: [EXP-IEP]
Reference(s): [22] Zaslaver A., et al., 2006


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -12.6 4620835 4620860 atggatttggGCGGAGCGTTGACTCCGCCTTTGTTatgtcacaaa
  terminator -7.7 4617293 4617319 gcaaggtgaaTTTTATTGGCGACAAGCCAGGAGAATgaaatgactg
  anti-terminator -16.19 4620771 4620841 tcggccagacTCTGGCAAAATATTTTGGTACTTCTGATATGGAATATGGCAAAGCCATGTTCTGATGGATTTGGGCGGAGcgttgactcc
  anti-anti-terminator -13.3 4620738 4620811 gctcactgggTCATCGTGAAACCTTCGCGGATATCGGCCAGACTCTGGCAAAATATTTTGGTACTTCTGATATGGAATATGGCaaagccatgt
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

 [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

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

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

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

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing

 [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] Inferred from expression pattern


Reference(s)    

 [1] Albrechtsen H., Ahmad SI., 1980, Regulation of the synthesis of nucleoside catabolic enzymes in Escherichia coli: further analysis of a deo Oc mutant strain., Mol Gen Genet 179(2):457-60

 [2] Svenningsen BA., 1975, Regulated in vitro synthesis of the enzymes of the deo operon of Escerichia coli. properties of the DNA directed system., Mol Gen Genet 137(4):289-304

 [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] Valentin-Hansen P., Aiba H., Schumperli D., 1982, The structure of tandem regulatory regions in the deo operon of Escherichia coli K12., EMBO J 1(3):317-322

 [5] Larsen JE., Albrechtsen B., Valentin-Hansen P., 1987, Analysis of the terminator region after the deoCABD operon of Escherichia coli K-12 using a new class of single copy number operon-fusion vectors., Nucleic Acids Res 15(13):5125-40

 [6] Gonzalez-Gil G., Bringmann P., Kahmann R., 1996, FIS is a regulator of metabolism in Escherichia coli., Mol Microbiol 22(1):21-9

 [7] Chahla M., Wooll J., Laue TM., Nguyen N., Senear DF., 2003, Role of protein-protein bridging interactions on cooperative assembly of DNA-bound CRP-CytR-CRP complex and regulation of the Escherichia coli CytR regulon., Biochemistry 42(13):3812-25

 [8] Mollegaard NE., Rasmussen PB., Valentin-Hansen P., Nielsen PE., 1993, Characterization of promoter recognition complexes formed by CRP and CytR for repression and by CRP and RNA polymerase for activation of transcription on the Escherichia coli deoP2 promoter., J Biol Chem 268(23):17471-7

 [9] Pedersen H., Sogaard-Andersen L., Holst B., Valentin-Hansen P., 1991, Heterologous cooperativity in Escherichia coli. The CytR repressor both contacts DNA and the cAMP receptor protein when binding to the deoP2 promoter., J Biol Chem 266(27):17804-8

 [10] Perini LT., Doherty EA., Werner E., Senear DF., 1996, Multiple specific CytR binding sites at the Escherichia coli deoP2 promoter mediate both cooperative and competitive interactions between CytR and cAMP receptor protein., J Biol Chem 271(52):33242-55

 [11] Shin M., Kang S., Hyun SJ., Fujita N., Ishihama A., Valentin-Hansen P., Choy HE., 2001, Repression of deoP2 in Escherichia coli by CytR: conversion of a transcription activator into a repressor., EMBO J 20(19):5392-9

 [12] Sogaard-Andersen L., Martinussen J., Mollegaard NE., Douthwaite SR., Valentin-Hansen P., 1990, The CytR repressor antagonizes cyclic AMP-cyclic AMP receptor protein activation of the deoCp2 promoter of Escherichia coli K-12., J Bacteriol 172(10):5706-13

 [13] Sogaard-Andersen L., Mironov AS., Pedersen H., Sukhodelets VV., Valentin-Hansen P., 1991, Single amino acid substitutions in the cAMP receptor protein specifically abolish regulation by the CytR repressor in Escherichia coli., Proc Natl Acad Sci U S A 88(11):4921-5

 [14] Sogaard-Andersen L., Mollegaard NE., Douthwaite SR., Valentin-Hansen P., 1990, Tandem DNA-bound cAMP-CRP complexes are required for transcriptional repression of the deoP2 promoter by the CytR repressor in Escherichia coli., Mol Microbiol 4(9):1595-601

 [15] Sogaard-Andersen L., Valentin-Hansen P., 1991, Restored DNA-binding of the cAMP-CRP activator complex reestablishes negative regulation by the CytR repressor in the deoP2 promoter in Escherichia coli., Mol Gen Genet 231(1):76-80

 [16] Sogaard-Andersen L., Valentin-Hansen P., 1993, Protein-protein interactions in gene regulation: the cAMP-CRP complex sets the specificity of a second DNA-binding protein, the CytR repressor., Cell 75(3):557-66

 [17] 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

 [18] Sogaard-Andersen L., Pedersen H., Holst B., Valentin-Hansen P., 1991, A novel function of the cAMP-CRP complex in Escherichia coli: cAMP-CRP functions as an adaptor for the CytR repressor in the deo operon., Mol Microbiol 5(4):969-75

 [19] Tao H., Hasona A., Do PM., Ingram LO., Shanmugam KT., 2005, Global gene expression analysis revealed an unsuspected deo operon under the control of molybdate sensor, ModE protein, in Escherichia coli., Arch Microbiol 184(4):225-33

 [20] Valentin-Hansen P., Hammer K., Love Larsen JE., Svendsen I., 1984, The internal regulated promoter of the deo operon of Escherichia coli K-12., Nucleic Acids Res 12(13):5211-24

 [21] 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.

 [22] Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette MG., Alon U., 2006, A comprehensive library of fluorescent transcriptional reporters for Escherichia coli., Nat Methods 3(8):623-8

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