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GlpR DNA-binding transcriptional repressor

Synonyms: GlpR-sn-glycerol 3-phosphate, GlpR-glycerol, GlpR
Summary:
The sn-Glycerol-3-phosphate repressor," GlpR, acts as the repressor of the glycerol-3-phosphate regulon, which is organized in different operons [1, 2, 4, 6, 7, 8, 9]. However, the array of promoters repressed by GlpR has been expanded [10].This regulator is part of the glpEGR operon, yet it can also be constitutively expressed as an independent (glpR) transcription unit [11, 12]. In addition, the operons regulated are induced when Escherichia coli is grown in the presence of inductor, glycerol, or glycerol-3-phosphate (G3P), and the absence of glucose [8] In the absence of inductor, this repressor binds in tandem to inverted repeat sequences that consist of 20-nucleotide-long DNA target sites [2, 3, 8]. In contrast, [10] discovered operons whose regulation appears to be mediated by a single GlpR site per operon. Binding of GlpR to DNA is diminished in the presence of the inducers glycerol or G3P.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
GlpR Functional   Apo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IPI] S [1]
GlpR-sn-glycerol 3-phosphate Non-Functional Allosteric Holo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IPI] S [1]
GlpR-glycerol Non-Functional   Holo nd nd nd
Evolutionary Family: DeoR
TFBs length: 20
TFBs symmetry: inverted-repeat
Sensing class: Sensing external and internal signals
Connectivity class: Local Regulator
Gene name: glpR
  Genome position: 3559848-3560605
  Length: 758 bp / 251 aa
Operon name: glpEGR
TU(s) encoding the TF:
Transcription unit        Promoter
glpEGR
glpEp
glpGR
glpGp
glpR
glpRp1
glpR
glpRp2


Regulon       
Regulated gene(s) glpA, glpB, glpC, glpD, glpF, glpK, glpQ, glpT, glpX
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
misc. glycerol metabolism (8)
membrane (5)
anaerobic respiration (4)
electron donors (4)
aerobic respiration (2)
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Regulated operon(s) glpABC, glpD, glpFKX, glpTQ
First gene in the operon(s) glpA, glpD, glpF, glpT
Simple and complex regulons ArcA,CRP,FNR,Fis,FlhDC,GlpR
ArcA,CRP,GlpR
CRP,FNR,Fis,GlpR,IHF
CRP,GlpR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[GlpR,-](4)


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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
  GlpR repressor glpABCp Sigma70 -90.5 -154.5 glpA, glpB, glpC
tcataaattaAATGTGAATTGCCGCACACAttattaaata
 2352483 2352502 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2], [2], [3]
  GlpR repressor glpABCp Sigma70 -50.5 -114.5 glpA, glpB, glpC
agatttacaaAATGTTCAAAATGACGCATGaaatcacgtt
 2352523 2352542 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2], [2], [3]
  GlpR repressor glpABCp Sigma70 -18.5 -82.5 glpA, glpB, glpC
atcacgtttcACTTTCGAATTATGAGCGAAtatgcgcgaa
 2352555 2352574 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2], [2], [3]
  GlpR repressor glpABCp Sigma70 1.5 -63.5 glpA, glpB, glpC
ttatgagcgaATATGCGCGAAATCAAACAAttcatgtttt
 2352574 2352593 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2], [2], [3]
  GlpR repressor glpABCp Sigma70 41.5 -23.5 glpA, glpB, glpC
tactatggctAAATGGTAAAAAACGAACTTcagagggata
 2352614 2352633 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2], [2], [3]
  GlpR repressor glpDp Sigma70 -0.5 -42.5 glpD
tctttgctaaTATGTTCGATAACGAACATTtatgagcttt
 3561961 3561980 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [3], [4], [4], [5], [5]
  GlpR repressor glpDp Sigma70 19.5 -23.5 glpD
taacgaacatTTATGAGCTTTAACGAAAGTgaatgagggc
 3561980 3561999 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [3], [4], [4], [5], [5]
  GlpR repressor glpDp Sigma70 414.5 372.5 glpD
cgggatcaacTGGTTTGCGTTTTGGCGCAAattcagtgtt
 3562375 3562394 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4], [4]
  GlpR repressor glpDp Sigma70 455.5 413.5 glpD
aaaccggaaaTTAAGCGCGGATTCGAATATtctgactgtt
 3562416 3562435 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4], [4]
  GlpR repressor glpFp Sigma70 -79.5 -150.5 glpF, glpK, glpX
gatggaataaATGGCGCGATAACGCTCATTttatgacgag
 4118231 4118250 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [6], [6]
  GlpR repressor glpFp Sigma70 -58.5 -129.5 glpF, glpK, glpX
acgctcatttTATGACGAGGCACACACATTttaagttcga
 4118210 4118229 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [6], [6]
  GlpR repressor glpFp Sigma70 -37.5 -108.5 glpF, glpK, glpX
acacacatttTAAGTTCGATATTTCTCGTTtttgctcgtt
 4118189 4118208 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [6], [6]
  GlpR repressor glpFp Sigma70 -17.5 -88.5 glpF, glpK, glpX
atttctcgttTTTGCTCGTTAACGATAAGTttacagcatg
 4118169 4118188 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [6], [6]
  GlpR repressor glpFp Sigma70 1001.5 930.5 glpF, glpK, glpX
accagctcccGCGCGGTCGTAATGGATCACgatgccaata
 4117151 4117170 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [6], [6]
  GlpR repressor glpFp Sigma70 1043.5 972.5 glpF, glpK, glpX
attagcgtgtCGCAGCGCGAATTTGAGCAAatctacccaa
 4117109 4117128 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [6], [6]
  GlpR repressor glpTQp Sigma70 -172.5 -249.5 glpT, glpQ
tatccctctgAAGTTCGTTTTTTACCATTTagccatagta
 2352614 2352633 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2], [2], [3], [7]
  GlpR repressor glpTQp Sigma70 -132.5 -209.5 glpT, glpQ
aaaacatgaaTTGTTTGATTTCGCGCATATtcgctcataa
 2352574 2352593 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2], [2], [3], [7]
  GlpR repressor glpTQp Sigma70 -113.5 -190.5 glpT, glpQ
ttcgcgcataTTCGCTCATAATTCGAAAGTgaaacgtgat
 2352555 2352574 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2], [2], [3], [7]
  GlpR repressor glpTQp Sigma70 -81.5 -158.5 glpT, glpQ
aacgtgatttCATGCGTCATTTTGAACATTttgtaaatct
 2352523 2352542 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2], [2], [3], [7]
  GlpR repressor glpTQp Sigma70 -41.5 -118.5 glpT, glpQ
tatttaataaTGTGTGCGGCAATTCACATTtaatttatga
 2352483 2352502 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2], [2], [3]
  GlpR repressor glpTQp Sigma70 315.5 238.5 glpT, glpQ
gattgcttatGGATTTTCGAAATTCATCATgggttcggta
 2352127 2352146 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [7], [7]
  GlpR repressor glpTQp Sigma70 333.5 256.5 glpT, glpQ
gaaattcatcATGGGTTCGGTATCGGATCGctcgaatccg
 2352109 2352128 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [7], [7]
  GlpR repressor glpTQp Sigma70 348.5 271.5 glpT, glpQ
ttcggtatcgGATCGCTCGAATCCGCGCGTtttcctgccc
 2352094 2352113 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [7], [7]


Alignment and PSSM for GlpR TFBSs    

Aligned TFBS of GlpR   
  Sequence
  AATATGTTCGATAACGAACATT
  AATATGCGCGAAATCAAACAAT
  AATTTGCGCCAAAACGCAAACC
  AAATGGCGCGATAACGCTCATT
  AAAACGCGCGGATTCGAGCGAT
  ATTAAGCGCGGATTCGAATATT
  TTTTTGCTCGTTAACGATAAGT
  GATTTGCTCAAATTCGCGCTGC
  TAAATGGTAAAAAACGAACTTC
  TTTATGAGCTTTAACGAAAGTG
  AAAACGAGAAATATCGAACTTA
  AAAATGTTCAAAATGACGCATG
  AATGTGTGCGGCAATTCACATT
  CCCATGATGAATTTCGAAAATC
  ATCGTGATCCATTACGACCGCG
  TTTATGACGAGGCACACACATT
  TATTCGCTCATAATTCGAAAGT

Position weight matrix (PWM). GlpR matrix-quality result    
A	10	11	5	10	1	0	5	0	2	7	10	8	11	9	0	3	10	11	5	11	2	1
C	1	1	2	0	3	0	8	1	13	2	0	1	1	0	14	1	6	1	11	0	2	4
G	1	0	0	2	1	17	1	8	2	7	4	1	0	0	1	12	1	3	0	3	3	3
T	5	5	10	5	12	0	3	8	0	1	3	7	5	8	2	1	0	2	1	3	10	9

Consensus    
;	consensus.strict             	aatatGcgCgaaaaCGaaCatt
;	consensus.strict.rc          	AATGTTCGTTTTCGCGCATATT
;	consensus.IUPAC              	aawatGmkCrrwawCGmaMaty
;	consensus.IUPAC.rc           	RATKTKCGWTWYYGMKCATWTT
;	consensus.regexp             	aa[at]atG[ac][gt]C[ag][ag][at]a[at]CG[ac]a[AC]at[ct]
;	consensus.regexp.rc          	[AG]AT[GT]T[GT]CG[AT]T[AT][CT][CT]G[AC][GT]CAT[AT]TT

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


Evidence    

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IPI] Inferred from physical interaction

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis


Reference(s)    

 [1] Larson TJ., Ye SZ., Weissenborn DL., Hoffmann HJ., Schweizer H., 1987, Purification and characterization of the repressor for the sn-glycerol 3-phosphate regulon of Escherichia coli K12., J Biol Chem 262(33):15869-74

 [2] Larson TJ., Cantwell JS., van Loo-Bhattacharya AT., 1992, Interaction at a distance between multiple operators controls the adjacent, divergently transcribed glpTQ-glpACB operons of Escherichia coli K-12., J Biol Chem 267(9):6114-21

 [3] Zhao N., Oh W., Trybul D., Thrasher KS., Kingsbury TJ., Larson TJ., 1994, Characterization of the interaction of the glp repressor of Escherichia coli K-12 with single and tandem glp operator variants., J Bacteriol 176(8):2393-7

 [4] Yang B., Larson TJ., 1996, Action at a distance for negative control of transcription of the glpD gene encoding sn-glycerol 3-phosphate dehydrogenase of Escherichia coli K-12., J Bacteriol 178(24):7090-8

 [5] Ye SZ., Larson TJ., 1988, Structures of the promoter and operator of the glpD gene encoding aerobic sn-glycerol-3-phosphate dehydrogenase of Escherichia coli K-12., J Bacteriol 170(9):4209-15

 [6] Weissenborn DL., Wittekindt N., Larson TJ., 1992, Structure and regulation of the glpFK operon encoding glycerol diffusion facilitator and glycerol kinase of Escherichia coli K-12., J Biol Chem 267(9):6122-31

 [7] Yang B., Gerhardt SG., Larson TJ., 1997, Action at a distance for glp repressor control of glpTQ transcription in Escherichia coli K-12., Mol Microbiol 24(3):511-21

 [8] Lin EC, 1976, Glycerol dissimilation and its regulation in bacteria., Annu Rev Microbiol, 30(None):535 10.1146/annurev.mi.30.100176.002535

 [9] Truniger V., Boos W., Sweet G., 1992, Molecular analysis of the glpFKX regions of Escherichia coli and Shigella flexneri., J Bacteriol 174(21):6981-91

 [10] Ireland WT, Beeler SM, Flores-Bautista E, McCarty NS, Röschinger T, Belliveau NM, Sweredoski MJ, Moradian A, Kinney JB, Phillips R, 2020, Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time., Elife, 9(None):None 10.7554/eLife.55308

 [11] Yang B., Larson TJ., 1998, Multiple promoters are responsible for transcription of the glpEGR operon of Escherichia coli K-12., Biochim Biophys Acta 1396(1):114-26

 [12] Schweizer H, Boos W, Larson TJ, 1985, Repressor for the sn-glycerol-3-phosphate regulon of Escherichia coli K-12: cloning of the glpR gene and identification of its product., J Bacteriol, 161(2):563 10.1128/jb.161.2.563-566.1985

 [13] Vimala A., Harinarayanan R., 2016, Transketolase activity modulates glycerol-3-phosphate levels in Escherichia coli., Mol Microbiol 100(2):263-77

 [14] Zeng G., Ye S., Larson TJ., 1996, Repressor for the sn-glycerol 3-phosphate regulon of Escherichia coli K-12: primary structure and identification of the DNA-binding domain., J Bacteriol 178(24):7080-9

 [15] Freddolino PL, Amini S, Tavazoie S, 2012, Newly identified genetic variations in common Escherichia coli MG1655 stock cultures., J Bacteriol, 194(2):303 10.1128/JB.06087-11


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