RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
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 23421615.
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 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: [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
Promoter
Name: pspAp
+1: 1368038
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 41
Sequence: aatcagatctttataaatcaaaaagataaaaaattggcacgcaaattgtattaacagttcAgcaggacaatcctgaacgca
                                   -24         -12          +1                   
Evidence: [AIPP]
[ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [5] Huerta AM., et al., 2003
[6] Salgado H, et al., 2012
[7] Weiner L., et al., 1991
TF binding sites (TFBSs)
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF1 activator pspAp 1367989 1368001 -42.5 atcagatcttTATAAATCAAAAAGataaaaaatt nd [APIORCISFBSCS], [BCE], [BPP], [GEA] [4], [9]
[PspF,+] Phrase
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 gtattctgccATGATGAAATTCGCCACTtgttagtgta nd [BCE], [BPP], [GEA] [8], [9], [10]
remote PspF activator pspAp 1367931 1367947 -99.0 tcgccacttgTTAGTGTAATTCGCTAACtcatcctggc nd [BCE], [BPP], [GEA] [8], [9], [10]
Note(s): 1IHF and PspF proteins bind cooperatively to regulate the pspA promoter.3IHF and PspF proteins bind cooperatively to regulate the pspA promoter.


Transcription unit       
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


Transcription unit       
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"


Evidence    

 [AIPP] Automated inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [TIM] Transcription initiation mapping

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BCE] Binding of cellular extracts

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [IEP] Inferred from expression pattern


Reference(s)    

 [1] Brissette JL., Weiner L., Ripmaster TL., Model P., 1991, Characterization and sequence of the Escherichia coli stress-induced psp operon., J Mol Biol 220(1):35-48

 [2] Fozo EM., Kawano M., Fontaine F., Kaya Y., Mendieta KS., Jones KL., Ocampo A., Rudd KE., Storz G., 2008, Repression of small toxic protein synthesis by the Sib and OhsC small RNAs., Mol Microbiol 70(5):1076-93

 [3] Jovanovic G., Weiner L., Model P., 1996, Identification, nucleotide sequence, and characterization of PspF, the transcriptional activator of the Escherichia coli stress-induced psp operon., J Bacteriol 178(7):1936-45

 [4] Weiner L., Brissette JL., Ramani N., Model P., 1995, Analysis of the proteins and cis-acting elements regulating the stress-induced phage shock protein operon., Nucleic Acids Res 23(11):2030-6

 [5] 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

 [6] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [7] Weiner L., Brissette JL., Model P., 1991, Stress-induced expression of the Escherichia coli phage shock protein operon is dependent on sigma 54 and modulated by positive and negative feedback mechanisms., Genes Dev 5(10):1912-23

 [8] Engl C., Jovanovic G., Brackston RD., Kotta-Loizou I., Buck M., 2020, The route to transcription initiation determines the mode of transcriptional bursting in E. coli., Nat Commun 11(1):2422

 [9] Jovanovic G., Model P., 1997, PspF and IHF bind co-operatively in the psp promoter-regulatory region of Escherichia coli., Mol Microbiol 25(3):473-81

 [10] Jovanovic G., Rakonjac J., Model P., 1999, In vivo and in vitro activities of the Escherichia coli sigma54 transcription activator, PspF, and its DNA-binding mutant, PspFDeltaHTH., J Mol Biol 285(2):469-83

 [11] Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette MG., Alon U., 2006, A comprehensive library of fluorescent transcriptional reporters for Escherichia coli., Nat Methods 3(8):623-8

 [12] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.

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