Escherichia coli K-12 substr. MG1655 Polypeptide: LrhA DNA-binding transcriptional dual regulator

Gene: lrhA Accession Numbers: EG12123 (EcoCyc), b2289, ECK2283

Synonyms: genR

Regulation Summary Diagram: ?

Regulation summary diagram for lrhA

LrhA, "LysR homologue A," regulates the transcription of genes involved in the synthesis of type 1 fimbriae [Blumer05]. 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 [Lehnen02].

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 [Peterson06].

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 [Bongaerts95]. The activity of most members of this family is controlled by small molecules; however, the effector of LrhA was not known until now [Lehnen02]. LrhA has high degree of homology to HexA from Erwinia carotovora (64% identity ) and PecT from Erwinia chrysanthemi (61% identity) [Harris98, Surgey96].

LrhA appears to recognize and bind to a partial palindromic DNA sequence of 13 bp that shows low similarity to the general consensus for LysR family members [Lehnen02].

The lrhA gene is transcribed alone, and it is under positive autoregulation by LrhA. Unlike the majority of LysR-type regulators, LrhA does not regulate the expression of adjacent genes to lrhA [Lehnen02]. The expression of lrhA is repressed by the RcsCDB phosphorelay system and by the DNA motor protein FtsK [Peterson06].

Citations: [Gibson99]

Locations: cytosol

Map Position: [2,403,725 <- 2,404,663] (51.81 centisomes, 187°)
Length: 939 bp / 312 aa

Molecular Weight of Polypeptide: 34.594 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0007555 , CGSC:32685 , EchoBASE:EB2044 , EcoGene:EG12123 , EcoliWiki:b2289 , ModBase:P36771 , OU-Microarray:b2289 , PortEco:lrhA , Protein Model Portal:P36771 , RefSeq:NP_416792 , RegulonDB:EG12123 , SMR:P36771 , String:511145.b2289 , UniProt:P36771

Relationship Links: InterPro:IN-FAMILY:IPR000847 , InterPro:IN-FAMILY:IPR005119 , InterPro:IN-FAMILY:IPR011991 , Pfam:IN-FAMILY:PF00126 , Pfam:IN-FAMILY:PF03466 , Prints:IN-FAMILY:PR00039 , Prosite:IN-FAMILY:PS50931

In Paralogous Gene Group: 6 (42 members)

Genetic Regulation Schematic: ?

Genetic regulation schematic for lrhA

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Lehnen02, Bongaerts95, Gibson99]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a, GOA01a, Gaudet10]
Molecular Function: GO:0043565 - sequence-specific DNA binding Inferred from experiment [Lehnen02]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01a, Gaudet10]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
regulation genetic unit regulated operon
regulation type of regulation transcriptional level repressor

DNA binding site length: 15 base-pairs

Symmetry: Inverted Repeat

Regulated Transcription Units (3 total): ?


Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Essentiality data for lrhA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Last-Curated ? 15-Aug-2008 by Gama-Castro S , UNAM

Sequence Features

Protein sequence of LrhA DNA-binding transcriptional dual regulator with features indicated

Feature Class Location Citations Comment
Conserved-Region 11 -> 68
UniProt: HTH lysR-type;
DNA-Binding-Region 28 -> 47
UniProt: H-T-H motif; Non-Experimental Qualifier: potential;
Sequence-Conflict 291 -> 312
[Bongaerts95, UniProt10a]
UniProt: (in Ref. 1; CAA52637);

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b2289 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12123; confirmed by SwissProt match.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Blumer05: 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. PMID: 16207912

Bongaerts95: 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. PMID: 7565112

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

Gibson99: 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. PMID: 9882671

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Harris98: 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);705-17. PMID: 9643539

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Lehnen02: 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 2002;45(2);521-32. PMID: 12123461

Peterson06: 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);3175-81. PMID: 16621809

Surgey96: Surgey N, Robert-Baudouy J, Condemine G (1996). "The Erwinia chrysanthemi pecT gene regulates pectinase gene expression." J Bacteriol 178(6);1593-9. PMID: 8626286

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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