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SutR DNA-binding transcriptional dual regulator

Synonyms: SutR
SutR (formely YdcN) regulates a set of genes involved in the utilization of sulfur |CITS: [25406449]|. SutR is a small transcription factor with a helix-turn-helix (HTH) motif and belongs to the Cro-C1-type superfamily |CITS: [20491932]|. 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 |CITS: [25406449]|.
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 |CITS: [25406449]|.
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 |CITS: [25406449]|. On the other hand, in the group B spacers, the direct repeat GCGT was identified upstream of the tdcF, yfgM, and ynfG genes while the palindromic GCGT(Nn)ACGC sequence was found in the fliZ gene |CITS: [25406449]|.
Genes identified by microarray analysis include several for repression by SutR, sutR, ydcO, pfkB, fliZ, and cysE, while activation of SutR was identified only for ypfN |CITS: [25406449]|.
The following genes were identified via chromatin immunoprecipitation (ChIP) in vivo: sutR, cysE, and fliZ |CITS: [25406449]|.
The highest level of SutR binding was found in the spacer in the ydcO-sutR region.
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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     nd nd
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

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,MatA,NsrR,SutR
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
  SutR repressor cysEp nd nd nd cysE nd nd [BPP], [GEA] [1]
  SutR repressor fliAp1 Sigma70 nd nd fliA, fliZ, tcyJ nd nd [AIBSCS], [BPP], [GEA] [1]
  SutR activator sutRp Sigma70 -54.5 -76.5 sutR
1506085 1506106 [BPP], [GEA], [HIBSCS] [1]
  SutR repressor sutRp Sigma70 -16.5 -38.5 sutR
1506125 1506142 [BPP], [GEA], [HIBSCS] [1]

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


 [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


 [1] 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