RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit          
Name: dadAX
Gene(s): dadA, dadX   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcript of dadAX is decreased after σE induction, as observed in high-throughput analysis of gene expression Lacoux C,2020.
dadAX operon expression is upregulated upon L-valine addition (isoleucine starvation) in the cellular growth medium Gummesson B, Shah SA, Borum AS, Fessler M, Mitarai N, Sørensen MA, Svenningsen SL,2020.

A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for dadA . 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: [ITCR] Inferred through co-regulation
[PAGTSBP] Products of adjacent genes in the same biological process
Reference(s): [1] Lobocka M., et al., 1994
[2] Wild J., et al., 1985
Promoter
Name: dadAp1
+1: 1237509
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 62
Sequence: tcagggagatgtgagccagctcaccataaaaaagccgcatgttgaataatattttcaactGagttatcaagatgtgattag
                          -35                     -10       +1                   
Evidence: [ICWHO]
[IHBCE]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[4] Mathew E., et al., 1996
[5] Zhi J., et al., 1999
[6] Zhi J., et al., 1998
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cyclic-AMP activator dadAp1 1237455 1237477 -43.5 agagtcagggAGATGTGAGCCAGCTCACCATAAaaaagccgca nd [GEA], [APIORCISFBSCS], [BPP] [4], [5], [6]
proximal CRP-cyclic-AMP activator dadAp1 1237518 1237539 20.5 tgagttatcaAGATGTGATTAGATTATTATTCttttactgta nd [GEA], [APIORCISFBSCS], [BPP] [4], [5]
[CRP,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cyclic-AMP repressor dadAp1 1237518 1237539 20.5 tgagttatcaAGATGTGATTAGATTATTATTCttttactgta nd [GEA], [APIORCISFBSCS], [BPP] [4], [5]
[Lrp,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Lrp repressor dadAp1 1237252 1237266 -250.0 acgcgcacctCATTGTTGTCGGCGCtctctgtgtg nd [GEA], [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [5], [7]
remote Lrp repressor dadAp1 1237277 1237291 -225.0 tctctgtgtgGAGCACCTCATTTCAagcatagaac nd [GEA], [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [5], [7]
remote Lrp repressor dadAp1 1237325 1237339 -177.0 cgcgtcgccgGAGAATTTTTTTCTTtgcgatttct nd [EME], [GEA], [RSE], [AIBSPD], [APIORCISFBSCS], [BPP], [CCE], [CSE], [SM] [4], [5], [7], [8]
remote Lrp repressor dadAp1 1237356 1237370 -146.0 ttcttattatCAGAGTGCCACTAATccgcttctga nd [GEA], [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [5], [7]
remote Lrp repressor dadAp1 1237382 1237396 -120.0 cgcttctgaaCGGAATTTTATGCTGgataaaaagg nd [EME], [GEA], [RSE], [AIBSPD], [APIORCISFBSCS], [BPP], [CCE], [CSE], [SM] [4], [5], [7], [8]
proximal Lrp repressor dadAp1 1237412 1237426 -90.0 aaagggcgttCAGCAGGAGATACTAaagacgccat nd [GEA], [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [5], [7]
proximal Lrp repressor dadAp1 1237450 1237464 -52.0 gccgcagagtCAGGGAGATGTGAGCcagctcacca nd [GEA], [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [5], [7]
proximal Lrp repressor dadAp1 1237495 1237509 -7.0 gcatgttgaaTAATATTTTCAACTGagttatcaag nd [EME], [GEA], [RSE], [AIBSPD], [APIORCISFBSCS], [BPP], [CCE], [CSE], [SM] [4], [5], [7], [8]
proximal Lrp repressor dadAp1 1237527 1237541 26.0 aagatgtgatTAGATTATTATTCTTttactgtatc nd [EME], [GEA], [RSE], [AIBSPD], [APIORCISFBSCS], [BPP], [CCE], [CSE], [SM] [4], [5], [7], [8]
remote Lrp repressor dadAp1 1237574 1237588 73.0 agtggctatgCGAGTTGTCATACTGggaagtggtg nd [GEA], [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [5], [7]
remote Lrp repressor dadAp1 1237596 1237610 95.0 ctgggaagtgGTGTGGTAGGCGTTGccagcgcctg nd [GEA], [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [5], [7]


Transcription unit          
Name: dadAX
Synonym(s): dad
Gene(s): dadA, dadX   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcript of dadAX is decreased after σE induction, as observed in high-throughput analysis of gene expression Lacoux C,2020.
dadAX operon expression is upregulated upon L-valine addition (isoleucine starvation) in the cellular growth medium Gummesson B, Shah SA, Borum AS, Fessler M, Mitarai N, Sørensen MA, Svenningsen SL,2020.
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for dadA . 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: [ITCR] Inferred through co-regulation
[PAGTSBP] Products of adjacent genes in the same biological process
Reference(s): [1] Lobocka M., et al., 1994
[2] Wild J., et al., 1985
Promoter
Name: dadAp2
+1: 1237525
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 46
Sequence: cagctcaccataaaaaagccgcatgttgaataatattttcaactgagttatcaagatgtgAttagattattattcttttac
                          -35                       -10     +1                   
Evidence: [ICWHO]
[IHBCE]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[1] Lobocka M., et al., 1994
[4] Mathew E., et al., 1996
[5] Zhi J., et al., 1999
[6] Zhi J., et al., 1998
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cyclic-AMP activator dadAp2 1237455 1237477 -59.5 agagtcagggAGATGTGAGCCAGCTCACCATAAaaaagccgca nd [GEA], [APIORCISFBSCS], [BPP] [4], [5], [6]
proximal CRP-cyclic-AMP activator dadAp2 1237520 1237541 7.0 agttatcaagATGTGATTAGATTATTATTCTTttactgtatc nd [GEA], [APIORCISFBSCS], [BPP] nd
[Lrp,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Lrp repressor dadAp2 1237252 1237266 -266.0 acgcgcacctCATTGTTGTCGGCGCtctctgtgtg nd [GEA], [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [5], [7]
remote Lrp repressor dadAp2 1237277 1237291 -241.0 tctctgtgtgGAGCACCTCATTTCAagcatagaac nd [GEA], [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [5], [7]
remote Lrp repressor dadAp2 1237325 1237339 -193.0 cgcgtcgccgGAGAATTTTTTTCTTtgcgatttct nd [EME], [GEA], [RSE], [AIBSPD], [APIORCISFBSCS], [BPP], [CCE], [CSE], [SM] [4], [5], [7], [8]
remote Lrp repressor dadAp2 1237356 1237370 -162.0 ttcttattatCAGAGTGCCACTAATccgcttctga nd [GEA], [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [5], [7]
remote Lrp repressor dadAp2 1237382 1237396 -136.0 cgcttctgaaCGGAATTTTATGCTGgataaaaagg nd [EME], [GEA], [RSE], [AIBSPD], [APIORCISFBSCS], [BPP], [CCE], [CSE], [SM] [4], [5], [7], [8]
remote Lrp repressor dadAp2 1237412 1237426 -106.0 aaagggcgttCAGCAGGAGATACTAaagacgccat nd [GEA], [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [5], [7]
proximal Lrp repressor dadAp2 1237450 1237464 -68.0 gccgcagagtCAGGGAGATGTGAGCcagctcacca nd [GEA], [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [5], [7]
proximal Lrp repressor dadAp2 1237495 1237509 -23.0 gcatgttgaaTAATATTTTCAACTGagttatcaag nd [EME], [GEA], [RSE], [AIBSPD], [APIORCISFBSCS], [BPP], [CCE], [CSE], [SM] [4], [5], [7], [8]
proximal Lrp repressor dadAp2 1237527 1237541 10.0 aagatgtgatTAGATTATTATTCTTttactgtatc nd [EME], [GEA], [RSE], [AIBSPD], [APIORCISFBSCS], [BPP], [CCE], [CSE], [SM] [4], [5], [7], [8]
remote Lrp repressor dadAp2 1237574 1237588 57.0 agtggctatgCGAGTTGTCATACTGggaagtggtg nd [GEA], [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [5], [7]
remote Lrp repressor dadAp2 1237596 1237610 79.0 ctgggaagtgGTGTGGTAGGCGTTGccagcgcctg nd [GEA], [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [5], [7]


Transcription unit          
Name: dadAX
Gene(s): dadA, dadX   Genome Browser M3D Gene expression COLOMBOS
Note(s): dadAX operon expression is upregulated upon L-valine addition (isoleucine starvation) in the cellular growth medium Gummesson B, Shah SA, Borum AS, Fessler M, Mitarai N, Sørensen MA, Svenningsen SL,2020.
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for dadA . 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: [ITCR] Inferred through co-regulation
[PAGTSBP] Products of adjacent genes in the same biological process
Reference(s): [1] Lobocka M., et al., 1994
[2] Wild J., et al., 1985
Promoter
Name: dadAp3
+1: 1237538
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 33
Sequence: aaaagccgcatgttgaataatattttcaactgagttatcaagatgtgattagattattatTcttttactgtatctaccgtt
                              -35                      -10  +1                   
Evidence: [ICWHO]
[IHBCE]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[4] Mathew E., et al., 1996
[5] Zhi J., et al., 1999
[6] Zhi J., et al., 1998
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cyclic-AMP activator dadAp3 1237455 1237477 -72.5 agagtcagggAGATGTGAGCCAGCTCACCATAAaaaagccgca nd [GEA], [APIORCISFBSCS], [BPP] [4], [5], [6]
proximal CRP-cyclic-AMP activator dadAp3 1237518 1237539 -9.5 tgagttatcaAGATGTGATTAGATTATTATTCttttactgta nd [APIORCISFBSCS], [BPP], [GEA], [APIORCISFBSCS], [BPP] [4], [5], [6]
[Lrp,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Lrp repressor dadAp3 1237252 1237266 -279.0 acgcgcacctCATTGTTGTCGGCGCtctctgtgtg nd [APIORCISFBSCS], [BPP], [GEA], [RSE], [SM], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [5], [7]
remote Lrp repressor dadAp3 1237277 1237291 -254.0 tctctgtgtgGAGCACCTCATTTCAagcatagaac nd [APIORCISFBSCS], [BPP], [GEA], [RSE], [SM], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [5], [7]
remote Lrp repressor dadAp3 1237325 1237339 -206.0 cgcgtcgccgGAGAATTTTTTTCTTtgcgatttct nd [APIORCISFBSCS], [BPP], [EME], [GEA], [RSE], [SM], [AIBSPD], [APIORCISFBSCS], [BPP], [CCE], [CSE], [SM] [4], [5], [7], [8]
remote Lrp repressor dadAp3 1237356 1237370 -175.0 ttcttattatCAGAGTGCCACTAATccgcttctga nd [APIORCISFBSCS], [BPP], [GEA], [RSE], [SM], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [5], [7]
remote Lrp repressor dadAp3 1237382 1237396 -149.0 cgcttctgaaCGGAATTTTATGCTGgataaaaagg nd [APIORCISFBSCS], [BPP], [EME], [GEA], [RSE], [SM], [AIBSPD], [APIORCISFBSCS], [BPP], [CCE], [CSE], [SM] [4], [5], [7], [8]
remote Lrp repressor dadAp3 1237412 1237426 -119.0 aaagggcgttCAGCAGGAGATACTAaagacgccat nd [APIORCISFBSCS], [BPP], [GEA], [RSE], [SM], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [5], [7]
proximal Lrp repressor dadAp3 1237450 1237464 -81.0 gccgcagagtCAGGGAGATGTGAGCcagctcacca nd [GEA], [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [5], [7]
proximal Lrp repressor dadAp3 1237495 1237509 -36.0 gcatgttgaaTAATATTTTCAACTGagttatcaag nd [EME], [GEA], [RSE], [AIBSPD], [APIORCISFBSCS], [BPP], [CCE], [CSE], [SM] [4], [5], [7], [8]
proximal Lrp repressor dadAp3 1237527 1237541 -4.0 aagatgtgatTAGATTATTATTCTTttactgtatc nd [EME], [GEA], [RSE], [AIBSPD], [APIORCISFBSCS], [BPP], [CCE], [CSE], [SM] [4], [5], [7], [8]
remote Lrp repressor dadAp3 1237574 1237588 44.0 agtggctatgCGAGTTGTCATACTGggaagtggtg nd [GEA], [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [5], [7]
remote Lrp repressor dadAp3 1237596 1237610 66.0 ctgggaagtgGTGTGGTAGGCGTTGccagcgcctg nd [GEA], [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [5], [7]


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [IHBCE] Inferred by a human based on computational evidence

 [TIM] Transcription initiation mapping

 [GEA] Gene expression analysis

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BPP] Binding of purified proteins

 [RSE] RNA-seq evidence

 [CSE] ChIP-seq evidence

 [SM] Site mutation

 [EME] Expression microarray evidence

 [AIBSPD] Automated inference based on sequence pattern discovery

 [CCE] ChIP-chip evidence


Reference(s)    

 [1] Lobocka M., Hennig J., Wild J., Klopotowski T., 1994, Organization and expression of the Escherichia coli K-12 dad operon encoding the smaller subunit of D-amino acid dehydrogenase and the catabolic alanine racemase., J Bacteriol 176(5):1500-10

 [2] Wild J., Hennig J., Lobocka M., Walczak W., Klopotowski T., 1985, Identification of the dadX gene coding for the predominant isozyme of alanine racemase in Escherichia coli K12., Mol Gen Genet 198(2):315-22

 [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] Mathew E., Zhi J., Freundlich M., 1996, Lrp is a direct repressor of the dad operon in Escherichia coli., J Bacteriol 178(24):7234-40

 [5] Zhi J., Mathew E., Freundlich M., 1999, Lrp binds to two regions in the dadAX promoter region of Escherichia coli to repress and activate transcription directly., Mol Microbiol 32(1):29-40

 [6] Zhi J., Mathew E., Freundlich M., 1998, In vitro and in vivo characterization of three major dadAX promoters in Escherichia coli that are regulated by cyclic AMP-CRP and Lrp., Mol Gen Genet 258(4):442-7

 [7] Kroner GM., Wolfe MB., Freddolino PL., 2019, Escherichia coli Lrp Regulates One-Third of the Genome via Direct, Cooperative, and Indirect Routes., J Bacteriol 201(3)

 [8] Cho BK., Barrett CL., Knight EM., Park YS., Palsson BO., 2008, Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli., Proc Natl Acad Sci U S A 105(49):19462-7

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