RegulonDB RegulonDB 10.6.3: Operon Form
   

lrp operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: lrp
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: lrp
Synonym(s): OP00251
Gene(s): lrp   Genome Browser M3D Gene expression COLOMBOS
Note(s): It is not yet clear whether there are other genes dowstream of lrp that are transcribed from the lrpp promoter. ftsK is a gene regulated by LexA, and the ts gene immediately dowstream of lrp is transcribed in the same direction. It is likely that ftsK has a separate promoter, because the expression of ftsK is markedly increased after treatment of E. coli with mitomycin.
Reference(s): [1] Wang Q., et al., 1994
Promoter
Name: lrpp
+1: 932328
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 267
Sequence: ttgtactaaaaatcgatgttttgctttgacaatcccctggtgttttgcgaaaacattcgaGgaagaaaaaaaacagtattc
                          -35                    -10        +1                   
Note(s): The lrpp promoter was identified both by primer extension and by a deletion analysis. At -35 there is a perfect match to the consensus, but only three of six bases match the -10 consensus. The similarity score of the lrpp promoter to the E. coli promoter consensus is 52%, calculated as described by Mulligan et al.
Evidence: [TIM] ; Method: Primer Extension
[TIM]
Reference(s): [1] Wang Q., et al., 1994
TF binding sites (TFBSs)
[GadE,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd GadE activator lrpp nd nd nd nd nd [GEA] [6]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS repressor lrpp nd nd nd nd nd [BPP], [GEA] [7]
[Lrp,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Lrp1 repressor lrpp 932265 932279 -56.0 aatatctggcATGTTGTACTAAAAAtcgatgtttt nd [BCE], [SM] [1]
proximal Lrp-leucine repressor lrpp 932328 932343 8.0 aaacattcgaGGAAGAAAAAAAACAGtattcttata nd [AIBSCS], [GEA] [2]
remote Lrp-leucine repressor lrpp 932351 932368 32.0 cagtattcttATATGCGCATAACCATGCatgtaaatac nd [AIBSCS], [GEA] [2]
remote Lrp repressor lrpp 932369 932383 49.0 ataaccatgcATGTAAATACCATGTttaccgtgct nd [HIBSCS], [SM] [1], [3], [4]
[NsrR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote NsrR repressor lrpp 932374 932385 52.0 catgcatgtaAATACCATGTTTaccgtgctag nd [GEA], [HIBSCS] [5]
Note(s): 1Lrp binds to one or more sites within the region from -80 to -32 relative to the start point of lrp transcription. In vitro Lrp binds a region just upstream from the lrp promoter. With the deletion of this region, autogenous regulation by Lrp in vivo is lost. The region protected by Lrp from the DNase I cleavage is at 105 to -20 relative to the start point of lrp transcription. There are two sequences that match with the consensus of Lrp located at -67 to -53 and at +14 to +28. A cluster of single-base substitutions within the region -60 to -53 prevents binding of lrp in vitro and significantly reduces repression of lrp caused by lrp
in vivo.
1Lrp binds to one or more sites within the region from -80 to -32 relative to the start point of lrp transcription. In vitro Lrp binds a region just upstream from the lrp promoter. With the deletion of this region, autogenous regulation by Lrp in vivo is lost. The region protected by Lrp from the DNase I cleavage is at 105 to -20 relative to the start point of lrp transcription. There are two sequences that match with the consensus of Lrp located at -67 to -53 and at +14 to +28. A cluster of single-base substitutions within the region -60 to -53 prevents binding of lrp in vitro and significantly reduces repression of lrp caused by lrp
in vivo.
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation lrpp ppGpp regulates positively the expression of lrp, but it may not be entirely responsible for growth-phase regulation |CITS:[8955316]|. [GEA] [8]
Evidence: [GEA] Gene expression analysis
Reference(s): [8] Landgraf JR., et al., 1996


Evidence    

 [TIM] Transcription initiation mapping

 [GEA] Gene expression analysis

 [BPP] Binding of purified proteins

 [BCE] Binding of cellular extracts

 [SM] Site mutation

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [HIBSCS] Human inference based on similarity to consensus sequences


Reference(s)    

 [1] Wang Q., Wu J., Friedberg D., Plakto J., Calvo JM., 1994, Regulation of the Escherichia coli lrp gene., J Bacteriol 176(7):1831-9

 [2] Lintner RE., Mishra PK., Srivastava P., Martinez-Vaz BM., Khodursky AB., Blumenthal RM., 2008, Limited functional conservation of a global regulator among related bacterial genera: Lrp in Escherichia, Proteus and Vibrio., BMC Microbiol 8:60

 [3] Fraenkel YM., Mandel Y., Friedberg D., Margalit H., 1995, Identification of common motifs in unaligned DNA sequences: application to Escherichia coli Lrp regulon., Comput Appl Biosci 11(4):379-87

 [4] Lin R., D'Ari R., Newman EB., 1992, Lambda placMu insertions in genes of the leucine regulon: extension of the regulon to genes not regulated by leucine., J Bacteriol 174(6):1948-55

 [5] Partridge JD., Bodenmiller DM., Humphrys MS., Spiro S., 2009, NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility., Mol Microbiol 73(4):680-94

 [6] Hommais F., Krin E., Coppee JY., Lacroix C., Yeramian E., Danchin A., Bertin P., 2004, GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli., Microbiology 150(Pt 1):61-72

 [7] Oshima T., Ito K., Kabayama H., Nakamura Y., 1995, Regulation of lrp gene expression by H-NS and Lrp proteins in Escherichia coli: dominant negative mutations in lrp., Mol Gen Genet 247(5):521-8

 [8] Landgraf JR., Wu J., Calvo JM., 1996, Effects of nutrition and growth rate on Lrp levels in Escherichia coli., J Bacteriol 178(23):6930-6

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