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NemR DNA-binding transcriptional repressor

Synonyms: NemR
Summary:
N-ethylmaleimide reductase repressor, [1] represses the nemA gene, which is involved in reductive degradation of N-ethylmaleimide (NEM) and other toxic nitrous compounds, and it also represses its own expression. NemR belongs to the TetR family of HTH-type DNA-binding transcription factors [2, 3]
NemR binds to a region 16 bp in length, and its consensus is a palindromic sequence, TAGACCnnnnGGTCTA, which is referred as the NemR box [1] This box sequence, TAGACCnnnnGGTCTA, is close to the recognition sequence, TTGACCAnnTGGTCAA, of RutR (the RutR box). RutR can bind upstream of the nemRA operon; however, it does not play an important role in regulation of nemRA expression in vivo [1]
Presently, the nemRA operon is the unique member of the NemR regulon. Based on genomic SELEX and gene expression analyses, NemR could be affecting other genes, such as ydhF-ydhL, gloA, sapABCDF, yeaU, pck yeaT, and yhgE [1] however, the regulation of the genes under control of NemR requires more detailed studies before it can be solved.
The NemRA system plays an important role in Escherichia coli survival in the presence of the toxic compound N-ethylmaleimide (NEM), which is the inducer for depression of the nemRA operon [1] It has been experimentally verified that methylglyoxal (MG) and not NEM is the real inducer for the nemRA operon [4] This induction was determined by ChIP-chip analysis with DNA-RNAP occupancy when cells were exposed to growth-inhibitory concentrations of MG [4] NemR is a transcriptional repressor that is sensitive to HOCl and related reactive chlorine species (RCS), and its gene products contribute to increased bleach resistance by detoxifying reactive electrophiles produced during this process [5]
The NemR regulator is controlled by alkylation of one or more of its Cys residues.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
NemR     nd nd
Evolutionary Family: TetR/AcrR
Connectivity class: Local Regulator
Gene name: nemR
  Genome position: 1726023-1726622
  Length: 600 bp / 199 aa
Operon name: nemRA-gloA
TU(s) encoding the TF:
Transcription unit        Promoter
nemR
null
nemRA
nemRp
nemRA-gloA
nemRp


Regulon       
Regulated gene(s) gloA, nemA, nemR
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
methylglyoxal metabolism (1)
unassigned reversible reactions (1)
detoxification (1)
transcriptional level (1)
Regulated operon(s) nemRA-gloA
First gene in the operon(s) nemR, nemR
Simple and complex regulons NemR,RutR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[NemR,-](1)


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
  NemR repressor nemRp Sigma70 -20.5 -22.5 nemR, nemA, gloA
ttgcttgcacTAGACCGACTGGTCTActacactcca
1725993 1726008 [AIBSCS], [BPP], [GEA] [1]


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


Evidence    

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis



Reference(s)    

 [1] Umezawa Y., Shimada T., Kori A., Yamada K., Ishihama A., 2008, Uncharacterized Transcription Factor YdhM is the Regulator of the nemA Gene Encoding N-ethylmaleimide (NEM) Reductase., J Bacteriol. 190(17):5890-7

 [2] Riley M., Abe T., Arnaud MB., Berlyn MK., Blattner FR., Chaudhuri RR., Glasner JD., Horiuchi T., Keseler IM., Kosuge T., Mori H., Perna NT., Plunkett G., Rudd KE., Serres MH., Thomas GH., Thomson NR., Wishart D., Wanner BL., 2006, Escherichia coli K-12: a cooperatively developed annotation snapshot--2005., Nucleic Acids Res. 34(1):1-9

 [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] Ozyamak E., de Almeida C., de Moura AP., Miller S., Booth IR., 2013, Integrated stress response of Escherichia coli to methylglyoxal: transcriptional readthrough from the nemRA operon enhances protection through increased expression of glyoxalase I., Mol Microbiol. 88(5):936-50

 [5] Gray MJ., Wholey WY., Parker BW., Kim M., Jakob U., 2013, NemR is a bleach-sensing transcription factor., J Biol Chem. 288(19):13789-98

 [6] Lee C., Shin J., Park C., 2013, Novel regulatory system nemRA-gloA for electrophile reduction in Escherichia coli K-12., Mol Microbiol. 88(2):395-412

 [7] Gray MJ., Li Y., Leichert LI., Xu Z., Jakob U., 2015, Does the Transcription Factor NemR Use a Regulatory Sulfenamide Bond to Sense Bleach?, Antioxid Redox Signal. 23(9):747-54

 [8] 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



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