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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 [11, 31] as well as its own synthesis [32] This regulation is known as the SOS response [31] When DNA is damaged, the RecA coprotease binds to the single-stranded DNA in the damaged region to form a filament [33, 34] 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 [35, 36] RecF appears to facilitate RecA filament formation on the leading-strand single-stranded DNA gaps generated by replisome lesion skipping [37] Phenylboronic compounds are able to inhibit the self-cleavage of the transcriptional repressor LexA, presumably through the formation of an acyl-enzyme intermediate [38] The conformational flexibility of unbound LexA is the key element in establishing a coordinated SOS response [39] A structurally dynamic peptide loop encoding residues 75-84 of LexA appears to be necessary for the recognition of RecA [40]. In addition to the degradation of LexA in response to DNA damage, spontaneous self-cleavage activity of LexA has been observed under normal growth, triggering SOS response pulses [41].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
LexA Functional   nd nd
Evolutionary Family: LexA
TFBs length: 20
TFBs symmetry: inverted-repeat
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, mraY, murC, murD, murE, murF, murG, phr, polB, ptrA, recA, recB, recD, recN, recQ, recX, rpoD, rpsU, ruvA, ruvB, sbmC, ssb, sulA, symE, tisB, umuC, umuD, uvrA, uvrB, uvrC, uvrD, uvrY, yafN, yafO, yafP, yafQ, ybfE, ybiB, ydjM, yebG, yehF
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
SOS response (25)
DNA repair (23)
cell division (9)
DNA recombination (9)
murein (peptidoglycan) (8)
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Regulated operon(s) cho, dinB-yafNOP, dinD, dinG-ybiB, dinI, dinJ-yafQ, dinQ, ftsK, hokE, insK, lexA-dinF, mraZ-rsmH-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ-lpxC, polB, ptrA-recBD, recAX, recN, recQ, rpsU-dnaG-rpoD, ruvAB, sbmC, ssb, sulA, symE, tisB, umuDC, uvrA, uvrB, uvrD, uvrYC, ybfE, ybgA-phr, ydjM, yebG, yehF
First gene in the operon(s) cho, dinB, dinD, dinG, dinI, dinJ, dinQ, ftsK, ftsL, hokE, insK, lexA, phr, polB, ptrA, recA, recN, recQ, rpsU, ruvA, sbmC, ssb, sulA, symE, tisB, umuD, uvrA, uvrB, uvrC, uvrD, uvrY, yafN, ybfE, ydjM, yebG, yehF
Simple and complex regulons ArcA,LexA
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

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 (Confirmed, Strong, Weak) References
  LexA repressor chop Sigma70 -0.5 -23.5 cho
1823482 1823501 [AIBSCS], [APIORCISFBSCS] [1], [2]
  LexA repressor dinBp Sigma70 -6.5 -24.5 dinB, yafN, yafO, yafP
250864 250883 [AIBSCS], [APIORCISFBSCS], [ICWHO] [1], [3]
  LexA repressor dinBp2 Sigma38 -6.5 -24.5 dinB, yafN, yafO, yafP
250864 250883 [AIBSCS], [APIORCISFBSCS], [ICWHO] [1], [3]
  LexA repressor dinDp nd 8.5 -53.5 dinD
3817697 3817716 [GEA], [AIBSCS], [APIORCISFBSCS] [4]
  LexA repressor dinGp Sigma70 -27.5 -24.5 dinG, ybiB
833036 833055 [GEA], [AIBSCS], [BPP] [5], [6]
  LexA repressor dinIp Sigma70 -7.5 -29.5 dinI
1121507 1121526 [GEA], [AIBSCS], [APIORCISFBSCS], [BPP], [IHBCE], [SM] [7], [8]
  LexA repressor dinJp Sigma70 89.5 -24.5 dinJ, yafQ
246517 246536 [GEA], [AIBSCS] [7], [9]
  LexA repressor dinQp Sigma70 -29.5 -223.5 dinQ
3648002 3648021 [APIORCISFBSCS] [10]
  LexA repressor dinQp Sigma70 -7.5 -201.5 dinQ
3647980 3647999 [GEA], [AIBSCS], [APIORCISFBSCS] [10], [11]
  LexA repressor ftsKp1 Sigma70 -0.5 -86.5 ftsK
933128 933147 [AIBSCS], [GEA], [AIBSCS], [BPP] [5], [12]
  LexA repressor ftsLp2 nd 3.0 -18.0 ftsL, ftsI, murE, murF, mraY, murD, ftsW, murG, murC, ddlB, ftsQ, ftsA, ftsZ, lpxC
91004 91023 [APIORCISFBSCS] [13], [14]
  LexA repressor hokEp Sigma24 -81.5 -186.5 hokE
607640 607659 [AIBSCS] [1]
  LexA repressor insKp Sigma24 nd nd insK nd nd [GEA], [BPP] [11]
  LexA repressor lexAp Sigma70 -9.0 -37.0 lexA, dinF
4257068 4257087 [GEA], [APIORCISFBSCS], [BPP], [SM] [15]
  LexA repressor lexAp Sigma70 13.0 -16.0 lexA, dinF
4257089 4257108 [GEA], [APIORCISFBSCS], [BPP], [SM] [15]
  LexA repressor phrp nd -66.5 -152.5 phr
739345 739364 [APIORCISFBSCS] [7], [16]
  LexA repressor phrp nd 25.5 -61.5 phr
739436 739455 [GEA], [APIORCISFBSCS] [17]
  LexA repressor polBp Sigma70 -40.5 -63.5 polB
65834 65853 [GEA], [AIBSCS], [BPP] [5]
  LexA repressor ptrAp Sigma70 20.5 -107.5 ptrA, recB, recD
2958982 2959001 [BPP], [SM] [18]
  LexA repressor recAp Sigma70 -20.0 -70.0 recA, recX
2823829 2823848 [BPP] [19]
  LexA repressor recNp Sigma70 -22.5 -58.5 recN
2751727 2751746 [GEA], [AIBSCS], [BPP] [20], [21]
  LexA repressor recNp Sigma70 -0.5 -36.5 recN
2751749 2751768 [GEA], [AIBSCS], [BPP] [20], [21]
  LexA repressor recQp Sigma70 6.0 -23.0 recQ
4005834 4005849 [GEA], [APIORCISFBSCS] [22]
  LexA repressor rpsUp3 Sigma70 4.5 -42.5 rpsU, dnaG, rpoD
3210729 3210748 [BCE], [SM]
  LexA repressor ruvAp1 nd -63.5 -111.5 ruvA, ruvB
1946078 1946097 [APIORCISFBSCS]
  LexA repressor ruvAp1 nd -12.5 -60.5 ruvA, ruvB
1946027 1946046 [APIORCISFBSCS], [BPP] [23]
  LexA repressor ruvAp2 nd -72.5 -112.5 ruvA, ruvB
1946079 1946098 [APIORCISFBSCS]
  LexA repressor ruvAp2 nd -19.5 -59.5 ruvA, ruvB
1946026 1946045 [APIORCISFBSCS], [BPP] [23]
  LexA repressor sbmCp2 nd 17.5 -24.5 sbmC
2081277 2081296 [GEA], [IHBCE] [24]
  LexA repressor ssbp3 Sigma70 -46.5 -160.5 ssb
4273955 4273974 [APIORCISFBSCS], [BCE]
  LexA repressor sulAp Sigma70 -5.0 -33.0 sulA
1020942 1020961 [BCE]
  LexA repressor symEp Sigma70 -8.5 -85.5 symE
4579916 4579935 [AIBSCS], [BPP] [11]
  LexA repressor tisBp nd -28.0 -244.0 tisB
3853299 3853318 [GEA], [ICA] [11]
  LexA repressor umuDp Sigma70 -20.5 -49.5 umuD, umuC
1230708 1230727 [APIORCISFBSCS] [7], [25]
  LexA repressor umuDp Sigma70 -0.5 -29.5 umuD, umuC
1230728 1230747 [BPP] [7], [25]
  LexA repressor uvrAp Sigma70 -28.5 -93.5 uvrA
4273955 4273974 [APIORCISFBSCS], [BCE]
  LexA repressor uvrBp1 Sigma70 -51.5 -84.5 uvrB
813434 813450 [GEA], [APIORCISFBSCS], [BPP], [ICA], [SM] [21], [26]
  LexA repressor uvrBp2 Sigma70 -220.5 -284.5 uvrB
813234 813250 [GEA], [BPP], [ICA] [21]
  LexA repressor uvrBp2 Sigma70 -167.5 -231.5 uvrB
813287 813303 [GEA], [BPP], [ICA] [21]
  LexA repressor uvrBp2 Sigma70 -20.5 -84.5 uvrB
813434 813450 [BPP], [GEA], [SM], [APIORCISFBSCS], [BPP], [ICA], [SM] [21], [26]
  LexA repressor uvrBp3 Sigma70 -24.5 -398.5 uvrB
813120 813136 [GEA], [BPP], [ICA], [SM] [21]
  LexA repressor uvrCp3 Sigma70 nd nd uvrC nd nd [GEA], [BPP] [27]
  LexA repressor uvrDp1 Sigma70 11.0 -66.0 uvrD
3997907 3997926 [APIORCISFBSCS]
  LexA repressor uvrYp2 Sigma70 -129.5 -176.5 uvrY, uvrC
1995526 1995545 [GEA], [AIBSCS] [27]
  LexA repressor yafNp Sigma70 -1.5 -37.5 yafN, yafO, yafP
251958 251977 [APIORCISFBSCS] [28]
  LexA repressor ybfEp Sigma32 -85.5 -126.5 ybfE
712015 712034 [AIBSCS] [1]
  LexA repressor ydjMp Sigma70 -1.5 -42.5 ydjM
1810159 1810178 [GEA], [AIBSCS], [BPP] [11]
  LexA repressor ydjMp Sigma70 17.5 -24.5 ydjM
1810177 1810196 [GEA], [AIBSCS], [BPP] [11]
  LexA repressor yebGp Sigma70 -9.5 -27.5 yebG
1930765 1930784 [GEA], [AIBSCS], [APIORCISFBSCS], [IHBCE] [29]
  LexA repressor yehFp Sigma70 11.5 -18.5 yehF
2196446 2196465 [AIBSCS] [11]

High-throughput Transcription factor binding sites (TFBSs)

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Center Position Growth Condition Evidence (Confirmed, Strong, Weak) References
  LexA repressor yoaA Gene nd
1893242 1893261 1893251.5 nd [GEA], [APIORCISFBSCS], [SM] [30]
Other High-throughput regulatory interactions with weak evidence

Alignment and PSSM for LexA TFBSs    

Aligned TFBS of LexA   

Position weight matrix (PWM). LexA matrix-quality result   
A	9	20	3	2	3	0	12	10	15	6	16	3	32	6	24	1	40	0	2	20	17	20
C	9	9	36	2	1	1	3	5	1	1	7	6	6	1	11	42	0	0	9	1	5	3
G	5	11	1	2	39	15	11	2	8	0	6	1	3	6	3	1	2	43	5	5	6	6
T	21	4	4	38	1	28	18	27	20	37	15	34	3	31	6	0	2	1	28	18	16	15

;	consensus.strict             	taCTGttttTatataCAGtaaa
;	consensus.strict.rc          	TTTACTGTATATAAAAACAGTA
;	consensus.IUPAC              	trCTGkktwTwtatmCAGtwww
;	consensus.IUPAC.rc           	WWWACTGKATAWAWAMMCAGYA
;	consensus.regexp             	t[ag]CTG[gt][gt]t[at]T[at]tat[ac]CAGt[at][at][at]
;	consensus.regexp.rc          	[AT][AT][AT]ACTG[GT]ATA[AT]A[AT]A[AC][AC]CAG[CT]A

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


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 [32] Brent R, Ptashne M, 1980, The lexA gene product represses its own promoter., Proc Natl Acad Sci U S A, 77(4):1932 10.1073/pnas.77.4.1932

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