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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 [1]. SutR is a small transcription factor with a helix-turn-helix (HTH) motif and belongs to the Cro-C1-type superfamily [3]. 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 [1]. 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 [1]. 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 [1].
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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
SutR Functional   nd nd nd
Evolutionary Family: HTH_3
TFBs symmetry: inverted-repeat
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,-](3)
[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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
  SutR repressor cysEp nd nd nd cysE
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  SutR repressor fliAp1 Sigma70 nd nd fliA, fliZ, tcyJ
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  SutR activator sutRp Sigma70 -54.5 -76.5 sutR
acgcatagtcACCTCGTGCGTTATAGCGTACAGgcaccgtagc
 1506085 1506107 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [1], [2]
  SutR repressor sutRp Sigma70 -16.5 -38.5 sutR
agcatttgtcCGTTATAACGCACAAGTGAtaaacttccg
 1506125 1506143 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Center Position Growth Condition Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  SutR repressor ydcO Transcription-Unit nd
acgcatagtcACCTCGTGCGTTATAGCGTACAGgcaccgtagc
1506085 1506107 1506095.5 nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1]
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    

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

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-CHIP-EXO] high throughput ChIP-exo evidence


Reference(s)    

 [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

 [2] Gao Y., Lim HG., Verkler H., Szubin R., Quach D., Rodionova I., Chen K., Yurkovich JT., Cho BK., Palsson BO., 2021, Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo., Nucleic Acids Res 49(17):9696-9710

 [3] Ishihama A, 2010, Prokaryotic genome regulation: multifactor promoters, multitarget regulators and hierarchic networks., FEMS Microbiol Rev, 34(5):628 10.1111/j.1574-6976.2010.00227.x


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