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LexA DNA-binding transcriptional repressor

Synonyms: LexA
LexA represses the transcription of several genes involved in the cellular response to DNA damage or inhibition of DNA replication [1, 37] as well as its own synthesis [38] This regulation is known as the SOS response [37]
When DNA is damaged, the RecA coprotease binds to the single-stranded DNA in the damaged region to form a filament [39, 40] This filament interacts with the LexA dimer to activate its self-cleavage activity by an allosteric mechanism, causing the dissociation of LexA from its DNA targets and the induction of the SOS regulon for the repair of broken DNA [41, 42] The conformational flexibility of unbound LexA is the key element in establishing a coordinated SOS response [43]
LexA is widely distributed in bacteria, and it appears that it emerged from the gram-positive group [44] It shows two domains, the N-terminal domain involved in DNA binding via a helix-turn-helix [45]and the C-terminal domain involved in dimerization and in cleavage activity [46, 47]
To repress transcription, LexA blocks the access of RNA polymerase to target promoters [16]
LexA dimer [48]recognizes and binds to an imperfect inverted repeat DNA sequence called the LexA box or SOS box [49, 50] Although, the majority of the LexA-regulated genes have only one SOS box, some have two or three boxes which sometimes overlap [2]
The crystal structure of the LexA-DNA complex has been determined [51] The DNA-binding domains of the LexA dimer interact with the DNA in the classical fashion of a winged helix-turn-helix (HTH) motif, and they bind to the same minor groove of the DNA [51]
lexA is the first gene in the lexA-dinF operon [52] dinF encodes a member of the MATE family of multidrug efflux transporters [53]
The SOS system is induced by methylglyoxal (MG), based on ChIP-chip analysis with DNA-RNAP occupancy, and this involves LexA-regulated genes such as recAX, lexA-dinF, and dinB [54]
Reviews: [50, 50, 55]24097899]|. Read more >

Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
LexA     nd nd
Evolutionary Family: LexA
Sensing class: Using internal synthesized signals
Connectivity class: Local Regulator
Gene name: lexA
  Genome position: 4257115-4257723
  Length: 609 bp / 202 aa
Operon name: lexA-dinF
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) cho, ddlB, dinB, dinD, dinF, dinG, dinI, dinJ, dinQ, dnaG, ftsA, ftsI, ftsK, ftsL, ftsQ, ftsW, ftsZ, hokE, insK, lexA, lpxC, molR_1, mraY, murC, murD, murE, murF, murG, phr, polB, ptrA, recA, recB, recD, recN, recX, rpoD, rpsU, ruvA, ruvB, sbmC, ssb, sulA, symE, tisB, umuC, umuD, uvrA, uvrB, uvrC, uvrD, uvrY, yafN, yafO, yafP, yafQ, ybfE, ydjM, yebG
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
SOS response (26)
DNA repair (23)
cell division (9)
murein (peptidoglycan) (8)
murein (8)
Read more >
Regulated operon(s) cho, dinB-yafNOP, dinD, dinG, dinI, dinJ-yafQ, dinQ, ftsK, hokE, insK, lexA-dinF, molR_1, mraZ-rsmH-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ-lpxC, polB, ptrA-recBD, recAX, recN, rpsU-dnaG-rpoD, ruvAB, sbmC, ssb, sulA, symE, tisB, umuDC, uvrA, uvrB, uvrD, uvrYC, ybfE, ybgA-phr, ydjM, yebG
First gene in the operon(s) cho, dinB, dinD, dinG, dinI, dinJ, dinQ, ftsK, ftsL, hokE, insK, lexA, molR_1, phr, polB, ptrA, ptrA, recA, recA, recN, rpsU, ruvA, ruvA, sbmC, ssb, sulA, symE, tisB, umuD, uvrA, uvrB, uvrC, uvrD, uvrY, yafN, ybfE, ydjM, yebG
Simple and complex regulons ArcA,LexA
Read more >
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

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
  LexA repressor chop Sigma70 -0.5 -23.5 cho
1823482 1823501 [AIBSCS], [HIBSCS] [1], [2], [3], [4]
  LexA repressor dinBp Sigma70 -6.5 -24.5 dinB, yafN, yafO, yafP
250864 250883 [AIBSCS], [HIBSCS], [ICWHO] [1], [2], [3], [4], [5]
  LexA repressor dinDp nd 8.5 -53.5 dinD
3817697 3817716 [AIBSCS], [GEA], [HIBSCS] [1], [3], [4], [6], [7]
  LexA repressor dinGp Sigma70 -27.5 -24.5 dinG
833036 833055 [AIBSCS], [BPP], [GEA] [8], [9]
  LexA repressor dinIp Sigma70 -7.5 -29.5 dinI
1121507 1121526 [AIBSCS], [BPP], [GEA], [HIBSCS], [IHBCE], [SM] [1], [3], [4], [6], [10]
  LexA repressor dinJp Sigma70 89.5 -24.5 dinJ, yafQ
246517 246536 [AIBSCS], [GEA] [6], [11]
  LexA repressor dinQp Sigma70 -29.5 -223.5 dinQ
3648002 3648021 [HIBSCS] [12]
  LexA repressor dinQp Sigma70 -7.5 -201.5 dinQ
3647980 3647999 [AIBSCS], [GEA], [HIBSCS] [1], [12]
  LexA repressor ftsKp1 Sigma70 -0.5 -86.5 ftsK
933128 933147 [AIBSCS], [BPP], [GEA] [6], [8], [13]
  LexA repressor ftsLp2 nd 3.0 -18.5 ftsL, ftsI, murE, murF, mraY, murD, ftsW, murG, murC, ddlB, ftsQ, ftsA, ftsZ, lpxC
91004 91023 [HIBSCS] [14], [15]
  LexA repressor hokEp Sigma24 -81.5 -186.5 hokE
607640 607659 [AIBSCS] [2]
  LexA repressor insKp Sigma24 nd nd insK nd nd [AIBSCS], [GEA] [1]
  LexA repressor lexAp Sigma70 -50.5 -78.5 lexA, dinF
4257027 4257046 [HIBSCS] [6], [16]
  LexA repressor lexAp Sigma70 -9.0 -37.5 lexA, dinF
4257068 4257087 [BPP], [HIBSCS] [16], [17]
  LexA repressor lexAp Sigma70 13.0 -16.5 lexA, dinF
4257089 4257108 [BPP], [HIBSCS] [16], [17]
  LexA repressor molR_1p Sigma70 11.5 -18.5 molR_1
2196446 2196465 [AIBSCS] [1]
  LexA repressor phrBp nd -66.5 -152.5 phr
739345 739364 [HIBSCS] [6], [18]
  LexA repressor phrBp nd 25.5 -61.5 phr
739436 739455 [GEA], [HIBSCS] [19]
  LexA repressor polBp Sigma70 -40.5 -63.5 polB
65834 65853 [AIBSCS], [BPP], [GEA] [6], [8]
  LexA repressor ptrAp Sigma70 20.5 -107.5 ptrA, recB, recD
2958982 2959001 [BPP], [SM] [4]
  LexA repressor recAp Sigma70 -20.0 -69.5 recA, recX
2823829 2823848 [BPP] [16], [17]
  LexA repressor recNp Sigma70 -22.5 -58.5 recN
2751727 2751746 [AIBSCS], [BPP] [20]
  LexA repressor recNp Sigma70 -0.5 -36.5 recN
2751749 2751768 [AIBSCS], [BPP] [20]
  LexA repressor rpsUp3 Sigma70 4.5 -42.5 rpsU, dnaG, rpoD
3210729 3210748 [BCE], [SM] [21], [22]
  LexA repressor ruvAp1 nd -63.5 -111.5 ruvA, ruvB
1946078 1946097 [HIBSCS] [6], [23]
  LexA repressor ruvAp1 nd -12.5 -60.5 ruvA, ruvB
1946027 1946046 [BPP], [HIBSCS] [1], [6], [23], [24]
  LexA repressor ruvAp2 nd -72.5 -112.5 ruvA, ruvB
1946079 1946098 [HIBSCS] [6], [23]
  LexA repressor ruvAp2 nd -19.5 -59.5 ruvA, ruvB
1946026 1946045 [BPP], [HIBSCS] [1], [6], [23], [24]
  LexA repressor sbmCp2 nd 17.5 -24.5 sbmC
2081277 2081296 [GEA], [IHBCE] [25]
  LexA repressor ssbp3 Sigma70 -46.5 -160.5 ssb
4273955 4273974 [BCE], [HIBSCS] [26], [27]
  LexA repressor sulAp Sigma70 -2.0 -29.5 sulA
1020939 1020958 [BCE] [28]
  LexA repressor symEp Sigma70 -8.5 -85.5 symE
4579916 4579935 [AIBSCS], [BPP] [1], [6]
  LexA repressor tisBp nd -28.0 -244.5 tisB
3853299 3853318 [GEA], [ICA] [1], [29]
  LexA repressor umuDp Sigma70 -20.5 -49.5 umuD, umuC
1230708 1230727 [HIBSCS] [6], [30], [31]
  LexA repressor umuDp Sigma70 -0.5 -29.5 umuD, umuC
1230728 1230747 [BPP] [6], [30]
  LexA repressor uvrAp Sigma70 -28.5 -93.5 uvrA
4273955 4273974 [BCE], [HIBSCS] [26], [27]
  LexA repressor uvrBp2 Sigma70 -20.0 -84.5 uvrB
813432 813451 [BPP], [HIBSCS] [32]
  LexA repressor uvrCp3 Sigma70 nd nd uvrC nd nd [GEA] [33]
  LexA repressor uvrDp1 Sigma70 11.0 -66.5 uvrD
3997907 3997926 [HIBSCS] [34]
  LexA repressor uvrYp2 Sigma70 -129.5 -176.5 uvrY, uvrC
1995526 1995545 [AIBSCS], [GEA] [33]
  LexA repressor yafNp Sigma70 -1.5 -37.5 yafN, yafO, yafP
251958 251977 [HIBSCS] [35]
  LexA repressor ybfEp Sigma32 -85.5 -126.5 ybfE
712015 712034 [AIBSCS] [2]
  LexA repressor ydjMp Sigma70 -1.5 -42.5 ydjM
1810159 1810178 [AIBSCS], [BPP], [GEA] [1]
  LexA repressor ydjMp Sigma70 17.5 -24.5 ydjM
1810177 1810196 [AIBSCS], [BPP], [GEA] [1]
  LexA repressor yebGp Sigma70 -9.5 -27.5 yebG
1930765 1930784 [AIBSCS], [GEA], [HIBSCS], [IHBCE] [1], [3], [4], [36]

Alignment and PSSM for LexA TFBSs    

Aligned TFBS of LexA   

Position weight matrix (PWM).   
A	16	26	1	2	0	6	30	1	31	16	33	18	25	16	23	1	37	4	2	21
C	6	4	39	1	1	3	5	3	1	4	0	7	1	9	16	38	1	0	12	4
G	1	7	0	0	39	8	0	5	6	6	2	1	5	3	1	1	0	35	7	7
T	17	3	0	37	0	23	5	31	2	14	5	14	9	12	0	0	2	1	19	8

PWM logo   


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


 [AIBSCS] Automated inference based on similarity to consensus sequences

 [HIBSCS] Human inference based on similarity to consensus sequences

 [ICWHO] Inferred computationally without human oversight

 [GEA] Gene expression analysis

 [BPP] Binding of purified proteins

 [IHBCE] Inferred by a human based on computational evidence

 [SM] Site mutation

 [BCE] Binding of cellular extracts

 [ICA] Inferred by computational analysis


 [1] Fernandez De Henestrosa AR., Ogi T., Aoyagi S., Chafin D., Hayes JJ., Ohmori H., Woodgate R., 2000, Identification of additional genes belonging to the LexA regulon in Escherichia coli., Mol Microbiol. 35(6):1560-72

 [2] Gillor O., Vriezen JA., Riley MA., 2008, The role of SOS boxes in enteric bacteriocin regulation., Microbiology. 154(Pt 6):1783-92

 [3] Kaleta C., Gohler A., Schuster S., Jahreis K., Guthke R., Nikolajewa S., 2010, Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis., BMC Syst Biol. 4:116

 [4] Wade JT., Reppas NB., Church GM., Struhl K., 2005, Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites., Genes Dev. 19(21):2619-30

 [5] Ohmori H., Hatada E., Qiao Y., Tsuji M., Fukuda R., 1995, dinP, a new gene in Escherichia coli, whose product shows similarities to UmuC and its homologues., Mutat Res. 347(1):1-7

 [6] Lewis LK., Harlow GR., Gregg-Jolly LA., Mount DW., 1994, Identification of high affinity binding sites for LexA which define new DNA damage-inducible genes in Escherichia coli., J Mol Biol. 241(4):507-23

 [7] Ohmori H., Saito M., Yasuda T., Nagata T., Fujii T., Wachi M., Nagai K., 1995, The pcsA gene is identical to dinD in Escherichia coli., J Bacteriol. 177(1):156-65

 [8] Lewis LK., Jenkins ME., Mount DW., 1992, Isolation of DNA damage-inducible promoters in Escherichia coli: regulation of polB (dinA), dinG, and dinH by LexA repressor., J Bacteriol. 174(10):3377-85

 [9] Lewis LK., Mount DW., 1992, Interaction of LexA repressor with the asymmetric dinG operator and complete nucleotide sequence of the gene., J Bacteriol. 174(15):5110-6

 [10] Yasuda T., Nagata T., Ohmori H., 1996, Multicopy suppressors of the cold-sensitive phenotype of the pcsA68 (dinD68) mutation in Escherichia coli., J Bacteriol. 178(13):3854-9

 [11] Ruangprasert A., Maehigashi T., Miles SJ., Giridharan N., Liu JX., Dunham CM., 2014, Mechanisms of toxin inhibition and transcriptional repression by Escherichia coli DinJ-YafQ., J Biol Chem. 289(30):20559-69

 [12] Weel-Sneve R., Kristiansen KI., Odsbu I., Dalhus B., Booth J., Rognes T., Skarstad K., Bjoras M., 2013, Single Transmembrane Peptide DinQ Modulates Membrane-Dependent Activities., PLoS Genet. 9(2):e1003260

 [13] Dorazi R., Dewar SJ., 2000, The SOS promoter dinH is essential for ftsK transcription during cell division., Microbiology. 146 ( Pt 11):2891-9

 [14] Ishino F., Jung HK., Ikeda M., Doi M., Wachi M., Matsuhashi M., 1989, New mutations fts-36, lts-33, and ftsW clustered in the mra region of the Escherichia coli chromosome induce thermosensitive cell growth and division., J Bacteriol. 171(10):5523-30

 [15] Vicente M., Gomez MJ., Ayala JA., 1998, Regulation of transcription of cell division genes in the Escherichia coli dcw cluster., Cell Mol Life Sci. 54(4):317-24

 [16] Little JW., Mount DW., Yanisch-Perron CR., 1981, Purified lexA protein is a repressor of the recA and lexA genes., Proc Natl Acad Sci U S A. 78(7):4199-203

 [17] Brent R., Ptashne M., 1981, Mechanism of action of the lexA gene product., Proc Natl Acad Sci U S A. 78(7):4204-8

 [18] Payne NS., Sancar A., 1989, The LexA protein does not bind specifically to the two SOS box-like sequences immediately 5' to the phr gene., Mutat Res. 218(3):207-10

 [19] Ma C., Rupert CS., 1995, Promoters of the phr gene in Escherichia coli K-12., Mol Gen Genet. 248(1):52-8

 [20] Rostas K., Morton SJ., Picksley SM., Lloyd RG., 1987, Nucleotide sequence and LexA regulation of the Escherichia coli recN gene., Nucleic Acids Res. 15(13):5041-9

 [21] Lupski JR., Ruiz AA., Godson GN., 1984, Promotion, termination, and anti-termination in the rpsU-dnaG-rpoD macromolecular synthesis operon of E. coli K-12., Mol Gen Genet. 195(3):391-401

 [22] Lupski JR., Smiley BL., Godson GN., 1983, Regulation of the rpsU-dnaG-rpoD macromolecular synthesis operon and the initiation of DNA replication in Escherichia coli K-12., Mol Gen Genet. 189(1):48-57

 [23] Benson FE., Illing GT., Sharples GJ., Lloyd RG., 1988, Nucleotide sequencing of the ruv region of Escherichia coli K-12 reveals a LexA regulated operon encoding two genes., Nucleic Acids Res. 16(4):1541-9

 [24] Shinagawa H., Makino K., Amemura M., Kimura S., Iwasaki H., Nakata A., 1988, Structure and regulation of the Escherichia coli ruv operon involved in DNA repair and recombination., J Bacteriol. 170(9):4322-9

 [25] Baquero MR., Bouzon M., Varea J., Moreno F., 1995, sbmC, a stationary-phase induced SOS Escherichia coli gene, whose product protects cells from the DNA replication inhibitor microcin B17., Mol Microbiol. 18(2):301-11

 [26] Brandsma JA., Bosch D., de Ruyter M., van de Putte P., 1985, Analysis of the regulatory region of the ssb gene of Escherichia coli., Nucleic Acids Res. 13(14):5095-109

 [27] Sancar A., Sancar GB., Rupp WD., Little JW., Mount DW., 1982, LexA protein inhibits transcription of the E. coli uvrA gene in vitro., Nature. 298(5869):96-8

 [28] Mizusawa S., Court D., Gottesman S., 1983, Transcription of the sulA gene and repression by LexA., J Mol Biol. 171(3):337-43

 [29] Vogel J., Argaman L., Wagner EG., Altuvia S., 2004, The small RNA IstR inhibits synthesis of an SOS-induced toxic peptide., Curr Biol. 14(24):2271-6

 [30] Kitagawa Y., Akaboshi E., Shinagawa H., Horii T., Ogawa H., Kato T., 1985, Structural analysis of the umu operon required for inducible mutagenesis in Escherichia coli., Proc Natl Acad Sci U S A. 82(13):4336-40

 [31] Otsuka J., Watanabe H., Mori KT., 1996, Evolution of transcriptional regulation system through promiscuous coupling of regulatory proteins with operons; suggestion from protein sequence similarities in Escherichia coli., J Theor Biol. 178(2):183-204

 [32] Sancar GB., Sancar A., Little JW., Rupp WD., 1982, The uvrB gene of Escherichia coli has both lexA-repressed and lexA-independent promoters., Cell. 28(3):523-30

 [33] Stark T., Moses RE., 1989, Interaction of the LexA repressor and the uvrC regulatory region., FEBS Lett. 258(1):39-41

 [34] Easton AM., Kushner SR., 1983, Transcription of the uvrD gene of Escherichia coli is controlled by the lexA repressor and by attenuation., Nucleic Acids Res. 11(24):8625-40

 [35] Christensen-Dalsgaard M., Jorgensen MG., Gerdes K., 2010, Three new RelE-homologous mRNA interferases of Escherichia coli differentially induced by environmental stresses., Mol Microbiol. 75(2):333-48

 [36] Lomba MR., Vasconcelos AT., Pacheco AB., de Almeida DF., 1997, Identification of yebG as a DNA damage-inducible Escherichia coli gene., FEMS Microbiol Lett. 156(1):119-22

 [37] d'Ari R., 1985, The SOS system., Biochimie. 67(3-4):343-7

 [38] Brent R., Ptashne M., 1980, The lexA gene product represses its own promoter., Proc Natl Acad Sci U S A. 77(4):1932-6

 [39] Chen Z., Yang H., Pavletich NP., 2008, Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures., Nature. 453(7194):489-4

 [40] Cox MM., 2007, Regulation of bacterial RecA protein function., Crit Rev Biochem Mol Biol. 42(1):41-63

 [41] Giese KC., Michalowski CB., Little JW., 2008, RecA-dependent cleavage of LexA dimers., J Mol Biol. 377(1):148-61

 [42] Little JW., 1991, Mechanism of specific LexA cleavage: autodigestion and the role of RecA coprotease., Biochimie. 73(4):411-21

 [43] Butala M., Klose D., Hodnik V., Rems A., Podlesek Z., Klare JP., Anderluh G., Busby SJ., Steinhoff HJ., Zgur-Bertok D., 2011, Interconversion between bound and free conformations of LexA orchestrates the bacterial SOS response., Nucleic Acids Res. 39(15):6546-57

 [44] Mazon G., Erill I., Campoy S., Cortes P., Forano E., Barbe J., 2004, Reconstruction of the evolutionary history of the LexA-binding sequence., Microbiology. 150(Pt 11):3783-95

 [45] Fogh RH., Ottleben G., Ruterjans H., Schnarr M., Boelens R., Kaptein R., 1994, Solution structure of the LexA repressor DNA binding domain determined by 1H NMR spectroscopy., EMBO J. 13(17):3936-44

 [46] Luo Y., Pfuetzner RA., Mosimann S., Paetzel M., Frey EA., Cherney M., Kim B., Little JW., Strynadka NC., 2001, Crystal structure of LexA: a conformational switch for regulation of self-cleavage., Cell. 106(5):585-94

 [47] Schnarr M., Granger-Schnarr M., Hurstel S., Pouyet J., 1988, The carboxy-terminal domain of the LexA repressor oligomerises essentially as the entire protein., FEBS Lett. 234(1):56-60

 [48] Mohana-Borges R., Pacheco AB., Sousa FJ., Foguel D., Almeida DF., Silva JL., 2000, LexA repressor forms stable dimers in solution. The role of specific dna in tightening protein-protein interactions., J Biol Chem. 275(7):4708-12

 [49] Erill I., Escribano M., Campoy S., Barbe J., 2003, In silico analysis reveals substantial variability in the gene contents of the gamma proteobacteria LexA-regulon., Bioinformatics. 19(17):2225-36

 [50] Walker GC., 1984, Mutagenesis and inducible responses to deoxyribonucleic acid damage in Escherichia coli., Microbiol Rev. 48(1):60-93

 [51] Zhang AP., Pigli YZ., Rice PA., 2010, Structure of the LexA-DNA complex and implications for SOS box measurement., Nature. 466(7308):883-6

 [52] Krueger JH., Elledge SJ., Walker GC., 1983, Isolation and characterization of Tn5 insertion mutations in the lexA gene of Escherichia coli., J Bacteriol. 153(3):1368-78

 [53] Brown MH., Paulsen IT., Skurray RA., 1999, The multidrug efflux protein NorM is a prototype of a new family of transporters., Mol Microbiol. 31(1):394-5

 [54] Ozyamak E., de Almeida C., de Moura AP., Miller S., Booth IR., 2013, Integrated stress response of Escherichia coli to methylglyoxal: transcriptional readthrough from the nemRA operon enhances protection through increased expression of glyoxalase I., Mol Microbiol. 88(5):936-50

 [55] Butala M., Zgur-Bertok D., Busby SJ., 2009, The bacterial LexA transcriptional repressor., Cell Mol Life Sci. 66(1):82-93