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SutR DNA-binding transcriptional dual regulator

Synonyms: SutR
Summary:
SutR (formely YdcN) regulates a set of genes involved in the utilization of sulfur [4]. SutR is a small transcription factor with a helix-turn-helix (HTH) motif and belongs to the Cro-C1-type superfamily []. Based on genomic SELEX screen analysis, it was identified as a highly probable regulator for 12-16 operons involved in various steps of sulfur utilization, playing an important role in the coordination of expression of the genes involved in this metabolic pathway [4]. Genes identified by SELEX analysis include the following: paoC, xseB, thiI, ydcO, sutR, ynfG, ydiY, pfkB, fliZ, ypfN, yfgM, yfiC, tdcF, cysE, and yjcS. Four peaks were located in type A spacers of divergent transcription units (TUs), and eight peaks were identified within type B spacers upstream of one TU but downstream of the preceding TUs [4]. A direct repeat GCGT motif of the SutR box was found in the yfiC, ydcO, and sutR genes, which are associated with group A spacers, and the palindromic sequence of GCGT(Nn)ACGC was identified for yfiC, thiI, ydcO, and sutR genes [4].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
SutR Functional   [AIFS], [APPHINH], [IEP] [1], [2], [3], [4]
Evolutionary Family: HTH_3
Connectivity class: Local Regulator
Gene name: sutR
  Genome position: 1506172-1506708
  Length: 537 bp / 178 aa
Operon name: sutR
TU(s) encoding the TF:
Transcription unit        Promoter
sutR
sutRp


Regulon       
Regulated gene(s) cysE, fliA, fliZ, sutR, tcyJ
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
cysteine (1)
Transcription related (1)
sigma factors, anti-sigmafactors (1)
stimulon (1)
motility, chemotaxis, energytaxis (aerotaxis, redoxtaxis etc) (1)
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Regulated operon(s) cysE, fliAZ-tcyJ, sutR
First gene in the operon(s) cysE, fliA, sutR
Simple and complex regulons CsgD,FlhDC,H-NS,IHF,MatA,NsrR,SutR
SutR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[SutR,+](1)
[SutR,-](1)


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
  SutR repressor cysEp nd nd 3782562.0 cysE nd nd [BPP], [GEA] [4]
  SutR repressor fliAp1 Sigma70 nd 2001789.0 fliA, fliZ, tcyJ nd nd [AIBSCS], [BPP], [GEA] [4]
  SutR activator sutRp Sigma70 -54.5 -76.0 sutR
ctacggtgccTGTACGCTATAACGCACGAGGTgactatgcgt
1506085 1506107 [BPP], [GEA], [HIBSCS] [4]
  SutR repressor sutRp Sigma70 -16.5 -38.0 sutR
agcatttgtcCGTTATAACGCACAAGTGataaacttcc
1506125 1506143 [BPP], [GEA], [HIBSCS] [4]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  SutR repressor ydcO nd nd 1506085 1506107 [AISGDTU] nd
Other High-throughput regulatory interactions with weak evidence


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
Promoter-target gene evolutionary conservation


Evidence    

 [AIFS] Automated inference of function from sequence

 [APPHINH] Assay of protein purified to homogeneity from its native host

 [IEP] Inferred from expression pattern

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [HIBSCS] Human inference based on similarity to consensus sequences

 [AISGDTU] Automated inference that a single-gene directon is a transcription unit



Reference(s)    

 [1] Paradis-Bleau C., Kritikos G., Orlova K., Typas A., Bernhardt TG., 2014, A genome-wide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism., PLoS Genet 10(1):e1004056

 [2] Perez-Rueda E., Collado-Vides J., 2000, The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12., Nucleic Acids Res 28(8):1838-47

 [3] Perez-Rueda E., Collado-Vides J., Segovia L., 2004, Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea., Comput Biol Chem 28(5-6):341-50

 [4] Yamamoto K., Nakano M., Ishihama A., 2015, Regulatory role of transcription factor SutR (YdcN) in sulfur utilization in Escherichia coli., Microbiology 161(Pt 1):99-111



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