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LrhA DNA-binding transcriptional dual regulator

Synonyms: LrhA
Summary:
LrhA, "LysR homologue A," regulates the transcription of genes involved in the synthesis of type 1 fimbriae [4]. Indirectly, this protein also regulates the transcription of several genes involved in motility, chemotaxis, and flagellum synthesis by directly controlling the expression of the master regulator FlhDC [3]. On the other hand, LrhA also regulates negatively and partially the translation of rpoS through two mechanisms, one of which is RprA dependent and the other one is RprA independent. RprA is a small RNA that regulates positively the translation of rpoS. Both mechanisms of regulation require the presence of the sRNA chaperone Hfq; therefore, it was suggested that another small RNA, in addition to RprA, that regulates rpoS translation is regulated by LrhA []. LrhA is a protein that belongs to the LysR family and, like the members of this family, LrhA contains three different domains: an N-terminal helix-turn-helix domain for DNA binding, a coinducer recognition domain in the center of the protein, and a C-terminal domain that contains a cluster of four cysteine and two histidine residues [1].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
LrhA Functional   [APPH], [GEA], [HIFS] [1], [2], [3]
Evolutionary Family: LysR
Connectivity class: Local Regulator
Gene name: lrhA
  Genome position: 2405703-2406641
  Length: 939 bp / 312 aa
Operon name: lrhA
TU(s) encoding the TF:
Transcription unit        Promoter
lrhA
lrhAp


Regulon       
Regulated gene(s) fimE, flhC, flhD, leuO, lrhA
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
operon (5)
Transcription related (4)
activator (3)
repressor (3)
flagellum (2)
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Regulated operon(s) fimE, flhDC, leuO, lrhA
First gene in the operon(s) fimE, flhD, leuO, leuO, leuO, lrhA
Simple and complex regulons AcrR,CRP,FliZ,Fur,H-NS,HdfR,IHF,LrhA,MatA,OmpR,QseB,RcsAB,YjjQ
H-NS,LeuO,LrhA,SlyA
H-NS,LrhA,Lrp
LrhA
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[LrhA,+](3)
[LrhA,-](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
  LrhA activator fimEp Sigma70 nd -4542037.0 fimE nd nd [BPP], [GEA] [4]
  LrhA repressor flhDp Sigma70 -112.0 -310.0 flhD, flhC
cttaacataaATGGGTAATGACTCCaacttattga
1978500 1978514 [BPP], [GEA] [3]
  LrhA activator leuOp Sigma70 -143.0 -322.5 leuO
attatatgttTTGCGATTTTTTTTGATATTGATTTGGTGAATATTATTGATCAATTAATGTTAAGAATTAATGCATTAAATATATAAATTAATTATTAAATaagcacattt
84000 84091 [BPP], [GEA] [5]
  LrhA activator leuOp1 nd -109.0 -322.5 leuO
attatatgttTTGCGATTTTTTTTGATATTGATTTGGTGAATATTATTGATCAATTAATGTTAAGAATTAATGCATTAAATATATAAATTAATTATTAAATaagcacattt
84000 84091 [BPP], [GEA] [5]
  LrhA activator leuOp3 nd -253.0 -322.5 leuO
attatatgttTTGCGATTTTTTTTGATATTGATTTGGTGAATATTATTGATCAATTAATGTTAAGAATTAATGCATTAAATATATAAATTAATTATTAAATaagcacattt
84000 84091 [BPP], [GEA] [5]
  LrhA activator lrhAp nd nd 2406641.0 lrhA nd nd [BPP], [GEA] [3]


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

 [GEA] Gene expression analysis

 [HIFS] Human inference of function from sequence

 [BPP] Binding of purified proteins



Reference(s)    

 [1] Bongaerts J., Zoske S., Weidner U., Unden G., 1995, Transcriptional regulation of the proton translocating NADH dehydrogenase genes (nuoA-N) of Escherichia coli by electron acceptors, electron donors and gene regulators., Mol Microbiol 16(3):521-34

 [2] Gibson KE., Silhavy TJ., 1999, The LysR homolog LrhA promotes RpoS degradation by modulating activity of the response regulator sprE., J Bacteriol 181(2):563-71

 [3] Lehnen D., Blumer C., Polen T., Wackwitz B., Wendisch VF., Unden G., 2002, LrhA as a new transcriptional key regulator of flagella, motility and chemotaxis genes in Escherichia coli., Mol Microbiol 45(2):521-32

 [4] Blumer C., Kleefeld A., Lehnen D., Heintz M., Dobrindt U., Nagy G., Michaelis K., Emody L., Polen T., Rachel R., Wendisch VF., Unden G., 2005, Regulation of type 1 fimbriae synthesis and biofilm formation by the transcriptional regulator LrhA of Escherichia coli., Microbiology 151(Pt 10):3287-98

 [5] Breddermann H., Schnetz K., 2017, Activation of leuO by LrhA in Escherichia coli., Mol Microbiol



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