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| Operon |  |
|---|---|
| Name: | pspF |
| This page displays every known transcription unit of this operon and their known regulation. | |
| 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 Bury-Moné S, Nomane Y, Reymond N, Barbet R, Jacquet E, Imbeaud S, Jacq A, Bouloc P,2009 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 Bury-Moné S, Nomane Y, Reymond N, Barbet R, Jacquet E, Imbeaud S, Jacq A, Bouloc P,2009 |
| Evidence: | [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit [EXP-IDA-BOUNDARIES-DEFINED] 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: |
[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
| Reference(s): |
[3] Huerta AM., et al., 2003 [2] Jovanovic G., et al., 1996 |
| Terminator(s) | |
| Type: | rho-independent |
| Sequence: | gcgattaataGCCCAACGCAATAATGTCTGATGCGCTGCGCTTATCAGGCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCaagttgtatt |
| Reference(s): | [2] Jovanovic G., et al., 1996 |
| 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 Bury-Moné S, Nomane Y, Reymond N, Barbet R, Jacquet E, Imbeaud S, Jacq A, Bouloc P,2009 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 Bury-Moné S, Nomane Y, Reymond N, Barbet R, Jacquet E, Imbeaud S, Jacq A, Bouloc P,2009 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. |
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| Evidence: | [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified |
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| Reference(s): |
[1] Jovanovic G., et al., 1997 [2] Jovanovic G., et al., 1996 |
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| Promoter | |||||||||||
| Name: | pspFp1 | ||||||||||
| +1: | 1367945 | ||||||||||
| Sigma Factor: | Sigma70 Sigmulon | ||||||||||
| Distance from start of the gene: | 33 | ||||||||||
| Sequence: |
tatctttttgatttataaagatctgattgaagaatcaacagcaacatgccaggatgagttAgcgaattacactaacaagtg -35 -10 +1 |
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| 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: |
[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
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| Reference(s): |
[3] Huerta AM., et al., 2003 [2] Jovanovic G., et al., 1996 |
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| Terminator(s) | |||||||||||
| Type: | rho-independent | ||||||||||
| Sequence: | gcgattaataGCCCAACGCAATAATGTCTGATGCGCTGCGCTTATCAGGCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCaagttgtatt | ||||||||||
| Reference(s): | [2] Jovanovic G., et al., 1996 | ||||||||||
| 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 | repressor | pspFp1 | 1367911 | 1367927 | 27.0 | acactaacaaGTGGCGAATTTCATCATggcagaatac | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [1], [4] |
| proximal | PspF | repressor | pspFp1 | 1367931 | 1367947 | 7.0 | ccaggatgagTTAGCGAATTACACTAAcaagtggcga | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [1], [4] |
| 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 Bury-Moné S, Nomane Y, Reymond N, Barbet R, Jacquet E, Imbeaud S, Jacq A, Bouloc P,2009 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 Bury-Moné S, Nomane Y, Reymond N, Barbet R, Jacquet E, Imbeaud S, Jacq A, Bouloc P,2009 |
| Evidence: | [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit [EXP-IDA-BOUNDARIES-DEFINED] 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: |
[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
| Reference(s): |
[3] Huerta AM., et al., 2003 [2] Jovanovic G., et al., 1996 |
| Terminator(s) | |
| Type: | rho-independent |
| Sequence: | gcgattaataGCCCAACGCAATAATGTCTGATGCGCTGCGCTTATCAGGCCTGCAAACGACGTATTGATTATGTATGCCGAATAAAGCATTCACGCCGCATCCGGCaagttgtatt |
| Reference(s): | [2] Jovanovic G., et al., 1996 |
| Reference(s) |
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|---|---|
[COMP-AINF] Inferred computationally without human oversight