RegulonDB

TRANSCRIPTION FACTOR:

Name:

Lrp	Weight Matrix Tractordb tool

Connectivity class

Global Regulator

Sensing Class

Sensing external and internal signals

Synonym(s):

AlsB, DNA-binding transcriptional dual regulator Lrp, Ihb, LivR, Lrs, Lss, LstR, Mbf, OppI, RblA

Gene name(s):

lrp

Functional conformation(s):

Lrp , Lrp-L-leucine

Coregulator(s):

AcrR, Ada, AdiY, AidB, ArcA, ArgP, ArgR, CRP, CadC, CpxR, Cra, DksA, DksA-ppGpp, EnvY, FNR, Fis, FliZ, Fur, GadE, GadE-RcsB, GadW, GadX, GcvA, GlaR, H-NS, HU, HdfR, IHF, LrhA, Lrp, MarA, Mlc, ModE, Nac, NarL, NhaR, NsrR, OmpR, PhoP, PurR, QseB, RcsB, Rob, SoxS, StpA, TorR, YeiL, YjjQ, ppGpp

Summary:

TF Summary ...[more]

REGULATION EXERTED BY Lrp

Info M3D | Colombos

KNOWN BINDING SITES (The central relative position is relative to the promoter +1)
Lrp activator
Transcription Factor		Regulated		Binding Sites				Evidence	References
Functional conformation	Function	Promoter	Gene(s)	LeftPos	RigthPos	Central Rel-Pos	Sequence
Lrp	activator	kblp	tdh , kbl	3792647	3792661	-77.0	agagacatcaAGTTACACGTTATTTatcctgaatt
Lrp	activator	kblp	tdh , kbl	3792636	3792650	-66.5	gttacacgttATTTATCCTGAATTTtgcagaagtg	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1]
Lrp-L-leucine	activator	yojIp	yojI	2308679	2308690	-43.5	aaaagaataaAAATAAGAATTAttattgctgt	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[2]
Lrp-L-leucine	activator	yojIp	yojI	2308690	2308701	-54.5	caggcaggtaAAAAAGAATAAAaataagaatt	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[2]
Lrp-L-leucine	activator	yojIp	yojI	2308830	2308841	-194.5	cgctcaaacgTTTGTTGTTGGAacatggcgat	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[2]
Lrp-L-leucine	activator	yojIp	yojI	2308876	2308887	-240.5	ggcttacccgCGATTTTTCAATttggcggcct	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[2]
Lrp-L-leucine	activator	yojIp	yojI	2308940	2308951	-304.5	actgtcgctgCATCAGGATAAAgacgaaccgg	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[2]
Lrp-L-leucine	activator	yojIp	yojI	2309048	2309059	-412.5	catgccacagAGTTTTCATAATttatgtcaac	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[2]
Lrp-L-leucine	activator	alaEp	alaE	2799068	2799083	-9.0	tagtcatagcCAGCGATATACGCTATgcgaaaatgc	[COMP-HINF-SIMILAR-TO-CONSENSUS] [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [EXP-IEP-RNA-SEQ]	[3] [4] [5] [6]
Lrp-L-leucine	activator	alaEp	alaE	2799019	2799034	-58.0	atattttatcTACAAAAACTGACTAAataaaaattt	[COMP-HINF-SIMILAR-TO-CONSENSUS] [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [EXP-IEP-RNA-SEQ]	[3] [4] [5] [6]
Lrp	activator	ridAp	ridA	4470995	4471009	-56.0	agagttttccCATAATGTGGTGCTGgccaattaat	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[7]
Lrp repressor
Transcription Factor		Regulated		Binding Sites				Evidence	References
Functional conformation	Function	Promoter	Gene(s)	LeftPos	RigthPos	Central Rel-Pos	Sequence
Lrp	repressor	ompCp2	ompC	2313199	2313213	-342.0	gtttttctgtGGTAGCACAGAATAAtgaaaagtgt	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[8] [9]
Lrp	repressor	ompCp2	ompC	2313163	2313177	-306.5	taaagaagggTAAAAAAAACCGAATgcgaggcatc	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[8] [9]
Lrp	repressor	ompCp2	ompC	2313134	2313148	-277.5	ggcatccggtTGAAATAGGGGTAAAcagacattca	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[8] [9]
Lrp	repressor	ompCp2	ompC	2313103	2313117	-246.5	ttcagaaatgAATGACGGTAATAAAtaaagttaat	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[8] [9]
Lrp	repressor	ompCp2	ompC	2313031	2313045	-174.0	tttgttttgaCATTCAGTGCTGTCAaatacttaag	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[8] [9]
Lrp	repressor	ompCp2	ompC	2312852	2312866	5.5	tatcatattcGTGTTGGATTATTCTgcatttttgg	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[8] [9] [10]
Lrp	repressor	ompCp2	ompC	2312822	2312836	36.0	tttggggagaATGGACTTGCCGACTgattaatgag	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[8] [9]
Lrp	repressor	ompCp2	ompC	2312738	2312752	120.0	gagggttaatAACATGAAAGTTAAAgtactgtccc	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[8] [9]
Lrp	repressor	lysUp1	lysU	4354856	4354870	-58.0	catttaaaccATTTTGATGGTTATTtattagtgat	[EXP-IEP-RNA-SEQ]	[5]
Lrp	repressor	ompCp2	ompC	2312759	2312773	98.5	agcaaataaaGGCATATAACAGAGGgttaataaca	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[8] [9]
Lrp-L-leucine	repressor	leuEp	leuE	1880868	1880879	-73.5	ctgattaatgATTCAATTATCGggttgatatc	[EXP-IEP-RNA-SEQ]	[5] [11]
Lrp-L-leucine	repressor	leuEp	leuE	1880835	1880846	-40.5	ggttaaaaccTGATTTTCTCCTttctaagccg	[EXP-IEP-RNA-SEQ]	[5] [11]
Lrp-L-leucine	repressor	leuEp	leuE	1880801	1880812	-6.5	acagattggtTAGCATATTCACctttaatcgc	[EXP-IEP-RNA-SEQ]	[5] [11]
Lrp-L-leucine	repressor	leuEp	leuE	1880764	1880775	31.5	atcgaaagatAATTAAAGAGGTtaatgtgttc	[EXP-IEP-RNA-SEQ]	[5] [11]
Lrp-L-leucine	repressor	alaAp9	alaA

Evidence:	[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence. [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins [EXP-IEP-RNA-SEQ] high throughput RNA-seq evidence
Reference(s):	[1] Rex JH., et al., 1991 [2] Socias SB., et al., 2009 [3] Free A., et al., 1997 [4] Ihara K., et al., 2017 [5] Kroner GM., et al., 2019 [6] Sonden B., et al., 1996 [7] Shukla S., et al., 2019 [8] Ernsting BR., et al., 1992 [9] Ferrario M., et al., 1995 [10] Fraenkel YM., et al., 1995 [11] Robison K., et al., 1998

Reference(s)
[1] Rex JH., Aronson BD., Somerville RL., 1991, The tdh and serA operons of Escherichia coli: mutational analysis of the regulatory elements of leucine-responsive genes., J Bacteriol 173(19):5944-53
[2] Socias SB., Vincent PA., Salomon RA., 2009, The leucine-responsive regulatory protein, Lrp, modulates microcin J25 intrinsic resistance in Escherichia coli by regulating expression of the YojI microcin exporter., J Bacteriol 191(4):1343-8
[3] Free A., Dorman CJ., 1997, The Escherichia coli stpA gene is transiently expressed during growth in rich medium and is induced in minimal medium and by stress conditions., J Bacteriol 179(3):909-18
[4] Ihara K., Sato K., Hori H., Makino Y., Shigenobu S., Ando T., Isogai E., Yoneyama H., 2017, Expression of the alaE gene is positively regulated by the global regulator Lrp in response to intracellular accumulation of l-alanine in Escherichia coli., J Biosci Bioeng 123(4):444-450
[5] Kroner GM., Wolfe MB., Freddolino PL., 2019, Escherichia coli Lrp Regulates One-Third of the Genome via Direct, Cooperative, and Indirect Routes., J Bacteriol 201(3)
[6] Sonden B., Uhlin BE., 1996, Coordinated and differential expression of histone-like proteins in Escherichia coli: regulation and function of the H-NS analog StpA., EMBO J 15(18):4970-80
[7] Shukla S., Mahadevan S., 2019, The ridA gene of E. coli is indirectly regulated by BglG through the transcriptional regulator Lrp in stationary phase., Microbiology 165(6):683-696
[8] Ernsting BR., Atkinson MR., Ninfa AJ., Matthews RG., 1992, Characterization of the regulon controlled by the leucine-responsive regulatory protein in Escherichia coli., J Bacteriol 174(4):1109-18
[9] Ferrario M., Ernsting BR., Borst DW., Wiese DE., Blumenthal RM., Matthews RG., 1995, The leucine-responsive regulatory protein of Escherichia coli negatively regulates transcription of ompC and micF and positively regulates translation of ompF., J Bacteriol 177(1):103-13
[10] 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
[11] Robison K., McGuire AM., Church GM., 1998, A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome., J Mol Biol 284(2):241-54
[12] Kim SH., Schneider BL., Reitzer L., 2010, Genetics and regulation of the major enzymes of alanine synthesis in Escherichia coli., J Bacteriol 192(20):5304-11
[13] Haney SA., Platko JV., Oxender DL., Calvo JM., 1992, Lrp, a leucine-responsive protein, regulates branched-chain amino acid transport genes in Escherichia coli., J Bacteriol 174(1):108-15