RegulonDB RegulonDB 10.7: Operon Form
   

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




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


Transcription unit       
Gene(s): gatD, gatC, gatB, gatA, gatZ   Genome Browser M3D Gene expression COLOMBOS
Note(s): gatABC were found to be downregulated in a MG1655 lysogen carrying the Stx2a phage O104 |CITS: 31208335|.
Evidence: [IC] Inferred by curator
Promoter
Name: gatZp
+1: 2176432
Distance from start of the gene: 111
Sequence: ccttctcgcaggcgttaaaaaattacctgaccgagcaccctgaagcgaccgatccccgggAttatttgcagtcggctaaat
Evidence: [HTIM]
[RS-EPT-CBR]
Reference(s): [1] Mendoza-Vargas A., et al., 2009
[2] Salgado H, et al., 2012


Transcription unit          
Name: gatYZABCD
Synonym(s): OP00231
Gene(s): gatD, gatC, gatB, gatA, gatZ, gatY   Genome Browser M3D Gene expression COLOMBOS
Note(s): gatABC were found to be downregulated in a MG1655 lysogen carrying the Stx2a phage O104 |CITS: 31208335|.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [3] Nobelmann B., et al., 1995
[4] Nobelmann B., et al., 1996
Promoter
Name: gatYp
+1: 2177234
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 30
Sequence: tattgtcgtttttgtgatcgttatctcgatatttaaaaacaaataatttcattatattttGaaatcgaaaacaaacgacag
                                -35                  -10    +1                   
Evidence: [RS-EPT-CBR]
[TIM]
Reference(s): [4] Nobelmann B., et al., 1996
[2] Salgado H, et al., 2012
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd ArcA-Phosphorylated1 repressor gatYp nd nd nd nd nd [AIBSCS], [GEA] [7]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP activator gatYp 2177264 2177285 -40.5 atattgtcgtTTTTGTGATCGTTATCTCGATAtttaaaaaca nd [AIBSCS], [BCE], [GEA], [SM] [5], [6]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd GatR repressor gatYp nd nd nd nd nd [GEA] [3], [4]
Note(s): 1ArcA represses gatY gene expression under anaerobiosis. Two putative ArcA-binding sites were identified upstream of this gene, but their sequence was not shown Salmon KA,2005.3ArcA represses gatY gene expression under anaerobiosis. Two putative ArcA-binding sites were identified upstream of this gene, but their sequence was not shown Salmon KA,2005.
External database links:
UNIPROT:
P36930


Regulation by sRNA    
  Small RNA name (Regulator) Regulation type Mechanism Function Binding Sites Evidence Reference
LeftPos RightPos Sequence (RNA-strand)
  gcvB unknown unknown repressor       [IMP] [8]
[9]
[10]
  gcvB unknown unknown repressor       [IMP] [10]
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'"


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
Evidence: [ICA] Inferred by computational analysis
Reference(s): [11] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -18.3 2177320 2177350 gcactttgctACGGCTTCCCTATCGGGAGGCCGTTTTTTTgcctttcact
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"




Reference(s)    

 [1] Mendoza-Vargas A., Olvera L., Olvera M., Grande R., Vega-Alvarado L., Taboada B., Jimenez-Jacinto V., Salgado H., Juarez K., Contreras-Moreira B., Huerta AM., Collado-Vides J., Morett E., 2009, Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli., PLoS One 4(10):e7526

 [2] 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.

 [3] Nobelmann B., Lengeler JW., 1995, Sequence of the gat operon for galactitol utilization from a wild-type strain EC3132 of Escherichia coli., Biochim Biophys Acta 1262(1):69-72

 [4] Nobelmann B., Lengeler JW., 1996, Molecular analysis of the gat genes from Escherichia coli and of their roles in galactitol transport and metabolism., J Bacteriol 178(23):6790-5

 [5] Hollands K., Busby SJ., Lloyd GS., 2007, New targets for the cyclic AMP receptor protein in the Escherichia coli K-12 genome., FEMS Microbiol Lett 274(1):89-94

 [6] 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

 [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] Lengeler J., 1975, Nature and properties of hexitol transport systems in Escherichia coli., J Bacteriol 124(1):39-47

 [9] Lengeler J., 1977, Analysis of mutations affecting the dissmilation of galactitol (dulcitol) in Escherichia coli K 12., Mol Gen Genet 152(1):83-91

 [10] Pulvermacher SC., Stauffer LT., Stauffer GV., 2009, Role of the sRNA GcvB in regulation of cycA in Escherichia coli., Microbiology 155(Pt 1):106-14

 [11] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.


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