RegulonDB RegulonDB 11.1: 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
Based on cells with plasmids and three inducible promoters of genes (matA, safA, and chbB), three novel fluorescent biosensors sensitive to terahertz (THz) radiation were developed, and they controlled the expression of a fluorescent protein Serdyukov DS, Goryachkovskaya TN, Mescheryakova IA, Bannikova SV, Kuznetsov SA, Cherkasova OP, Popik VM, Peltek SE,2020 The induction of these biosensors was manifested as fluorescent luminosity and reflected the activity of transcription units matA, safA-ydeO, and chbBCARFG, which contain the transcription factors MatA, YdeO, and ChbR, respectively Serdyukov DS, Goryachkovskaya TN, Mescheryakova IA, Bannikova SV, Kuznetsov SA, Cherkasova OP, Popik VM, Peltek SE,2020
Evidence: [EXP-IEP-COREGULATION] 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: [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 safAp 1584071 1584088 -51.5 tataaacttcTGCCTACAGCTGTAAGAAactccgctca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [3], [4]
[PhoP,-] 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
remote PhoP-phosphorylated repressor safAp 1583968 1583985 53.0 atttttaacgTTATCCGCTAAATAAACAtatttgaaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] W [5]
remote PhoP-phosphorylated repressor safAp 1583988 1584005 33.0 attaagcataCTGATTAACGATTTTTAAcgttatccgc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] W [5]
[RcsB,+] 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
nd RcsB-phosphorylated activator safAp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]
[YdeO,-] 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
nd YdeO repressor safAp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [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: [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Masuda N., et al., 2003
Promoter
Name: ydeOp
+1: Unknown
Sigma Factor: Sigma32 Sigmulon
Evidence: [EXP-IDA]
[EXP-IEP]
Reference(s): [7] Wade JT., et al., 2006
TF binding sites (TFBSs)
[H-NS,-] 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
nd H-NS repressor ydeOp nd nd nd nd nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [8]


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

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

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP-IDA] Inferred from direct assay

 [EXP-IEP] Inferred from expression pattern


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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