RegulonDB RegulonDB 11.1: Operon Form
   

yfdX-frc-oxc-yfdVE operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: yfdX-frc-oxc-yfdVE
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: frc
Synonym(s): yfdW
Gene(s): frc   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, seven operons were identified as induced by EvgA overexpressed and YdeO absent; on the other hand, twelve operons were identified as induced by YdeO overexpression. 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 frc gene is included.
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
Promoter
Name: frcp
+1: 2493439
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 185
Sequence: cacaaatgtcgcgactctctctgattaccacgaatcaatatttatcatattcttcttttcGtcctcactacttaccatgca
                              -35                    -10    +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Huerta AM., et al., 2003
[2] 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 frcp 2493506 2493523 -75.5 tcaccggcgcTTCTTACAGTTGTAAGAAtaacatcaca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [3]


Transcription unit          
Name: yfdX
Gene(s): yfdE, yfdV, oxc, frc, yfdX   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 by EvgA overexpressed and when YdeO is absent; on the other hand, 12 operons were identified as induced by YdeO overexpression. 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 yfdX gene is included.
The yfdX-frc-oxc-yfdVE operon is required for oxalate-induced acid tolerance (AR) Fontenot EM, Ezelle KE, Gabreski LN, Giglio ER, McAfee JM, Mills AC, Qureshi MN, Salmon KM, Toyota CG,2013
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [4] Masuda N., et al., 2002
[3] Masuda N., et al., 2003
Promoter
Name: yfdXp
+1: 2494433
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 31
Sequence: ttcaaaatgaccgttgctctctgatttctcatttcatgctcacccaatatgatggcggcgTtttctaaaactgttaaagaa
                               -35                   -10    +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Huerta AM., et al., 2003
[2] 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 yfdXp 2494500 2494517 -75.5 cttgcgataaTAACTACAACTGTAAGATaaccctttca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
remote EvgA-phosphorylated activator yfdXp 2494538 2494555 -113.5 aggaagcataTTCCTACAATTGTAAGACtaaaatactt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [3]


Transcription unit       
Name: yfdE
Gene(s): yfdE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight


Transcription unit       
Name: yfdV
Gene(s): yfdV   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight


Transcription unit       
Name: oxc
Gene(s): oxc   Genome Browser M3D Gene expression COLOMBOS
Note(s): 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: [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 -11.1 2489182 2489213 ttacataaatGCCGAAGTGTCTTTTCACCTTCGGCTTTTTTcaaggcataa
  terminator -9.3 2490192 2490224 gccaactcatTATGCGATGGTGAGGGGACCCTTATCGGAAATactattatgc
  terminator -9.8 2491980 2491996 tgatattaacGGGGGCTTCTGGCTCCcaatttataa
  anti-terminator -13.3 2489207 2489275 tcacggctccCTTGTGGATTTATGTCAGTCGACTGGTTTCATAATTAATCATGTTATTGATTTTACATAAATGCCGAAgtgtcttttc
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

 [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] 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

 [2] 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

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

 [4] Masuda N., Church GM., 2002, Escherichia coli gene expression responsive to levels of the response regulator EvgA., J Bacteriol 184(22):6225-34

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