RegulonDB RegulonDB 10.8: Operon Form
   

ynfEFGH-dmsD operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: ynfEFGH-dmsD
Synonym(s): ynfEFGHI
Gene(s): ynfE, ynfF, ynfG, ynfH, dmsD   Genome Browser M3D Gene expression COLOMBOS
Note(s): These genes are contiguous and their products participate in the same biological process (dimethyl sulfoxide reduction); therefore, the ynfEFGH-dmsD operon was inferred Lubitz SP,2003
Evidence: [PAGTSBP] Products of adjacent genes in the same biological process
Reference(s): [1] Lubitz SP., et al., 2003
Promoter
Name: ynfEp
+1: 1658003
Sigma Factor: Sigma70, Sigma38
Distance from start of the gene: 66
Sequence: tcatacccttctattgatatggattaataattcttaacccaaaatgggtagactccctctAttgttagcgcgctaaatatt
                        -35                 -10             +1                   
Evidence: [AIPP]
[RPF]
Reference(s): [2] Kang Y., et al., 2005
[3] Xu M., et al., 2009
TF binding sites (TFBSs)
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR activator ynfEp 1657956 1657970 -40.5 tacccttctaTTGATATGGATTAATaattcttaac nd [AIBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [2], [3], [4]
[NarL,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarL-Phosphorylated repressor ynfEp 1657972 1657987 -23.0 tggattaataATTCTTAACCCAAAATgggtagactc nd [AIBSCS], [BPP] [3]
proximal NarL-Phosphorylated repressor ynfEp 1657981 1657996 -14.0 aattcttaacCCAAAATGGGTAGACTccctctattg nd [AIBSCS], [BPP] [3]


Evidence    

 [AIPP] Automated inference of promoter position

 [RPF] RNA polymerase footprinting

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

 [CV(CHIP-SV/GEA/ROMA)] cross validation(CHIP-SV/GEA/ROMA)

 [CV(CHIP-SV/SM)] cross validation(CHIP-SV/SM)

 [CV(GEA/ROMA)] cross validation(GEA/ROMA)

 [CV(GEA/ROMA/SM)] cross validation(GEA/ROMA/SM)

 [GEA] Gene expression analysis

 [SM] Site mutation


Reference(s)    

 [1] Lubitz SP., Weiner JH., 2003, The Escherichia coli ynfEFGHI operon encodes polypeptides which are paralogues of dimethyl sulfoxide reductase (DmsABC)., Arch Biochem Biophys 418(2):205-16

 [2] Kang Y., Weber KD., Qiu Y., Kiley PJ., Blattner FR., 2005, Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function., J Bacteriol 187(3):1135-60

 [3] Xu M., Busby SJ., Browning DF., 2009, Activation and repression at the Escherichia coli ynfEFGHI operon promoter., J Bacteriol 191(9):3172-6

 [4] Constantinidou C., Hobman JL., Griffiths L., Patel MD., Penn CW., Cole JA., Overton TW., 2006, A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth., J Biol Chem 281(8):4802-15

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