RegulonDB RegulonDB 11.1: Operon Form
   

map-glnD-dapD operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: map-glnD-dapD
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: dapD
Gene(s): dapD   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Bouvier J., et al., 1992
[2] Richaud C., et al., 1984
Promoter
Name: dapDp
+1: 185977
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 30
Sequence: ttgcagcaggaagtgcatcagcggttgacagaggccctcaatccaaacgataaagggtgaTgtgtttactgatatgaaaag
                              -35                  -10      +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [3] Huerta AM., et al., 2003
[2] Richaud C., et al., 1984
[4] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: tgcaaaaaaaTCGGGCAGCGTCGTGCTGCCCGtgtgcatact
Reference(s): [2] Richaud C., et al., 1984
TF binding sites (TFBSs)
[ArgP,+] 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
nd ArgP activator dapDp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5]


Transcription unit          
Name: glnD
Gene(s): glnD   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under nitrogen-rich growth conditions, the expression of the glnD 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 Fnr mutant Kumar R,2011
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [6] van Heeswijk WC., et al., 1993
Promoter
Name: glnDp
+1: 188655
Distance from start of the gene: 5
Sequence: ataagatgaagccggcgaatgccggcttttttaatgcgataatttaatcttatgggtggcGcacaatgaatacccttccag
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [6] van Heeswijk WC., et al., 1993
TF binding sites (TFBSs)
[FNR,+] 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
nd FNR activator glnDp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [7]
[FNR,-] 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
nd FNR repressor glnDp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [7]
[Fur,-] 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
nd Fur-Fe2+ repressor glnDp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [7]


Transcription unit       
Name: map-glnD-dapD
Gene(s): dapD, glnD, map   Genome Browser M3D Gene expression COLOMBOS
Note(s): Activation of the SoxS and Rob regulators of the map-glnD-dapD operon was observed after treatment with paraquat and dipyridyl Martin RG,2002, and activation by MarA was observed after treatment with sodium salicylate Pomposiello PJ,2001. Blanchard JL, Wholey WY, Conlon EM, Pomposiello PJ,2007.
Evidence: [COMP-AINF] Inferred computationally without human oversight


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -12.9 188683 188706 aataagatgaAGCCGGCGAATGCCGGCTTTTTTaatgcgataa
  terminator -9.5 189634 189669 ccaataattgTTGGCGCTGTGTACAGCATCAGACGTCGAATTTTCtattatagaa
  anti-terminator -12.3 188698 188740 gatgacaccaTCCCGGCGATAATCTCGCACGACGAATAAGATGAAGCCGGCGaatgccggct
  anti-terminator -9.9 189658 189693 tataccacaaATACGTCGTGGACACCAATAATTGTTGGCGCTGTGtacagcatca
  anti-anti-terminator -14.2 188722 188774 tgataacggcTGCGAAATTCTGACGCTACGCAAGGATGACACCATCCCGGCGATAATCTCGCacgacgaata
  anti-anti-terminator -8.4 189678 189720 gaaatggatcGGAAGTCCGGCGCGCTTTATACCACAAATACGTCGTGGACACcaataattgt
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

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

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

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


Reference(s)    

 [1] Bouvier J., Richaud C., Higgins W., Bogler O., Stragier P., 1992, Cloning, characterization, and expression of the dapE gene of Escherichia coli., J Bacteriol 174(16):5265-71

 [2] Richaud C., Richaud F., Martin C., Haziza C., Patte JC., 1984, Regulation of expression and nucleotide sequence of the Escherichia coli dapD gene., J Biol Chem 259(23):14824-8

 [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] 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.

 [5] Marbaniang CN., Gowrishankar J., 2011, Role of ArgP (IciA) in Lysine-Mediated Repression in Escherichia coli., J Bacteriol 193(21):5985-96

 [6] van Heeswijk WC., Rabenberg M., Westerhoff HV., Kahn D., 1993, The genes of the glutamine synthetase adenylylation cascade are not regulated by nitrogen in Escherichia coli., Mol Microbiol 9(3):443-57

 [7] Kumar R., Shimizu K., 2011, Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures., Microb Cell Fact 10:3

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