RegulonDB RegulonDB 11.2: 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       
Name: gatZABCD
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 1208335|.
Evidence: [IC] Inferred by curator
Promoter
Name: gatZp
+1: 2176432
Distance from start of the gene: 111
Sequence: ccttctcgcaggcgttaaaaaattacctgaccgagcaccctgaagcgaccgatccccgggAttatttgcagtcggctaaat
Evidence: [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[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 1208335|.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] 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                  -1+1                   
Note(s): The activity of gatYp promoter appears to be decreased in the presence of σE. It is repressed during the first 5 minutes following σE induction and decreased from 5 to 10 minutes and from 10 to 20 minutes after induction of the σ factor Lacoux C,2020.
This promoter appears to have more transcriptional sites at positions 2177230/1/2/3, as determined by high-throughput screening of maps of promoters Lacoux C,2020.
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [5] Huerta AM., et al., 2003
[4] Nobelmann B., et al., 1996
[2] 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
nd ArcA-phosphorylated repressor gatYp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [8]
[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
proximal CRP-cyclic-AMP activator gatYp 2177264 2177285 -40.5 atattgtcgtTTTTGTGATCGTTATCTCGATAtttaaaaaca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [7]
[GatR,-] 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 GatR repressor gatYp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [4]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  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"


Evidence    

 [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput transcription initiation mapping

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

 [COMP-AINF] Inferred computationally without human oversight

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

 [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-CELLULAR-EXTRACTS] Binding of cellular extracts

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

 [EXP-IMP-SITE-MUTATION] Site mutation


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] 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

 [6] 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

 [7] 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

 [8] 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

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