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DeoR DNA-binding transcriptional repressor

Synonyms: DeoR-Deoxyribose-5-phosphate, DeoR
Summary:
The transcriptional repressor DeoR, for "Deoxyribose Regulator," is involved in the negative expression of genes related to transport and catabolism of deoxyribonucleoside nucleotides [2, 3, 3, 5, 7, 8, 10, 11, 12, 13] DeoR belongs to the DeoR family of transcriptional regulators [14, 15] This protein consists of two domains, an amino-terminal domain that contains a potential helix-turn-helix DNA-binding motif and a carboxy-terminal domain involved in the oligomerization and the recognition of a possible co-inducer [14, 15, 16] DeoR is an octamer in solution [1]and it forms multiple complexes (oligomers) in its target promoters; the cooperative binding of this regulator to different tandem inverted repeat sequences generates a repression DNA loop [1, 2, 3, 17, 18, 19, 20, 21, 22] The binding targets for DeoR consist of 16-nucleotide inverted repeat sequences that possess conserved motifs [3, 21, 23] Read more >


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
DeoR Functional   Apo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IPI] S [1]
DeoR-Deoxyribose-5-phosphate Non-Functional Allosteric Holo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IPI] S [1]
Evolutionary Family: DeoR
TFBs length: 16
TFBs symmetry: inverted-repeat
Sensing class: Using internal synthesized signals
Connectivity class: Local Regulator
Gene name: deoR
  Genome position: 881976-882734
  Length: 759 bp / 252 aa
Operon name: deoR
TU(s) encoding the TF:
Transcription unit        Promoter
deoR
deoRp


Regulon       
Regulated gene(s) deoA, deoB, deoC, deoD, nupG, tsx
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
nucleotide and nucleoside conversions (5)
carbon utilization (1)
Porters (Uni-, Sym- and Antiporters) (1)
membrane (1)
Beta barrel porins (The Outer Membrane Porin (OMP) Functional Superfamily) (1)
Read more >
Regulated operon(s) deoCABD, mutY-yggX-mltC-nupG, tsx
First gene in the operon(s) deoC, nupG, tsx
Simple and complex regulons CRP,CytR,DeoR
CRP,CytR,DeoR,Fis,ModE
DeoR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[DeoR,-](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
  DeoR repressor deoCp1 Sigma70 -608.0 -1252.0 deoC, deoA, deoB, deoD
cgcgcggcaaTCCCTTCTTTTTCACAcagcaagtta
 4616063 4616078 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] S [2], [3]
  DeoR repressor deoCp1 Sigma70 -8.0 -652.0 deoC, deoA, deoB, deoD
atctcgtcttGTGTTAGAATTCTAACatacggttgc
 4616663 4616678 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] S [2], [3]
  DeoR repressor deoCp1 Sigma70 269.0 -376.0 deoC, deoA, deoB, deoD
gcaggaagctGTGGGTAAGGCAGATTgttttctgct
 4616939 4616954 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] S [2], [3]
  DeoR repressor deoCp2 Sigma70 -887.0 -932.0 deoC, deoA, deoB, deoD
gtagccccctTTTGTGAAAATTTTATcatgcaccgg
 4616383 4616398 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] S [2], [3]
  DeoR repressor deoCp2 Sigma70 -308.0 -353.0 deoC, deoA, deoB, deoD
attgttttctGCTTCCAGTGCCAGAAaatggcgctt
 4616962 4616977 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] S [2], [3]
  DeoR repressor deoCp2 Sigma70 -8.0 -53.0 deoC, deoA, deoB, deoD
tgcggagtagATGTTAGAATACTAACaaactcgcaa
 4617262 4617277 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IMP-SITE-MUTATION] S [2], [3], [4]
  DeoR repressor nupGp Sigma70 nd nd nupG
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [5], [5], [6]
  DeoR repressor tsxp1 Sigma70 -7.5 -239.5 tsx
cccgtcatttTGTTACTCTGCTTACAtcacctggat
 432245 432260 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-DAP-SEQ], [EXP-GSELEX], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [4], [7], [7], [8], [9]


Alignment and PSSM for DeoR TFBSs    

Aligned TFBS of DeoR   
  Sequence
  TTTGTTAGTATTCTAACAT
  TGTGTTAGAATTCTAACAT
  TTTGTTACTCTGCTTACAT
  TTTGTGAAAATTTTATCAT
  TTTCTGGCACTGGAAGCAG
  TGTGTGAAAAAGAAGGGAT
  GCTGTGGGTAAGGCAGATT

Position weight matrix (PWM). DeoR matrix-quality result    
A	0	0	0	0	0	0	5	2	4	5	2	0	1	2	5	3	1	6	0
C	0	1	0	1	0	0	0	2	0	2	0	0	3	1	0	0	5	0	0
G	1	2	0	6	0	4	2	3	0	0	0	4	2	0	1	3	1	0	1
T	6	4	7	0	7	3	0	0	3	0	5	3	1	4	1	1	0	1	6

Consensus    
;	consensus.strict             	ttTGTgagaatgctagCat
;	consensus.strict.rc          	ATGCTAGCATTCTCACAAA
;	consensus.IUPAC              	tkTGTkrswmtkstarCat
;	consensus.IUPAC.rc           	ATGYTASMAKWSYMACAMA
;	consensus.regexp             	t[gt]TGT[gt][ag][cg][at][ac]t[gt][cg]ta[ag]Cat
;	consensus.regexp.rc          	ATG[CT]TA[CG][AC]A[GT][AT][CG][CT][AC]ACA[AC]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


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-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing

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

 [EXP-GSELEX] high throughput Genomic SELEX-chip evidence

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts


Reference(s)    

 [1] Mortensen L., Dandanell G., Hammer K., 1989, Purification and characterization of the deoR repressor of Escherichia coli., EMBO J 8(1):325-31

 [2] Amouyal M., Mortensen L., Buc H., Hammer K., 1989, Single and double loop formation when deoR repressor binds to its natural operator sites., Cell 58(3):545-51

 [3] Valentin-Hansen P., Albrechtsen B., Love Larsen JE., 1986, DNA-protein recognition: demonstration of three genetically separated operator elements that are required for repression of the Escherichia coli deoCABD promoters by the DeoR repressor., EMBO J 5(8):2015-21

 [4] Baumgart LA, Lee JE, Salamov A, Dilworth DJ, Na H, Mingay M, Blow MJ, Zhang Y, Yoshinaga Y, Daum CG, O'Malley RC, 2021, Persistence and plasticity in bacterial gene regulation., Nat Methods, 18(12):1499 10.1038/s41592-021-01312-2

 [5] Munch-Petersen A., Jensen N., 1990, Analysis of the regulatory region of the Escherichia coli nupG gene, encoding a nucleoside-transport protein., Eur J Biochem 190(3):547-51

 [6] 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

 [7] Bremer E., Gerlach P., Middendorf A., 1988, Double negative and positive control of tsx expression in Escherichia coli., J Bacteriol 170(1):108-16

 [8] Bremer E., Middendorf A., Martinussen J., Valentin-Hansen P., 1990, Analysis of the tsx gene, which encodes a nucleoside-specific channel-forming protein (Tsx) in the outer membrane of Escherichia coli., Gene 96(1):59-65

 [9] Ishihama A, Shimada T, Yamazaki Y, 2016, Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors., Nucleic Acids Res, 44(5):2058 10.1093/nar/gkw051

 [10] Hammer-Jespersen K., Munch-Ptersen A., 1975, Multiple regulation of nucleoside catabolizing enzymes: regulation of the deo operon by the cytR and deoR gene products., Mol Gen Genet 137(4):327-35

 [11] Short SA, Singer JT, 1984, Studies on deo operon regulation in Escherichia coli: cloning and expression of the deoR structural gene., Gene, 31(1-3):205 10.1016/0378-1119(84)90211-7

 [12] Barbier CS, Short SA, 1985, Studies on deo operon regulation in Escherichia coli: cloning and expression of the cytR structural gene., Gene, 36(1-2):37 10.1016/0378-1119(85)90067-8

 [13] Dandanell G, Hammer K, 1991, deoP1 promoter and operator mutants in Escherichia coli: isolation and characterization., Mol Microbiol, 5(10):2371 10.1111/j.1365-2958.1991.tb02083.x

 [14] Valentin-Hansen P., Hojrup P., Short S., 1985, The primary structure of the DeoR repressor from Escherichia coli K-12., Nucleic Acids Res 13(16):5927-36

 [15] 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

 [16] Garces F., Fernandez FJ., Gomez AM., Perez-Luque R., Campos E., Prohens R., Aguilar J., Baldoma L., Coll M., Badia J., Vega MC., 2008, Quaternary structural transitions in the DeoR-type repressor UlaR control transcriptional readout from the L-ascorbate utilization regulon in Escherichia coli., Biochemistry 47(44):11424-33

 [17] Mochul'skaia NA, Mironov AS, Mashko SV, 1994, [Decrease in the level of DeoR-dependent repression of the deo operon as a result of integration of foreign DNA fragments into the interoperator deoO1-deoO2 region of the Escherichia coli chromosome]., Genetika, 30(9):1175 None

 [18] Dandanell G, Norris K, Hammer K, 1991, Long-distance deoR regulation of gene expression in Escherichia coli., Ann N Y Acad Sci, 646(None):19 10.1111/j.1749-6632.1991.tb18559.x

 [19] Dandanell G, Hammer K, 1985, Two operator sites separated by 599 base pairs are required for deoR repression of the deo operon of Escherichia coli., EMBO J, 4(12):3333 10.1002/j.1460-2075.1985.tb04085.x

 [20] Valentin-Hansen P., Aiba H., Schumperli D., 1982, The structure of tandem regulatory regions in the deo operon of Escherichia coli K12., EMBO J 1(3):317-322

 [21] Dandanell G, 1992, DeoR repression at-a-distance only weakly responds to changes in interoperator separation and DNA topology., Nucleic Acids Res, 20(20):5407 10.1093/nar/20.20.5407

 [22] Hao N, Sullivan AE, Shearwin KE, Dodd IB, 2021, The loopometer: a quantitative in vivo assay for DNA-looping proteins., Nucleic Acids Res, 49(7):e39 10.1093/nar/gkaa1284

 [23] Hammer K, Bech L, Hobolth P, Dandanell G, 1993, DNA specificity of Escherichia coli deoP1 operator-DeoR repressor recognition., Mol Gen Genet, 237(1-2):129 10.1007/BF00282793


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