RegulonDB RegulonDB 10.6.3: 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 |CITS:[21571995]|.
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
                         -10                   -35          +1                   
Evidence: [HIPP]
[TIM]
Reference(s): [2] 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 tataaacttcTGCCTACAGCTGTAAGAAactccgctca nd [AIBSCS], [BPP], [GEA] [1], [2], [3]
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 [GEA], [HIBSCS], [SM] [4]
remote PhoP-Phosphorylated repressor safAp 1583988 1584005 33.0 attaagcataCTGATTAACGATTTTTAAcgttatccgc nd [GEA], [HIBSCS], [SM] [4]
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 [GEA] [5]
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 [GEA] [4]


Transcription unit          
Name: ydeO
Gene(s): ydeO   Genome Browser M3D Gene expression COLOMBOS
Note(s): |CITS:[12694615]| proposed 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 |CITS:[12694615]|.
The expression of the gene ydeO is increased under acidic growth conditions in either aerobiosis or microaerobiosis |CITS:[23274360]|.
* 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) |CITS:[29468195]|.
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): [6] 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] [7]





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