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ArgP DNA-binding transcriptional dual regulator

Synonyms: ArgP-lysine, ArgP, ArgP-arginine
Summary:
ArgP, for "arginine protein," controls the transcription of genes involved in the arginine transport system and genes involved in DNA replication. DNA replication is also regulated directly by ArgP when the protein binds to three 13-mers located in the origin of replication (OriC), which blocks the DNA opening by DnaA and inhibits this cellular process [3] DNA binding by ArgP is prevented when the serine protease Do (DegP) hydrolyzes this transcriptional regulator []. ArgP was first identified as an inhibitor of oriC-initiated DNA replication in vitro. It has also subsequently been described as a nucleoid-associated protein that shows apparently sequence-nonspecific DNA-binding activity [15] ArgP is a noncanonical regulator, as it binds to a number of additional sites in the genome without an apparent direct regulatory effect, exhibiting low-affinity binding to these additional sites [5, 13] To activate transcription, ArgP recognizes AT-rich DNA-binding sites, but no consensus sequence has been identified.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
ArgP Functional   Apo [BPP], [HIFS], [IEP], [IPI] [1], [2], [3]
ArgP-arginine Functional Allosteric Holo [AIFS], [BPP], [GEA], [IPI] [3], [4]
ArgP-lysine Non-Functional Allosteric Holo [BPP], [GEA], [IPI] [1], [4]
Evolutionary Family: LysR
Sensing class: Using internal synthesized signals
Connectivity class: Local Regulator
Gene name: argP
  Genome position: 3059753-3060646
  Length: 894 bp / 297 aa
Operon name: argP
TU(s) encoding the TF:
Transcription unit        Promoter
argP
argPp


Regulon       
Regulated gene(s) argO, argP, dapB, dapD, dnaA, dnaN, gdhA, lysA, lysC, lysP, nrdA, nrdB, recF, yfaE
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
lysine (5)
DNA replication (4)
Porters (Uni-, Sym- and Antiporters) (2)
Transcription related (2)
nucleoproteins, basic proteins (2)
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Regulated operon(s) argO, argP, dapB, dnaAN-recF, gdhA, lysA, lysC, lysP, map-glnD-dapD, nrdAB-yfaE
First gene in the operon(s) argO, argP, dapB, dapD, dnaA, gdhA, lysA, lysC, lysP, nrdA
Simple and complex regulons ArgP
ArgP,CRP,DnaA,Fis,H-NS,NrdR
ArgP,CRP,FNR,Fur,Nac
ArgP,DnaA
ArgP,Lrp
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[ArgP,+](6)
[ArgP,-](1)


Transcription factor regulation    


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
  ArgP-arginine activator argOp Sigma70 -53.5 -82.0 argO
aaattgataaTATTAATTGGCAATCAGAAAaactaataag
3068880 3068900 [BPP], [GEA], [HIBSCS], [IC], [SM] [4], [5], [6], [7], [8]
  ArgP-arginine activator argOp Sigma70 -33.5 -61.5 argO
cgcgggattgTTATTAGCGGAAATTGATAAtattaattgg
3068860 3068879 [BCE], [BPP], [GEA], [HIBSCS], [SM] [1], [4], [5], [6], [7], [8]
  ArgP-arginine repressor argPp nd -36.5 -59.0 argP
acggcttcggTATATGCAACCTGACACAAAattgtgtcat
3059684 3059704 [HIBSCS], [IC] [9]
  ArgP-arginine repressor argPp nd -16.5 -39.5 argP
ctgacacaaaATTGTGTCATAGTGCAGGAAaaagcattta
3059704 3059723 [GEA], [HIBSCS], [IC] [9]
  ArgP activator dapBp1 Sigma70 -81.5 -112.5 dapB
gactcatgccTTTCACTGATATCCCTCCCTgtttatcatt
28252 28271 [BCE], [BPP], [GEA], [HIBSCS], [IC], [SM] [1], [5], [7]
  ArgP activator dapBp1 Sigma70 -61.5 -92.5 dapB
atccctccctGTTTATCATTAATTTCTAATtatcagcgtt
28272 28291 [BPP], [GEA], [SM] [7]
  ArgP activator dapDp Sigma70 nd nd dapD nd nd [BPP], [GEA] [5]
  ArgP activator dnaAp1 nd -69.5 -301.5 dnaA, dnaN, recF
atattggaaaATTTAATGACCATAGACAAAaattggctta
3884021 3884040 [BPP], [GEA], [IC] [5], [10], [11], [12]
  ArgP activator dnaAp1 nd -49.5 -281.5 dnaA, dnaN, recF
gcgggcacgaTTTACGCCGCATATTGGAAAatttaatgac
3884001 3884020 [BPP], [GEA], [IC] [5], [10], [11], [12]
  ArgP activator dnaAp1 nd 219.5 -13.5 dnaA, dnaN, recF
gtgacacggcGGACTCCACTCGAACAAAAGtcgataatga
3883733 3883752 [BPP], [GEA], [IC] [5], [10], [11], [12]
  ArgP activator gdhAp1 Sigma70 -79.5 -142.5 gdhA
atcgcatttgGTTATGAGATTACTCTCGTTattaatttgc
1842219 1842238 [BPP], [GEA], [SM] [5], [7]
  ArgP activator gdhAp1 Sigma70 -59.5 -122.5 gdhA
tactctcgttATTAATTTGCTTTCCTGGGTcatttttttc
1842239 1842258 [BPP], [GEA], [SM] [7]
  ArgP activator lysAp Sigma70 nd nd lysA nd nd [BPP], [GEA] [5]
  ArgP activator lysCp1 Sigma70 nd nd lysC nd nd [BPP], [GEA] [5]
  ArgP activator lysPp Sigma70 -82.5 -110.5 lysP
tcatgatcgcCCAGGGATTATAAGTAAAGCagccaatctc
2248633 2248652 [BPP], [GEA], [HIBSCS], [IC], [SM] [5], [7], [13]
  ArgP activator lysPp Sigma70 -62.5 -90.5 lysP
tacacggttaTAAGACACCTTCATGATCGCccagggatta
2248613 2248632 [BPP], [GEA], [HIBSCS], [IC], [SM] [5], [7], [13]
  ArgP activator nrdAp Sigma70 -334.5 -444.5 nrdA, nrdB, yfaE
atggcttagcATTTAACAATAACCGAATAGaaaacaacca
2344411 2344430 [BPP], [GEA], [IC] [5], [14]
  ArgP activator nrdAp Sigma70 -281.5 -391.5 nrdA, nrdB, yfaE
aatctcttacATTCGCTTATATATTGACCAcaactgatac
2344464 2344483 [BPP], [GEA], [IC] [2], [5]
  ArgP activator nrdAp Sigma70 -244.5 -354.5 nrdA, nrdB, yfaE
tacatcagatTATGTGATGACTCGTGCTTAgatcaatttt
2344501 2344520 [BPP], [GEA], [IC] [2], [5]
  ArgP activator nrdAp Sigma70 -218.5 -328.5 nrdA, nrdB, yfaE
cttagatcaaTTTTTGCAATCATTAGCAAAaagattaata
2344527 2344546 [BPP], [GEA], [IC] [2], [5]
  ArgP activator nrdAp Sigma70 -190.5 -300.5 nrdA, nrdB, yfaE
aaaagattaaTAAGCCATCTATATCAATTTatctaaccta
2344555 2344574 [BPP], [GEA], [IC] [2], [5]
  ArgP activator nrdAp Sigma70 -163.5 -273.5 nrdA, nrdB, yfaE
tttatctaacCTATTATGCCGTTCAAGAAAtcgccgaaca
2344582 2344601 [BPP], [GEA], [IC] [2], [5]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  ArgP activator asd nd nd nd nd [ICWHO] nd


Alignment and PSSM for ArgP TFBSs    

Aligned TFBS of ArgP   
  Sequence
  ATGCCTTTCACTGATATC
  ATGAAGGTGTCTTATAAC
  CTTATAATCCCTGGGCGA
  GTTATTGTTAAATGCTAA
  CTTACATTCGCTTATATA
  CAGATTATGTGATGACTC
  CTTTTTGCTAATGATTGC
  ATATAGATGGCTTATTAA
  CCTATTATGCCGTTCAAG
  AATTTTGTGTCAGGTTGC
  AAAATTGTGTCATAGTGC
  AATATTATCAATTTCCGC
  CTGATTGCCAATTAATAT
  CTTTTGTTCGAGTGGAGT
  CAATATGCGGCGTAAATC
  ATTTTTGTCTATGGTCAT

Position weight matrix (PWM).   
A	7	5	3	9	3	2	5	0	0	5	6	4	0	8	3	6	6	4
C	8	1	0	1	2	0	0	3	7	2	9	0	0	0	3	4	0	8
G	1	0	4	0	0	3	8	0	7	4	1	3	5	6	3	0	6	1
T	0	10	9	6	11	11	3	13	2	5	0	9	11	2	7	6	4	3

PWM logo   


 


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


Evidence    

 [BPP] Binding of purified proteins

 [HIFS] Human inference of function from sequence

 [IEP] Inferred from expression pattern

 [IPI] Inferred from physical interaction

 [AIFS] Automated inference of function from sequence

 [GEA] Gene expression analysis

 [HIBSCS] Human inference based on similarity to consensus sequences

 [IC] Inferred by curator

 [SM] Site mutation

 [BCE] Binding of cellular extracts

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Bouvier J., Stragier P., Morales V., Remy E., Gutierrez C., 2008, Lysine represses transcription of the Escherichia coli dapB gene by preventing its activation by the ArgP activator., J Bacteriol 190(15):5224-9

 [2] Han JS., Kwon HS., Yim JB., Hwang DS., 1998, Effect of IciA protein on the expression of the nrd gene encoding ribonucleoside diphosphate reductase in E. coli., Mol Gen Genet 259(6):610-4

 [3] Thony B., Hwang DS., Fradkin L., Kornberg A., 1991, iciA, an Escherichia coli gene encoding a specific inhibitor of chromosomal initiation of replication in vitro., Proc Natl Acad Sci U S A 88(10):4066-70

 [4] Laishram RS., Gowrishankar J., 2007, Environmental regulation operating at the promoter clearance step of bacterial transcription., Genes Dev 21(10):1258-72

 [5] Marbaniang CN., Gowrishankar J., 2011, Role of ArgP (IciA) in Lysine-Mediated Repression in Escherichia coli., J Bacteriol 193(21):5985-96

 [6] Nandineni MR., Gowrishankar J., 2004, Evidence for an arginine exporter encoded by yggA (argO) that is regulated by the LysR-type transcriptional regulator ArgP in Escherichia coli., J Bacteriol 186(11):3539-46

 [7] Nguyen Le Minh P., Velazquez Ruiz C., Vandermeeren S., Abwoyo P., Bervoets I., Charlier D., 2018, Differential protein-DNA contacts for activation and repression by ArgP, a LysR-type (LTTR) transcriptional regulator in Escherichia coli., Microbiol Res 206:141-158

 [8] Peeters E., Nguyen Le Minh P., Foulquie-Moreno M., Charlier D., 2009, Competitive activation of the Escherichia coli argO gene coding for an arginine exporter by the transcriptional regulators Lrp and ArgP., Mol Microbiol 74(6):1513-26

 [9] Celis RT., 1999, Repression and activation of arginine transport genes in Escherichia coli K 12 by the ArgP protein., J Mol Biol 294(5):1087-95

 [10] Lee Y., Lee H., Yim J., Hwang D., 1997, The binding of two dimers of IciA protein to the dnaA promoter 1P element enhances the binding of RNA polymerase to the dnaA promoter 1P., Nucleic Acids Res 25(17):3486-9

 [11] Lee YS., Hwang DS., 1997, Occlusion of RNA polymerase by oligomerization of DnaA protein over the dnaA promoter of Escherichia coli., J Biol Chem 272(1):83-8

 [12] Lee YS., Kim H., Hwang DS., 1996, Transcriptional activation of the dnaA gene encoding the initiator for oriC replication by IciA protein, an inhibitor of in vitro oriC replication in Escherichia coli., Mol Microbiol 19(2):389-96

 [13] Ruiz J., Haneburger I., Jung K., 2011, Identification of ArgP and Lrp as transcriptional regulators of lysP, the gene encoding the specific lysine permease of Escherichia coli., J Bacteriol 193(10):2536-48

 [14] Ohtsubo T., Matsuda O., Iba K., Terashima I., Sekiguchi M., Nakabeppu Y., 1998, Molecular cloning of AtMMH, an Arabidopsis thaliana ortholog of the Escherichia coli mutM gene, and analysis of functional domains of its product., Mol Gen Genet 259(6):577-90

 [15] Azam TA., Ishihama A., 1999, Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity., J Biol Chem 274(46):33105-13

 [16] Han JS., Park JY., Lee YS., Thony B., Hwang DS., 1999, PhoB-dependent transcriptional activation of the iciA gene during starvation for phosphate in Escherichia coli., Mol Gen Genet 262(3):448-52



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