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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 [1]. 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 [2]. 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 [4]. 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 [5].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
LrhA Functional   nd nd nd
Evolutionary Family: LysR
TFBs length: 15
TFBs symmetry: inverted-repeat
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, lrhA
Simple and complex regulons AcrR,CRP,FliZ,Fur,H-NS,HdfR,IHF,LrhA,MatA,OmpR,QseB,RcsAB,YjjQ
H-NS,LeuO,LrhA,SlyA,ppGpp
H-NS,LrhA,Lrp
LrhA
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[LrhA,+](5)
[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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
  LrhA activator fimEp Sigma70 nd nd fimE
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  LrhA repressor flhDp Sigma70 -112.0 -310.0 flhD, flhC
tcaataagttGGAGTCATTACCCATttatgttaag
 1978500 1978514 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2]
  LrhA activator leuOp Sigma70 -143.0 -323.0 leuO
attatatgttTTGCGATTTTTTTTGATATTGATTTGGTGAATATTATTGATCAATTAATGTTAAGAATTAATGCATTAAATATATAAATTAATTATTAAATAagcacattta
 84000 84091 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [3], [3]
  LrhA activator leuOp1 nd -109.0 -323.0 leuO
attatatgttTTGCGATTTTTTTTGATATTGATTTGGTGAATATTATTGATCAATTAATGTTAAGAATTAATGCATTAAATATATAAATTAATTATTAAATAagcacattta
 84000 84091 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [3], [3]
  LrhA activator leuOp3 nd -253.0 -323.0 leuO
attatatgttTTGCGATTTTTTTTGATATTGATTTGGTGAATATTATTGATCAATTAATGTTAAGAATTAATGCATTAAATATATAAATTAATTATTAAATAagcacattta
 84000 84091 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [3], [3]
  LrhA activator lrhAp nd nd nd lrhA
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2]


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


Evidence    

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins


Reference(s)    

 [1] 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

 [2] 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

 [3] Breddermann H., Schnetz K., 2017, Activation of leuO by LrhA in Escherichia coli., Mol Microbiol 104(4):664-676

 [4] Peterson CN, Carabetta VJ, Chowdhury T, Silhavy TJ, 2006, LrhA regulates rpoS translation in response to the Rcs phosphorelay system in Escherichia coli., J Bacteriol, 188(9):3175 10.1128/JB.188.9.3175-3181.2006

 [5] 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

 [6] Harris SJ, Shih YL, Bentley SD, Salmond GP, 1998, The hexA gene of Erwinia carotovora encodes a LysR homologue and regulates motility and the expression of multiple virulence determinants., Mol Microbiol, 28(4):705 10.1046/j.1365-2958.1998.00825.x

 [7] Surgey N, Robert-Baudouy J, Condemine G, 1996, The Erwinia chrysanthemi pecT gene regulates pectinase gene expression., J Bacteriol, 178(6):1593 10.1128/jb.178.6.1593-1599.1996

 [8] Yamanaka Y, Aizawa SI, Yamamoto K, 2022, The hdeD Gene Represses the Expression of Flagellum Biosynthesis via LrhA in Escherichia coli K-12., J Bacteriol, 204(1):e0042021 10.1128/JB.00420-21


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