RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: gcvB
Gene(s): gcvB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The gcvB gene responds to the same signals for expression of repression that the gcvTHP operon does. Overproduction of BglG in stationary phase brings about downregulation of both gcvA and gcvB Shukla S,2019
The mRNA produced by the gcvB gene has been observed mainly in the poles of the cell Kannaiah S, Livny J, Amster-Choder O,2019.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Argaman L., et al., 2001
[2] Urbanowski ML., et al., 2000
Promoter
Name: gcvBp
+1: 2942696
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 0
Sequence: aatctgagccattataaattgtccgttgagcttctaccagcaaatacctatagtggcggcActtcctgagccggaacgaaa
                          -35                    -10        +1                   
Note(s): gcvBp is a class II activator-dependent promoter (where activators bind to sites that are adjacent to or overlap the RNA polymerase-binding site) Stauffer LT,2005
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Argaman L., et al., 2001
[3] Huerta AM., et al., 2003
[4] Salgado H, et al., 2012
[5] Stauffer LT., et al., 2005
[2] Urbanowski ML., et al., 2000
TF binding sites (TFBSs)
[GcvA,+] 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 GcvA activator gcvBp 2942624 2942638 -65.0 tatgtaacctATTAGTTTTTTTAATctgagccatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [2], [5], [6], [7], [8]
proximal GcvA activator gcvBp 2942646 2942660 -43.0 aatctgagccATTATAAATTGTCCGttgagcttct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] C [2], [5], [6], [7], [8]


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

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts

 [EXP-IMP-SITE-MUTATION] Site mutation

 [IC] Inferred by curator

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

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


Reference(s)    

 [1] Argaman L., Hershberg R., Vogel J., Bejerano G., Wagner EG., Margalit H., Altuvia S., 2001, Novel small RNA-encoding genes in the intergenic regions of Escherichia coli., Curr Biol 11(12):941-50

 [2] Urbanowski ML., Stauffer LT., Stauffer GV., 2000, The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli., Mol Microbiol 37(4):856-68

 [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] Stauffer LT., Stauffer GV., 2005, GcvA interacts with both the alpha and sigma subunits of RNA polymerase to activate the Escherichia coli gcvB gene and the gcvTHP operon., FEMS Microbiol Lett 242(2):333-8

 [6] Jourdan AD., Stauffer GV., 1999, Genetic analysis of the GcvA binding site in the gcvA control region., Microbiology 145 ( Pt 8):2153-62

 [7] Wilson RL., Stauffer GV., 1994, DNA sequence and characterization of GcvA, a LysR family regulatory protein for the Escherichia coli glycine cleavage enzyme system., J Bacteriol 176(10):2862-8

 [8] Wilson RL., Urbanowski ML., Stauffer GV., 1995, DNA binding sites of the LysR-type regulator GcvA in the gcv and gcvA control regions of Escherichia coli., J Bacteriol 177(17):4940-6

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