RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: pspG
Synonym(s): yjbO
Gene(s): pspG, pspH   Genome Browser M3D Gene expression COLOMBOS
Note(s): pspG is physically unlike the psp operon but is coconserved and coregulated with the psp operon genes by σ54, PspF, IHF and PspA Lloyd LJ,2004.
Based on DNA microarray analysis, the mechanism of bacterial inactivation by carvacrol and citral was studied Chueca B, Pérez-Sáez E, Pagán R, García-Gonzalo D,2017. Treatment by both compounds caused membrane damage and activated metabolism through the production of nucleotides required for DNA and RNA synthesis and metabolic processes Chueca B, Pérez-Sáez E, Pagán R, García-Gonzalo D,2017. A total of 76 and 156 genes demonstrated significant transcriptional differences by carvacrol and citral, respectively. Genes upregulated by carvacrol treatment included the multidrug efflux pump genes acrA and mdtM, genes related to the phage shock response, pspA, pspB, pspC, pspD, pspF, and pspG, and genes whose products are important for biosynthesis of arginine (argC, argG, artJ) and purine nucleotides (purC, purM). Genes upregulated by citral treatment included purH, pyrB, and pyrI. On the other hand, mutations in several differentially expressed genes confirmed the roles of ygaV, yjbO, pspC, sdhA, yejG, and ygaV in mechanisms of inactivation by carvacrol and citral Chueca B, Pérez-Sáez E, Pagán R, García-Gonzalo D,2017.
Based on DNA microarray analysis, the mechanism of bacterial inactivation by carvacrol and citral was studied Chueca B, Pérez-Sáez E, Pagán R, García-Gonzalo D,2017. Treatment by both compounds caused membrane damage and activated metabolism through the production of nucleotides required for DNA and RNA synthesis and metabolic processes Chueca B, Pérez-Sáez E, Pagán R, García-Gonzalo D,2017. A total of 76 and 156 genes demonstrated significant transcriptional differences by carvacrol and citral, respectively. Genes upregulated by carvacrol treatment included the multidrug efflux pump genes acrA and mdtM, genes related to the phage shock response, pspA, pspB, pspC, pspD, pspF, and pspG, and genes whose products are important for biosynthesis of arginine (argC, argG, artJ) and purine nucleotides (purC, purM). Genes upregulated by citral treatment included purH, pyrB, and pyrI. On the other hand, mutations in several differentially expressed genes confirmed the roles of ygaV, yjbO, pspC, sdhA, yejG, and ygaV in mechanisms of inactivation by carvacrol and citral Chueca B, Pérez-Sáez E, Pagán R, García-Gonzalo D,2017.
Evidence: [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
Reference(s): [1] Lloyd LJ., et al., 2004
Promoter
Name: pspGp
+1: 4262816
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 24
Sequence: gggcgttttgctgttaaatcaatagattatttttggcatgattcttgtaatgccagcaagAgatttcatatttgggagagc
                                  -24         -12           +1                   
Note(s): Although the transcriptional start site position was not determined experimentally it was inferred by Lloyd LJ,2004, based on footprinting with the RNA polymerase and the identification of its -12 and -24 σ54 recognition boxes.
Evidence: [COMP]
[COMP-AINF]
[EXP-IDA-RNA-POLYMERASE-FOOTPRINTING]
Reference(s): [2] Huerta AM., et al., 2003
[1] Lloyd LJ., et al., 2004
TF binding sites (TFBSs)
[IHF,+] 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 IHF activator pspGp 4262771 4262783 -38.5 ttttgctgttAAATCAATAGATTatttttggca nd [COMP] nd [1]
[PspF,+] 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 PspF activator pspGp 4262721 4262737 -87.0 tcaccaaaaaGTAGTCAAATTCACCACgccctgcgca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1]


Evidence    

 [COMP] Inferred by computational analysis

 [COMP-AINF] Inferred computationally without human oversight

 [EXP-IDA-RNA-POLYMERASE-FOOTPRINTING] RNA polymerase footprinting

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins


Reference(s)    

 [1] Lloyd LJ., Jones SE., Jovanovic G., Gyaneshwar P., Rolfe MD., Thompson A., Hinton JC., Buck M., 2004, Identification of a new member of the phage shock protein response in Escherichia coli, the phage shock protein G (PspG)., J Biol Chem 279(53):55707-14

 [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

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