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RutR DNA-binding transcriptional dual regulator

Synonyms: RutR, RutR-Thymine, RutR-uracil
RutR regulates genes directly or indirectly involved in the complex pathway of pyrimidine metabolism [1, 5] and also plays a role in regulation of the genes for degradation of purines and genes for maintenance of pH homeostasis [1].
This protein belongs to the TetR family, whose members have an N-terminal DNA-binding domain that contains a helix-turn-helix motif and a C-terminal domain for dimerization and ligand binding [6].
RutR recognizes and binds a 16-bp (7-2-7) inverted repeat consensus sequence [1, 4], where the central A/T nucleotide in each half-site appears to be the most important for the site [4]. This binding is inhibited when uracil and thymine bind to RutR, although the effect is greater for uracil than for thymine [1].
It has been demonstrated, in E.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
RutR Functional   Apo [BPP], [IDA], [IEP] [1]
RutR-Thymine Non-Functional Allosteric Holo [BPP], [IDA], [IEP] [1]
RutR-uracil Non-Functional Allosteric Holo [BPP], [IDA], [IEP] [1]
Evolutionary Family: TetR/AcrR
Connectivity class: Local Regulator
Gene name: rutR
  Genome position: 1074242-1074880
  Length: 639 bp / 212 aa
Operon name: rutR
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) carA, carB, fepB, gadW, gadX, gloA, nemA, nemR, pdeR, rutA, rutB, rutC, rutD, rutE, rutF, rutG, rutR
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
nitrogen metabolism (6)
Transcription related (4)
arginine (2)
pyrimidine biosynthesis (2)
repressor (2)
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Regulated operon(s) carAB, fepB, gadAXW, nemRA-gloA, pdeR, rutABCDEFG, rutR
First gene in the operon(s) carA, fepB, gadX, gadX, nemR, nemR, pdeR, rutA, rutR
Simple and complex regulons ArcA,NtrC,PhoP,RutR
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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
  RutR activator carAp1 Sigma70 -184.0 -284.5 carA, carB
29359 29374 [AIBSCS], [BPP], [GEA], [SM] [1], [2], [3], [4]
  RutR repressor fepBp Sigma70 172.5 -45.5 fepB
624548 624563 [AIBSCS], [BPP], [GEA] [4]
  RutR repressor gadXp Sigma38 -824.5 -853.5 gadX, gadW
3666654 3666673 [BPP], [GEA] [1]
  RutR repressor gmrp Sigma38 nd nd pdeR nd nd [GEA] [1]
  RutR repressor nemRp Sigma70 -20.5 -22.5 nemR, nemA, gloA
1725993 1726008 [AIBSCS], [BPP], [GEA] [4]
  RutR repressor rutAp Sigma54 -102.5 -117.5 rutA, rutB, rutC, rutD, rutE, rutF, rutG
1074120 1074137 [AIBSCS], [BPP], [GEA], [SM] [1], [3], [4]
  RutR repressor rutRp2 Sigma70 16.5 -113.5 rutR
1074120 1074137 [AIBSCS], [BPP], [GEA], [SM] [1], [3], [4]

Alignment and PSSM for RutR TFBSs    

Aligned TFBS of RutR   

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

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


 [BPP] Binding of purified proteins

 [IDA] Inferred from direct assay

 [IEP] Inferred from expression pattern

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [GEA] Gene expression analysis

 [SM] Site mutation


 [1] Shimada T., Hirao K., Kori A., Yamamoto K., Ishihama A., 2007, RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines., Mol Microbiol. 66(3):744-57

 [2] Nguyen Le Minh P., Bervoets I., Maes D., Charlier D., 2010, The protein-DNA contacts in RutR{middle dot}carAB operator complexes., Nucleic Acids Res

 [3] Nguyen Le Minh P., de Cima S., Bervoets I., Maes D., Rubio V., Charlier D., 2015, Ligand binding specificity of RutR, a member of the TetR family of transcription regulators in Escherichia coli., FEBS Open Bio. 5:76-84

 [4] Shimada T., Ishihama A., Busby SJ., Grainger DC., 2008, The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions., Nucleic Acids Res. 36(12):3950-5

 [5] Loh KD., Gyaneshwar P., Markenscoff Papadimitriou E., Fong R., Kim KS., Parales R., Zhou Z., Inwood W., Kustu S., 2006, A previously undescribed pathway for pyrimidine catabolism., Proc Natl Acad Sci U S A. 103(13):5114-9

 [6] Ramos JL., Martinez-Bueno M., Molina-Henares AJ., Teran W., Watanabe K., Zhang X., Gallegos MT., Brennan R., Tobes R., 2005, The TetR family of transcriptional repressors., Microbiol Mol Biol Rev. 69(2):326-56