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| Operon |  |
|---|---|
| Name: | pspABCDE |
| This page displays every known transcription unit of this operon and their known regulation. | |
| Name: | pspABCDE | |||||||||
| Synonym(s): | pspABCE | |||||||||
| Gene(s): | pspA, pspB, pspC, pspD, pspE Genome Browser M3D Gene expression COLOMBOS | |||||||||
| Note(s): | The operon pspABCDE codes for proteins involved in the stress response system. This operon is divergently located from the pspF gene in the genome of E. coli. PspF encodes the transcriptional regulator of the psp operon. Evolutionary studies have shown that the psp operon grew in the head-to-tail direction from the 3' end of pspA, with pspE the more recent addition to the operon. The system appears to have evolved around the genes pspA and pspF. They form a minimal system for stress response Huvet M,2011. Contrary to findings in E. coli, the genes ycjX and ycjF are part of the psp operon in other species Huvet M,2011. This transcription unit is frequently called pspABCE, because the pspD product (73 amino acids) has not been detected either in vivo or in vitro Weiner L,1995. The pspABCDE operon was significantly upregulated in bacterial cells associated with lettuce roots in a microarray analysis Hou Z,2012. The expression of the operon is also increased when colicin (at 30 ng/ml) is added to the medium Kamen?ek S, ?gur-Bertok D,2013. The transition from low to high expression of the pspABCDE operon is regulated via the burst frequency of transcription but not by the burst size of transcription, as observed for operons transcribed from σ70 promoters Engl C,2020 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: | [LTED] Length of transcript experimentally determined | |||||||||
| Reference(s): |
[1] Brissette JL., et al., 1991 [2] Fozo EM., et al., 2008 [3] Jovanovic G., et al., 1996 [4] Weiner L., et al., 1995 |
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| Promoter | ||||||||||
| Name: | pspAp | |||||||||
| +1: | 1368038 | |||||||||
| Sigma Factor: | Sigma54 Sigmulon | |||||||||
| Distance from start of the gene: | 41 | |||||||||
| Sequence: |
aatcagatctttataaatcaaaaagataaaaaattggcacgcaaattgtattaacagttcAgcaggacaatcctgaacgca -24 -12 +1 |
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| Evidence: |
[AIPP] [ICWHO] [IHBCE] [IMP] [RS-EPT-CBR] [TIM] |
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| Reference(s): |
[5] Huerta AM., et al., 2003 [6] Salgado H, et al., 2012 [7] Weiner L., et al., 1991 |
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| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| remote | PspF | activator | pspAp | 1367911 | 1367927 | -119.0 | gtattctgccATGATGAAATTCGCCACttgttagtgt | nd | [GEA], [BCE], [BPP] | [8], [9], [10] |
| remote | PspF | activator | pspAp | 1367931 | 1367947 | -99.0 | tcgccacttgTTAGTGTAATTCGCTAActcatcctgg | nd | [GEA], [BCE], [BPP] | [8], [9], [10] |
| Name: | pspBCDE |
| Gene(s): | pspB, pspC, pspD, pspE Genome Browser M3D Gene expression COLOMBOS |
| Evidence: | [PAGTSBP] Products of adjacent genes in the same biological process |
| Promoter | |
| Name: | pspBp |
| +1: | Unknown |
| Note(s): | Zaslaver et al. demonstrated in 2006, by means of a library of fluorescent transcription fusions, that this promoter can be transcribed in vitro Zaslaver A,2006. Based on this, a putative promoter was suggested, but the +1 site of the transcription initiation has not been determined, although there exists promoter activity. |
| Evidence: | [IEP] |
| Reference(s): | [11] Zaslaver A., et al., 2006 |
| Name: | pspE |
| Gene(s): | pspE Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | The expression of the pspE gene is induced in a mutant at the YcjW transcriptional regulator; however, this appears to be an indirect effect of the regulator on gene expression Luhachack L,2019. |
| Promoter | |
| Name: | pspEp |
| +1: | Unknown |
| Evidence: | [IEP] |
| Reference(s): | [11] Zaslaver A., et al., 2006 |
| RNA cis-regulatory element | |
|---|
| Regulation, transcriptional elongation | |
| Attenuator type: | Translational |
| Strand: | forward |
| Evidence: | [ICA] Inferred by computational analysis |
| Reference(s): | [12] Merino E, et al., 2005 |
| Structure type | Energy | LeftPos | RightPos | Sequence (RNA-strand) | |
|---|---|---|---|---|---|
| terminator | -14.4 | 1369644 | 1369686 | ttaaatctcaGGCGTATAATGGATGGCAATTTTCATCCATAGAAGGACGCTTacatgtttaa |
| Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos" |
| Reference(s) |
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|---|---|
[AIPP] Automated inference of promoter position