RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: yegRZ
Gene(s): yegZ, yegR   Genome Browser M3D Gene expression COLOMBOS
Note(s): Masuda N,2003proposed a model of the regulatory network of the acid resistance genes, including evgA, ydeP, ydeO, yhiE, gadABC, and hdeAB, using a combination of microarray analysis and gene replacement techniques. With these assays, 7 operons were identified as induced when EvgA is overexpressed and YdeO is absent; on the other hand, 12 operons were identified as induced when YdeO is overexpressed. To confirm these regulatory interactions, the EvgA consensus site was searched with the ALIGNACE program, and the 18-bp site found was tested by gel shift analysis with the upstream regions of the corresponding operons. As a result, just six operons are regulated by EvgA, among which the yegRZ operon is included.
The specific position of the EvgA site has not been annotated because the +1 position has not been identified, but the experimental data are quoted as follows: regulator, EvgA; operon, yegR-b2084-yegZ; position(s), (-64 to -47)* and 2166445.5**;
Evidences: Consensus, Gene Expression Analysis, and Purified Protein Masuda N,2003
* Numbers relative to the start codon of the yegR gene.
** Absolute position on the E. coli genome.
Based on microarray and RT-qPCR analyses, it was determined that the asr, frc, oxc, ydeO, and yegR acid stress genes are significantly upregulated upon exposure to exogenous glutathione (GSH) Goswami M,2018
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Masuda N., et al., 2003
Promoter
Name: yegRp
+1: 2168349
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 43
Sequence: ttgtacagaacatttattataatcctattcaattataataatcatgccattattatatttAaacactagagagtgtcgttg
                                 -35                    -10 +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[3] Itou J., et al., 2009
TF binding sites (TFBSs)
[EvgA,+] 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 EvgA-phosphorylated activator yegRp 2168413 2168430 -72.5 atgtccgtaaTTCCTACTTATGTAGGAAatgttgtaca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [3]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [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-PURIFIED-PROTEINS] Binding of purified proteins


Reference(s)    

 [1] Masuda N., Church GM., 2003, Regulatory network of acid resistance genes in Escherichia coli., Mol Microbiol 48(3):699-712

 [2] 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

 [3] Itou J., Eguchi Y., Utsumi R., 2009, Molecular mechanism of transcriptional cascade initiated by the EvgS/EvgA system in Escherichia coli K-12., Biosci Biotechnol Biochem 73(4):870-8

RegulonDB