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MngR DNA-binding transcriptional repressor

Synonyms: MngR
Summary:
According to microarray analysis, the "mannosyl-d-glycerate regulator," MngR, regulates only two genes, mngA and mngB, involved in 2-O-α-mannosyl-D-glycerate utilization [2]. This regulator also autoregulates its own synthesis [1]. Previously, MngR, also called FarR, for fatty acyl-responsive regulator, had been proposed to regulate genes involved in the citric acid cycle in response to fatty acids, which release MngR from its DNA-binding site [1]. However, when it was found that this protein only regulates two genes, the suggestion was rejected and it was proposed that probably high concentrations of fatty acids could degrade the protein instead of it binding to the regulator [2]. MngR belongs to the GntR family of transcriptional regulators and has a helix-turn-helix motif in the N-terminal domain and a UbiC transcription regulator-associated domain that is predicted to be a sensor for small molecules.
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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
MngR Functional   nd nd nd
Evolutionary Family: GntR
TFBs length: 22
Sensing class: Using internal synthesized signals
Connectivity class: Local Regulator
Gene name: mngR
  Genome position: 765153-765875
  Length: 723 bp / 240 aa
Operon name: mngR
TU(s) encoding the TF:
Transcription unit        Promoter
mngR
mngRp


Regulon       
Regulated gene(s) mngA, mngB, mngR
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (2)
posttranslational modification (1)
Phosphotransferase Systems (PEP-dependent PTS) (1)
temperature extremes (1)
membrane (1)
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Regulated operon(s) mngAB, mngR
First gene in the operon(s) mngA, mngR
Simple and complex regulons MngR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[MngR,-](2)


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
  MngR repressor mngAp Sigma32 90.5 -83.5 mngA, mngB
agtatctcatTAATACGAATTTAACCATTATGcccgataaat
 765890 765911 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1], [2], [2]
  MngR repressor mngAp Sigma32 134.5 -39.5 mngA, mngB
atcctgtaaaTAATACAAATACAATACAAATAatttcaatca
 765934 765955 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [1], [2], [2], [3]
  MngR repressor mngRp Sigma70 -18.5 -69.5 mngR
tgattgaaatTATTTGTATTGTATTTGTATTAtttacaggat
 765934 765955 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [2], [2], [3]
  MngR repressor mngRp Sigma70 26.5 -25.5 mngR
atttatcgggCATAATGGTTAAATTCGTATTAatgagatact
 765890 765911 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [2], [2]


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


Evidence    

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

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

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

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing


Reference(s)    

 [1] Quail MA., Dempsey CE., Guest JR., 1994, Identification of a fatty acyl responsive regulator (FarR) in Escherichia coli., FEBS Lett 356(2-3):183-7

 [2] Sampaio MM., Chevance F., Dippel R., Eppler T., Schlegel A., Boos W., Lu YJ., Rock CO., 2004, Phosphotransferase-mediated transport of the osmolyte 2-O-alpha-mannosyl-D-glycerate in Escherichia coli occurs by the product of the mngA (hrsA) gene and is regulated by the mngR (farR) gene product acting as repressor., J Biol Chem 279(7):5537-48

 [3] Baumgart LA, Lee JE, Salamov A, Dilworth DJ, Na H, Mingay M, Blow MJ, Zhang Y, Yoshinaga Y, Daum CG, O'Malley RC, 2021, Persistence and plasticity in bacterial gene regulation., Nat Methods, 18(12):1499 10.1038/s41592-021-01312-2

 [4] Aravind L., Anantharaman V., 2003, HutC/FarR-like bacterial transcription factors of the GntR family contain a small molecule-binding domain of the chorismate lyase fold., FEMS Microbiol Lett 222(1):17-23

 [5] Krisko A, Copic T, Gabaldón T, Lehner B, Supek F, 2014, Inferring gene function from evolutionary change in signatures of translation efficiency., Genome Biol, 15(3):R44 10.1186/gb-2014-15-3-r44


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