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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, 4, 6, 7, 8, 9, 10, 11]
DeoR belongs to the DeoR family of transcriptional regulators [12, 13] 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 [12, 13, 14]
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, 15, 16, 17, 18, 19] The binding targets for DeoR consist of 16-nucleotide inverted repeat sequences that possess conserved motifs [3, 19, 20] Read more >


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
DeoR Functional   Apo [BPP], [IPI] [1]
DeoR-Deoxyribose-5-phosphate Non-Functional Allosteric Holo [BPP], [IPI] [1]
Evolutionary Family: DeoR
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 (6)
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, 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,-](3)


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
  DeoR repressor deoCp1 Sigma70 -608.0 -1252.5 deoC, deoA, deoB, deoD
cgcgcggcaaTCCCTTCTTTTTCACAcagcaagtta
4616063 4616078 [HIBSCS], [SM] [2], [3]
  DeoR repressor deoCp1 Sigma70 -8.0 -652.5 deoC, deoA, deoB, deoD
atctcgtcttGTGTTAGAATTCTAACatacggttgc
4616663 4616678 [HIBSCS], [SM] [2], [3]
  DeoR repressor deoCp1 Sigma70 269.0 -376.5 deoC, deoA, deoB, deoD
gcaggaagctGTGGGTAAGGCAGATTgttttctgct
4616939 4616954 [HIBSCS], [SM] [2], [3]
  DeoR repressor deoCp2 Sigma70 -887.0 -932.5 deoC, deoA, deoB, deoD
gtagccccctTTTGTGAAAATTTTATcatgcaccgg
4616383 4616398 [HIBSCS], [SM] [2], [3]
  DeoR repressor deoCp2 Sigma70 -308.0 -353.5 deoC, deoA, deoB, deoD
attgttttctGCTTCCAGTGCCAGAAaatggcgctt
4616962 4616977 [HIBSCS], [SM] [2], [3]
  DeoR repressor deoCp2 Sigma70 -8.0 -53.5 deoC, deoA, deoB, deoD
tgcggagtagATGTTAGAATACTAACaaactcgcaa
4617262 4617277 [HIBSCS], [SM] [2], [3]
  DeoR repressor nupGp Sigma70 nd nd nupG nd nd [GEA], [HIBSCS] [4], [5]
  DeoR repressor tsxp1 Sigma70 -7.5 -239.5 tsx
cccgtcatttTGTTACTCTGCTTACAtcacctggat
432245 432260 [BCE], [GEA] [6], [7]


Alignment and PSSM for DeoR TFBSs    

Aligned TFBS of DeoR   
  Sequence
  ATGTAAGCAGAGTAACAAA
  ATCCCTTCTTTTTCACACA
  ATGATAAAATTTTCACAAA
  ATGTTAGAATTCTAACACA
  AATCTGCCTTACCCACAGC
  CTGCTTCCAGTGCCAGAAA
  ATGTTAGAATACTAACAAA

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

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    

 [BPP] Binding of purified proteins

 [IPI] Inferred from physical interaction

 [HIBSCS] Human inference based on similarity to consensus sequences

 [SM] Site mutation

 [GEA] Gene expression analysis

 [BCE] 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] 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

 [5] 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

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

 [7] 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

 [8] 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

 [9] 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):205-11

 [10] 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):37-44

 [11] Dandanell G., Hammer K., 1991, deoP1 promoter and operator mutants in Escherichia coli: isolation and characterization., Mol Microbiol. 5(10):2371-6

 [12] 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

 [13] 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

 [14] 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

 [15] 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):1175-83

 [16] Dandanell G., Norris K., Hammer K., 1991, Long-distance deoR regulation of gene expression in Escherichia coli., Ann N Y Acad Sci. 646:19-30

 [17] 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):3333-8

 [18] 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

 [19] Dandanell G., 1992, DeoR repression at-a-distance only weakly responds to changes in interoperator separation and DNA topology., Nucleic Acids Res. 20(20):5407-12

 [20] 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):129-33



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