RegulonDB RegulonDB 10.9: Operon Form
   

safA-ydeO operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: safA-ydeO
Synonym(s): b1500-ydeO, yneN-ydeO
Gene(s): ydeO, safA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcription of safA appears to be increased under acidic growth conditions during the exponential phase in a RcsB-dependent manner, but not during stationary phase Johnson MD,2011
Evidence: [ITCR] Inferred through co-regulation
Reference(s): [1] Masuda N., et al., 2003
Promoter
Name: safAp
+1: 1584028
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 69
Sequence: tgcctacagctgtaagaaactccgctcagtactgaagcaccagtcctatttcctcttttcTccagcctgttatattaagca
                         -35                   -10          +1                   
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[3] Itou J., et al., 2009
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
proximal EvgA-Phosphorylated activator safAp 1584071 1584088 -51.5 atataaacttCTGCCTACAGCTGTAAGAAactccgctca nd [AIBSCS], [BPP], [GEA] [1], [3], [4]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote PhoP-Phosphorylated repressor safAp 1583968 1583985 53.0 atttttaacgTTATCCGCTAAATAAACAtatttgaaat nd [APIORCISFBSCS], [GEA], [SM] [5]
remote PhoP-Phosphorylated repressor safAp 1583988 1584005 33.0 attaagcataCTGATTAACGATTTTTAAcgttatccgc nd [APIORCISFBSCS], [GEA], [SM] [5]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd RcsB-Pasp56 activator safAp nd nd nd nd nd [BPP], [GEA], [IGI] [6]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd YdeO repressor safAp nd nd nd nd nd [BPP], [GEA], [IGI] [5]


Transcription unit          
Name: ydeO
Gene(s): ydeO   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 when 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 ydeO operon is included.
The specific position of the EvgA site has not been anotated because the +1 position has not been identified, but the experimental data are quoted as follows: regulator, EvgA; operon, b1500-ydeO; position(s), (-129 to -112)* and 1582103.5**. Evidences: Consensus, Gene Expression Analysis and Purified Protein Masuda N,2003
The expression of the gene ydeO is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013
* Numbers relative to the start codon of the b1500 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: [ITCR] Inferred through co-regulation
Reference(s): [1] Masuda N., et al., 2003
Promoter
Name: ydeOp
+1: Unknown
Sigma Factor: Sigma32 Sigmulon
Evidence: [IDA]
[IEP]
Reference(s): [7] Wade JT., et al., 2006
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 H-NS repressor ydeOp nd nd nd nd nd [BPP], [GEA], [IGI] [8]




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

 [4] Eguchi Y., Itou J., Yamane M., Demizu R., Yamato F., Okada A., Mori H., Kato A., Utsumi R., 2007, B1500, a small membrane protein, connects the two-component systems EvgS/EvgA and PhoQ/PhoP in Escherichia coli., Proc Natl Acad Sci U S A 104(47):18712-7

 [5] Burton NA., Johnson MD., Antczak P., Robinson A., Lund PA., 2010, Novel aspects of the acid response network of E. coli K-12 are revealed by a study of transcriptional dynamics., J Mol Biol 401(5):726-42

 [6] Johnson MD., Burton NA., Gutierrez B., Painter K., Lund PA., 2011, RcsB Is Required for Inducible Acid Resistance in Escherichia coli and Acts at gadE-Dependent and -Independent Promoters., J Bacteriol 193(14):3653-6

 [7] Wade JT., Roa DC., Grainger DC., Hurd D., Busby SJ., Struhl K., Nudler E., 2006, Extensive functional overlap between sigma factors in Escherichia coli., Nat Struct Mol Biol 13(9):806-14

 [8] Krin E., Danchin A., Soutourina O., 2010, Decrypting the H-NS-dependent regulatory cascade of acid stress resistance in Escherichia coli., BMC Microbiol 10:273


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