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YdeO DNA-binding transcriptional dual regulator

Synonyms: YdeO
Summary:
YdeO belongs to the AraC/XylS family of transcriptional regulators and shows more similarity to YhiW, AppY, AdiY, and GadX than the other AraC/XylS regulators [2, 8]. The members of this family exhibit two domains, an amino-terminal domain involved in coinducer recognition and dimerization and a carboxy-terminal domain that contains a potential helix-turn-helix DNA-binding motif [2, 9]. YdeO activates genes involved in the cellular response to acid resistance [3, 4, 5]. This protein, together with the proteins HNS, EvgA, and GadE, pertains to a specific regulatory circuit that is functional in exponential-phase cells growing in minimal medium [3, 4, 5]. Several of the genes directly regulated by YdeO are also directly regulated by GadX [5]. The YdeO regulon has been determined [6].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
YdeO Functional   [APPH], [APPHINH], [GEA], [HIFS], [IEP], [IMP] [1], [2], [3], [4], [5], [6]
Evolutionary Family: AraC/XylS
Connectivity class: Local Regulator
Gene name: ydeO
  Genome position: 1582926-1583687
  Length: 762 bp / 253 aa
Operon name: safA-ydeO
TU(s) encoding the TF:
Transcription unit        Promoter
safA-ydeO
safAp
ydeO
ydeOp


Regulon       
Regulated gene(s) appA, appB, appC, appX, dctR, gadE, gadF, gadW, hyaA, hyaB, hyaC, hyaD, hyaE, hyaF, mdtE, mdtF, safA, slp, uspD, ydeO, yiiS
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
aerobic respiration (6)
anaerobic respiration (6)
membrane (5)
Transcription related (3)
electron donors (3)
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Regulated operon(s) appCBXA, gadAXW, gadEF-mdtEF, hyaABCDEF, safA-ydeO, slp-dctR, yiiS-uspD
First gene in the operon(s) appC, gadE, gadE, gadW, hyaA, safA, slp, yiiS
Simple and complex regulons AppY,ArcA,Fis,IscR,NarL,NarP,YdeO
AppY,ArcA,YdeO
ArcA,GadX,YdeO
CRP,EvgA,FliZ,GadE,GadW,GadX,H-NS,YdeO
EvgA,PhoP,RcsB,YdeO
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[YdeO,+](7)
[YdeO,-](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
  YdeO activator appCp Sigma70, Sigma38 -27.5 -57.0 appC, appB, appX, appA
tggtcgtagaGTTTCAGGATAAAGAGGGAGATCtaccattatc
1037672 1037694 [BPP], [GEA], [IHBCE] [6]
  YdeO activator gadEp Sigma38 nd nd gadE, gadF, mdtE, mdtF nd nd [BPP], [GEA] [3]
  YdeO activator gadEp3 Sigma70 -41.0 -607.0 gadE, gadF
caaattagccATTTCAAACATTATCATGGCTGATATTttccgtagtc
3657746 3657772 [BPP], [GEA], [IHBCE] [6], [7]
  YdeO activator gadWp1 nd -13.0 -46.5 gadW
agtctggcatCATTTCATTAGTATACTGAAATtgaaataatc
3664654 3664675 [BPP], [GEA], [IHBCE] [6]
  YdeO activator hyaAp Sigma70, Sigma38 -61.0 -215.5 hyaA, hyaB, hyaC, hyaD, hyaE, hyaF
aaataggtccATTTTTATCGCTAAAAGATAAATCcacacagttt
1031912 1031935 [BPP], [GEA], [IHBCE] [6]
  YdeO repressor safAp Sigma70 nd nd safA, ydeO nd nd [GEA] [1]
  YdeO activator slpp Sigma70 -40.0 -64.5 slp, dctR
actatcaggcATATCACCTCAGAATCAGATGAAAACtataaagaaa
3653884 3653909 [BPP], [GEA], [IHBCE] [6]
  YdeO activator yiiSp Sigma24 -55.0 -152.5 yiiS, uspD
cgggattgttATTTCCACGATGCAAATGACAATACCCGGAAAATccttctgaac
4112798 4112831 [BPP], [GEA], [IHBCE] [6]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Growth Condition Evidence (Confirmed, Strong, Weak) References
  YdeO activator nhaR nd nd 17894 17927 nd [BPP], [GEA], [HIBSCS] [6]


Alignment and PSSM for YdeO TFBSs    

Aligned TFBS of YdeO   
  Sequence
  TGTTATTTCCACGATGCAAATGACAATACCC
  GTAGAGTTTCAGGATAAAGAGGGAGATCTAC
  TTTCAATTTCAGTATACTAATGAAATGATGC
  GTCCATTTTTATCGCTAAAAGATAAATCCAC
  TAGTTTTCATCTGATTCTGAGGTGATATGCC
  AGCCATTTCAAACATTATCATGGCTGATATT

Position weight matrix (PWM). YdeO matrix-quality result   
A	1	1	1	0	5	1	0	0	1	1	5	1	0	5	0	2	3	3	3	6	0	1	2	3	4	3	2	2	1	2	0
C	0	0	2	3	0	0	0	1	2	3	1	1	2	0	1	0	3	0	1	0	0	0	0	2	0	0	0	2	2	2	5
G	2	2	1	1	0	1	0	0	0	0	0	2	3	1	0	1	0	0	2	0	3	5	2	1	1	1	1	0	1	1	0
T	3	3	2	2	1	4	6	5	3	2	0	2	1	0	5	3	0	3	0	0	3	0	2	0	1	2	3	2	2	1	1

Consensus   
;	consensus.strict             	ttccatTttcaggattcaaAgGgaaatcccC
;	consensus.strict.rc          	GGGGATTTCCCTTTGAATCCTGAAAATGGAA
;	consensus.IUPAC              	kkyyatTtyyaksatwmwrAkGdmawwhymC
;	consensus.IUPAC.rc           	GKRDWWTKHCMTYWKWATSMTRRAAATRRMM
;	consensus.regexp             	[gt][gt][ct][ct]atTt[ct][ct]a[gt][cg]at[at][ac][at][ag]A[gt]G[agt][ac]a[at][at][act][ct][ac]C
;	consensus.regexp.rc          	G[GT][AG][AGT][AT][AT]T[GT][ACT]C[AC]T[CT][AT][GT][AT]AT[CG][AC]T[AG][AG]AAAT[AG][AG][AC][AC]

PWM logo   


 


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


Evidence    

 [APPH] Assay of protein purified to homogeneity

 [APPHINH] Assay of protein purified to homogeneity from its native host

 [GEA] Gene expression analysis

 [HIFS] Human inference of function from sequence

 [IEP] Inferred from expression pattern

 [IMP] Inferred from mutant phenotype

 [BPP] Binding of purified proteins

 [IHBCE] Inferred by a human based on computational evidence

 [HIBSCS] Human inference based on similarity to consensus sequences



Reference(s)    

 [1] Burton NA., Johnson MD., Antczak P., Robinson A., Lund PA., 2010, Novel aspects of the acid response network of E. coli K-12 are revealed by a study of transcriptional dynamics., J Mol Biol 401(5):726-42

 [2] Gallegos MT., Schleif R., Bairoch A., Hofmann K., Ramos JL., 1997, Arac/XylS family of transcriptional regulators., Microbiol Mol Biol Rev 61(4):393-410

 [3] Ma Z., Masuda N., Foster JW., 2004, Characterization of EvgAS-YdeO-GadE branched regulatory circuit governing glutamate-dependent acid resistance in Escherichia coli., J Bacteriol 186(21):7378-89

 [4] Masuda N., Church GM., 2002, Escherichia coli gene expression responsive to levels of the response regulator EvgA., J Bacteriol 184(22):6225-34

 [5] Masuda N., Church GM., 2003, Regulatory network of acid resistance genes in Escherichia coli., Mol Microbiol 48(3):699-712

 [6] Yamanaka Y., Oshima T., Ishihama A., Yamamoto K., 2014, Characterization of the YdeO regulon in Escherichia coli., PLoS One 9(11):e111962

 [7] Sayed AK., Foster JW., 2009, A 750 bp sensory integration region directs global control of the Escherichia coli GadE acid resistance regulator., Mol Microbiol 71(6):1435-50

 [8] Ibarra JA, Pérez-Rueda E, Segovia L, Puente JL, 2008, The DNA-binding domain as a functional indicator: the case of the AraC/XylS family of transcription factors., Genetica, 2008 May

 [9] Martin RG, Rosner JL, 2001, The AraC transcriptional activators., Curr Opin Microbiol, 2001 Apr

 [10] Eguchi Y., Itou J., Yamane M., Demizu R., Yamato F., Okada A., Mori H., Kato A., Utsumi R., 2007, B1500, a small membrane protein, connects the two-component systems EvgS/EvgA and PhoQ/PhoP in Escherichia coli., Proc Natl Acad Sci U S A 104(47):18712-7

 [11] Yamanaka Y, Ishihama A, Yamamoto K, 2012, Induction of YdeO, a regulator for acid resistance genes, by ultraviolet irradiation in Escherichia coli., Biosci Biotechnol Biochem, 2012



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