RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit       
Name: pspF
Gene(s): pspF   Genome Browser M3D Gene expression COLOMBOS
Note(s): An integrated transcriptomic study of the extracytoplasmic stress response, which detects and responds to alterations of the bacterial envelope, was performed by Bury-Moré et al. (2009). They investigated the interconnections and dynamics between Bae, Cpx, Psp, Rcs, and σE pathways and showed that these pathways can be activated simultaneously in response to exogenous or endogenous stimulation, while natural environmental stimuli provoke bacterial modifications that lead to multiple pathway responses 19763168
Each of these responses might be specialized to ensure a specific aspect of envelope biogenesis and maintenance; on the other hand, CpxR could have a role as a modulator of the response by integrating other endogenous signals. Bury-Moré et al. concluded that all five pathways are needed to mount a full response to extracytoplasmic stress 19763168
Evidence: [AISDTU] Automated inference that a single-gene directon is a transcription unit
[BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Jovanovic G., et al., 1997
[2] Jovanovic G., et al., 1996
Promoter
Name: pspFp2
+1: 1367929
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 17
Sequence: aaagatctgattgaagaatcaacagcaacatgccaggatgagttagcgaattacactaacAagtggcgaatttcatcatgg
                              -35                   -10     +1                   
Note(s): Evolutionary studies have shown that none of the three promoters transcribing the gene pspF reveal a conserved profile beyond enterobacteria Huvet M,2011
Evidence: [HIPP]
[TIM]
Reference(s): [2] Jovanovic G., et al., 1996
Terminator(s)
Type: rho-independent
Sequence: gcgattaataGCCCAACGCAATAATGTCTGATGCGCTGCGCTTATCAGGCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCaagttgtatt
Reference(s): [2] Jovanovic G., et al., 1996


Transcription unit          
Name: pspF
Gene(s): pspF   Genome Browser M3D Gene expression COLOMBOS
Note(s): An integrated transcriptomic study of the extracytoplasmic stress response, which detects and responds to alterations of the bacterial envelope, was performed by Bury-Moré et al. (2009). They investigated the interconnections and dynamics between Bae, Cpx, Psp, Rcs, and σE pathways and showed that these pathways can be activated simultaneously in response to exogenous or endogenous stimulation, while natural environmental stimuli provoke bacterial modifications that lead to multiple pathway responses 19763168
Each of these responses might be specialized to ensure a specific aspect of envelope biogenesis and maintenance; on the other hand, CpxR could have a role as a modulator of the response by integrating other endogenous signals. Bury-Moré et al. concluded that all five pathways are needed to mount a full response to extracytoplasmic stress 19763168
Based on DNA microarray analysis, the mechanism of bacterial inactivation by carvacrol and citral was studied 28644990. Treatment by both compounds caused membrane damage and activated metabolism through the production of nucleotides required for DNA and RNA synthesis and metabolic processes 28644990. 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 28644990.
Evidence: [AISDTU] Automated inference that a single-gene directon is a transcription unit
[BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Jovanovic G., et al., 1997
[2] Jovanovic G., et al., 1996
Promoter
Name: pspFp1
+1: 1367945
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 33
Sequence: tatctttttgatttataaagatctgattgaagaatcaacagcaacatgccaggatgagttAgcgaattacactaacaagtg
                           -35                    -10       +1                   
Note(s): Evolutionary studies have shown that none of the three promoters transcribing the gene pspF reveal a conserved profile beyond enterobacteria Huvet M,2011
Evidence: [HIPP]
[TIM]
Reference(s): [2] Jovanovic G., et al., 1996
Terminator(s)
Type: rho-independent
Sequence: gcgattaataGCCCAACGCAATAATGTCTGATGCGCTGCGCTTATCAGGCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCaagttgtatt
Reference(s): [2] Jovanovic G., et al., 1996
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 PspF repressor pspFp1 1367911 1367927 27.0 acactaacaaGTGGCGAATTTCATCATggcagaatac nd [BCE], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [1], [3], [4]
proximal PspF repressor pspFp1 1367931 1367947 7.0 ccaggatgagTTAGCGAATTACACTAAcaagtggcga nd [BCE], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [1], [3], [4]


Transcription unit       
Name: pspF
Gene(s): pspF   Genome Browser M3D Gene expression COLOMBOS
Note(s): An integrated transcriptomic study of the extracytoplasmic stress response, which detects and responds to alterations of the bacterial envelope, was performed by Bury-Moré et al. (2009). They investigated the interconnections and dynamics between Bae, Cpx, Psp, Rcs, and σE pathways and showed that these pathways can be activated simultaneously in response to exogenous or endogenous stimulation, while natural environmental stimuli provoke bacterial modifications that lead to multiple pathway responses 19763168
Each of these responses might be specialized to ensure a specific aspect of envelope biogenesis and maintenance; on the other hand, CpxR could have a role as a modulator of the response by integrating other endogenous signals. Bury-Moré et al. concluded that all five pathways are needed to mount a full response to extracytoplasmic stress 19763168
Evidence: [AISDTU] Automated inference that a single-gene directon is a transcription unit
[BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Jovanovic G., et al., 1997
[2] Jovanovic G., et al., 1996
Promoter
Name: pspFp3
+1: 1368040
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 128
Sequence: caaagcgagaaaaaatacccataatgttgtcctcttgatttctgcgttcaggattgtcctGctgaactgttaatacaattt
                           -35                      -10     +1                   
Note(s): Evolutionary studies have shown that none of the three promoters transcribing the gene pspF reveal a conserved profile beyond enterobacteria Huvet M,2011
Evidence: [HIPP]
[TIM]
Reference(s): [2] Jovanovic G., et al., 1996
Terminator(s)
Type: rho-independent
Sequence: gcgattaataGCCCAACGCAATAATGTCTGATGCGCTGCGCTTATCAGGCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCaagttgtatt
Reference(s): [2] Jovanovic G., et al., 1996





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