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PspF DNA-binding transcriptional dual regulator

Synonyms: PspF
Summary:
The transcription factor PspF, for Phage shock protein F, is a bacterial enhancer-binding protein required for σ54-dependent transcription activation [5, 6]. This regulator activates the transcription of the psp regulon, and it is negatively autoregulated and coordinately activated by transcription of the divergent operon psp [1, 4, 6, 7]. The integration host factor facilitates control of the psp regulon [2, 4, 8].
The psp regulon is defined like the phage shock protein system, which is involved in protecting the bacterium during infectious processes [4, 6]. The synthesis of this regulon is induced when Escherichia coli is grown under different extracytoplasmic stress conditions and upon infection by filamentous phage (phage shock) [7, 9, 10, 11, 12, 13, 14].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
PspF     nd nd
Evolutionary Family: EBP
Connectivity class: Local Regulator
Gene name: pspF
  Genome position: 1366935-1367912
  Length: 978 bp / 325 aa
Operon name: pspF
TU(s) encoding the TF:
Transcription unit        Promoter
pspF
pspFp1
pspF
pspFp2
pspF
pspFp3


Regulon       
Regulated gene(s) pspA, pspB, pspC, pspD, pspE, pspF, pspG
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
prophage genes and phage related functions (5)
operon (4)
inhibition / activation of enzymes (1)
cell killing (1)
Transcription related (1)
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Regulated operon(s) pspABCDE, pspF, pspG
First gene in the operon(s) pspA, pspF, pspG
Simple and complex regulons IHF,PspF
PspF
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[PspF,+](2)
[PspF,-](1)


Transcription factor binding sites (TFBSs) arrangements       

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  PspF activator pspAp Sigma54 -119.0 -160.0 pspA, pspB, pspC, pspD, pspE
gtattctgccATGATGAAATTCGCCACttgttagtgt
1367911 1367927 [BCE], [BPP], [GEA] [1], [2], [3]
  PspF activator pspAp Sigma54 -99.0 -140.0 pspA, pspB, pspC, pspD, pspE
tcgccacttgTTAGTGTAATTCGCTAActcatcctgg
1367931 1367947 [BCE], [BPP], [GEA] [1], [2], [3]
  PspF repressor pspFp1 Sigma70 7.0 -27.0 pspF
ccaggatgagTTAGCGAATTACACTAAcaagtggcga
1367931 1367947 [BCE], [BPP], [GEA] [1], [2], [3]
  PspF repressor pspFp1 Sigma70 27.0 -7.0 pspF
acactaacaaGTGGCGAATTTCATCATggcagaatac
1367911 1367927 [BCE], [BPP], [GEA] [1], [2], [3]
  PspF activator pspGp Sigma54 -87.0 -111.0 pspG
tcaccaaaaaGTAGTCAAATTCACCACgccctgcgca
4262721 4262737 [BPP], [GEA], [ICA] [4]


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
Promoter-target gene evolutionary conservation


Evidence    

 [BCE] Binding of cellular extracts

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [ICA] Inferred by computational analysis



Reference(s)    

 [1] Jovanovic G., Dworkin J., Model P., 1997, Autogenous control of PspF, a constitutively active enhancer-binding protein of Escherichia coli., J Bacteriol. 179(16):5232-7

 [2] 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

 [3] 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

 [4] 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

 [5] Rappas M., Bose D., Zhang X., 2007, Bacterial enhancer-binding proteins: unlocking sigma54-dependent gene transcription., Curr Opin Struct Biol. 17(1):110-6

 [6] 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

 [7] Amin MA., Awadein MR., Gabr H., 2005, Evaluation of the inhibitory effect of antisense oligodeoxynucleotides on the growth of hepatitis C-associated hepatocellular carcinoma cells in vitro., Chin J Dig Dis. 6(3):142-8

 [8] Dworkin J., Jovanovic G., Model P., 1997, Role of upstream activation sequences and integration host factor in transcriptional activation by the constitutively active prokaryotic enhancer-binding protein PspF., J Mol Biol. 273(2):377-88

 [9] 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

 [10] Jovanovic G., Lloyd LJ., Stumpf MP., Mayhew AJ., Buck M., 2006, Induction and function of the phage shock protein extracytoplasmic stress response in Escherichia coli., J Biol Chem. 281(30):21147-61

 [11] Model P., Jovanovic G., Dworkin J., 1997, The Escherichia coli phage-shock-protein (psp) operon., Mol Microbiol. 24(2):255-61

 [12] Darwin AJ., 2005, The phage-shock-protein response., Mol Microbiol. 57(3):621-8

 [13] 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

 [14] Kobayashi H., Yamamoto M., Aono R., 1998, Appearance of a stress-response protein, phage-shock protein A, in Escherichia coli exposed to hydrophobic organic solvents., Microbiology. 144 ( Pt 2):353-9

 [15] Elderkin S., Jones S., Schumacher J., Studholme D., Buck M., 2002, Mechanism of action of the Escherichia coli phage shock protein PspA in repression of the AAA family transcription factor PspF., J Mol Biol. 320(1):23-37

 [16] Dworkin J., Jovanovic G., Model P., 2000, The PspA protein of Escherichia coli is a negative regulator of sigma(54)-dependent transcription., J Bacteriol. 182(2):311-9

 [17] Zhang N., Simpson T., Lawton E., Uzdavinys P., Joly N., Burrows P., Buck M., 2013, A key hydrophobic patch identified in an AAA¿¿¿ protein essential for its in trans inhibitory regulation., J Mol Biol. 425(15):2656-69

 [18] Mehta P., Jovanovic G., Lenn T., Bruckbauer A., Engl C., Ying L., Buck M., 2013, Dynamics and stoichiometry of a regulated enhancer-binding protein in live Escherichia coli cells., Nat Commun. 4:1997

 [19] 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

 [20] Adams H., Teertstra W., Demmers J., Boesten R., Tommassen J., 2003, Interactions between phage-shock proteins in Escherichia coli., J Bacteriol. 185(4):1174-80

 [21] Chaney M., Grande R., Wigneshweraraj SR., Cannon W., Casaz P., Gallegos MT., Schumacher J., Jones S., Elderkin S., Dago AE., Morett E., Buck M., 2001, Binding of transcriptional activators to sigma 54 in the presence of the transition state analog ADP-aluminum fluoride: insights into activator mechanochemical action., Genes Dev. 15(17):2282-94

 [22] Cannon WV., Schumacher J., Buck M., 2004, Nucleotide-dependent interactions between a fork junction-RNA polymerase complex and an AAA+ transcriptional activator protein., Nucleic Acids Res. 32(15):4596-608

 [23] Lew CM., Gralla JD., 2002, New roles for conserved regions within a sigma 54-dependent enhancer-binding protein., J Biol Chem. 277(44):41517-24

 [24] Bordes P., Wigneshweraraj SR., Schumacher J., Zhang X., Chaney M., Buck M., 2003, The ATP hydrolyzing transcription activator phage shock protein F of Escherichia coli: identifying a surface that binds sigma 54., Proc Natl Acad Sci U S A. 100(5):2278-83

 [25] Cannon W., Bordes P., Wigneshweraraj SR., Buck M., 2003, Nucleotide-dependent Triggering of RNA Polymerase-DNA Interactions by an AAA Regulator of Transcription., J Biol Chem. 278(22):19815-25

 [26] Jovanovic G., Model P., 1997, The RIB element in the goaG-pspF intergenic region of Escherichia coli., J Bacteriol. 179(10):3095-102

 [27] Elderkin S., Bordes P., Jones S., Rappas M., Buck M., 2005, Molecular determinants for PspA-mediated repression of the AAA transcriptional activator PspF., J Bacteriol. 187(9):3238-48

 [28] Darbari VC., Lawton E., Lu D., Burrows PC., Wiesler S., Joly N., Zhang N., Zhang X., Buck M., 2014, Molecular basis of nucleotide-dependent substrate engagement and remodeling by an AAA+ activator., Nucleic Acids Res. 42(14):9249-61

 [29] Schumacher J., Zhang X., Jones S., Bordes P., Buck M., 2004, ATP-dependent transcriptional activation by bacterial PspF AAA+protein., J Mol Biol. 338(5):863-75

 [30] Joly N., Schumacher J., Buck M., 2006, Heterogeneous nucleotide occupancy stimulates functionality of phage shock protein F, an AAA+ transcriptional activator., J Biol Chem. 281(46):34997-5007

 [31] Bordes P., Wigneshweraraj SR., Zhang X., Buck M., 2004, Sigma54-dependent transcription activator phage shock protein F of Escherichia coli: a fragmentation approach to identify sequences that contribute to self-association., Biochem J. 378(Pt 3):735-44

 [32] Ogura T., Wilkinson AJ., 2001, AAA+ superfamily ATPases: common structure--diverse function., Genes Cells. 6(7):575-97

 [33] Walker JE., Saraste M., Runswick MJ., Gay NJ., 1982, Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold., EMBO J. 1(8):945-51

 [34] Bose D., Joly N., Pape T., Rappas M., Schumacher J., Buck M., Zhang X., 2008, Dissecting the ATP hydrolysis pathway of bacterial enhancer-binding proteins., Biochem Soc Trans. 36(Pt 1):83-8

 [35] Zhang N., Joly N., Buck M., 2012, A common feature from different subunits of a homomeric AAA+ protein contacts three spatially distinct transcription elements., Nucleic Acids Res. 40(18):9139-52

 [36] Dago AE., Wigneshweraraj SR., Buck M., Morett E., 2007, A role for the conserved GAFTGA motif of AAA+ transcription activators in sensing promoter DNA conformation., J Biol Chem. 282(2):1087-97

 [37] Bordes P., Wigneshweraraj SR., Chaney M., Dago AE., Morett E., Buck M., 2004, Communication between Esigma(54) , promoter DNA and the conserved threonine residue in the GAFTGA motif of the PspF sigma-dependent activator during transcription activation., Mol Microbiol. 54(2):489-506

 [38] Zhang N., Joly N., Burrows PC., Jovanovic M., Wigneshweraraj SR., Buck M., 2009, The role of the conserved phenylalanine in the sigma54-interacting GAFTGA motif of bacterial enhancer binding proteins., Nucleic Acids Res. 37(18):5981-92

 [39] Burrows PC., Schumacher J., Amartey S., Ghosh T., Burgis TA., Zhang X., Nixon BT., Buck M., 2009, Functional roles of the pre-sensor I insertion sequence in an AAA+ bacterial enhancer binding protein., Mol Microbiol. 73(4):519-33

 [40] Schumacher J., Joly N., Rappas M., Bradley D., Wigneshweraraj SR., Zhang X., Buck M., 2007, Sensor I threonine of the AAA+ ATPase transcriptional activator PspF is involved in coupling nucleotide triphosphate hydrolysis to the restructuring of sigma 54-RNA polymerase., J Biol Chem. 282(13):9825-33

 [41] Joly N., Buck M., 2011, Single chain forms of the enhancer binding protein PspF provide insights into geometric requirements for gene activation., J Biol Chem. 286(14):12734-42

 [42] Tucker PA., Sallai L., 2007, The AAA+ superfamily--a myriad of motions., Curr Opin Struct Biol. 17(6):641-52

 [43] Schumacher J., Joly N., Rappas M., Zhang X., Buck M., 2006, Structures and organisation of AAA+ enhancer binding proteins in transcriptional activation., J Struct Biol. 156(1):190-9



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