RegulonDB RegulonDB 10.8: Operon Form
   

nemRA-gloA operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: nemRA-gloA
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: nemRA-gloA
Gene(s): nemR, nemA, gloA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ITC] Inferred through co-regulation
[LTED] Length of transcript experimentally determined
Reference(s): [1] Lee C., et al., 2013
[2] Ozyamak E., et al., 2013
Promoter
Name: nemRp
+1: 1726021
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 2
Sequence: gttaatgtccaaagtagcaactttgcttgcactagaccgactggtctactacactccaacGcatgaacaaacacaccgaac
                       -35                        -10       +1                   
Evidence: [TIM]
Reference(s): [3] Umezawa Y., et al., 2008
TF binding sites (TFBSs)
[NemR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NemR1 repressor nemRp 1725993 1726009 -20.5 ttgcttgcacTAGACCGACTGGTCTACtacactccaa nd [AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [3]
[RutR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal RutR repressor nemRp 1725993 1726009 -20.5 ttgcttgcacTAGACCGACTGGTCTACtacactccaa nd [AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [4]
Note(s): 1The role for the nemRA-gloA operon is to sense electrophiles Lee C,2013
Bleach upregulates the NemR-controlled genes gloA and nemA and increases bacterial survival in bleach, and this finding provided the first evidence that resistance toward bleach relies on the ability of bacteria to detoxify methylglyoxal and reactive electrophiles 235361881The role for the nemRA-gloA operon is to sense electrophiles Lee C,2013
Bleach upregulates the NemR-controlled genes gloA and nemA and increases bacterial survival in bleach, and this finding provided the first evidence that resistance toward bleach relies on the ability of bacteria to detoxify methylglyoxal and reactive electrophiles 23536188


Transcription unit          
Name: nemRA
Gene(s): nemR, nemA   Genome Browser M3D Gene expression COLOMBOS
Note(s): nemRA and gloA transcripts appear to be generated from the processing of the nemRA-gloA transcript by RNase E CITS:[23506073]|.
Evidence: [ITC] Inferred through co-regulation
[LTED] Length of transcript experimentally determined
Reference(s): [1] Lee C., et al., 2013
[3] Umezawa Y., et al., 2008
Promoter
Name: nemRp
+1: 1726021
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 2
Sequence: gttaatgtccaaagtagcaactttgcttgcactagaccgactggtctactacactccaacGcatgaacaaacacaccgaac
                       -35                        -10       +1                   
Evidence: [TIM]
Reference(s): [3] Umezawa Y., et al., 2008
TF binding sites (TFBSs)
[NemR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NemR1 repressor nemRp 1725993 1726009 -20.5 ttgcttgcacTAGACCGACTGGTCTACtacactccaa nd [AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [3]
[RutR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal RutR repressor nemRp 1725993 1726009 -20.5 ttgcttgcacTAGACCGACTGGTCTACtacactccaa nd [AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [4]
Note(s): 1The role for the nemRA-gloA operon is to sense electrophiles Lee C,2013
Bleach upregulates the NemR-controlled genes gloA and nemA and increases bacterial survival in bleach, and this finding provided the first evidence that resistance toward bleach relies on the ability of bacteria to detoxify methylglyoxal and reactive electrophiles 235361881The role for the nemRA-gloA operon is to sense electrophiles Lee C,2013
Bleach upregulates the NemR-controlled genes gloA and nemA and increases bacterial survival in bleach, and this finding provided the first evidence that resistance toward bleach relies on the ability of bacteria to detoxify methylglyoxal and reactive electrophiles 23536188


Transcription unit       
Name: gloA
Gene(s): gloA   Genome Browser M3D Gene expression COLOMBOS
Note(s): nemRA and gloA transcripts appear to be generated from the processing of the nemRA-gloA transcript by RNase E CITS:[23506073]|.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Lee C., et al., 2013
Promoter
Name: gloAp
+1: 1727801
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 36
Sequence: ttacccgacgttgtaatccaacattgcgagcggcgtaaagccgccgctatactaaaacaaCattttgaatctgttagccat
                        -35                     -10         +1                   
Evidence: [HIPP]
Reference(s): [5] Clugston SL., et al., 1998


Transcription unit       
Name: ydhM
Gene(s): nemR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IHBCE] Inferred by a human based on computational evidence


Transcription unit       
Name: nemA
Gene(s): nemA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Although nemA and gloA are involved in the same metabolic pathway (degradation of toxic compounds for detoxification and reuse as nitrogen sources), it is not yet known whether these two genes are organized into a single operon Umezawa Y,2008
Evidence: [IHBCE] Inferred by a human based on computational evidence


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -17.5 1726060 1726107 gcgaacatctCCTGGCGACGGGCGAGCAACTTTGCCTGCAACGTGGATTCACCGGGAtggggctaag
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [TIM] Transcription initiation mapping

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

 [CV(GEA)] cross validation(GEA)

 [GEA] Gene expression analysis

 [HIPP] Human inference of promoter position


Reference(s)    

 [1] 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

 [2] 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

 [3] 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

 [4] Shimada T., Ishihama A., Busby SJ., Grainger DC., 2008, The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions., Nucleic Acids Res 36(12):3950-5

 [5] Clugston SL., Barnard JF., Kinach R., Miedema D., Ruman R., Daub E., Honek JF., 1998, Overproduction and characterization of a dimeric non-zinc glyoxalase I from Escherichia coli: evidence for optimal activation by nickel ions., Biochemistry 37(24):8754-63

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