RegulonDB RegulonDB 11.1: 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: [IC-ADJ-GENES-SAME-BIO-PROCESS] 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 Sigmulon
Distance from start of the gene: 66
Sequence: tcatacccttctattgatatggattaataattcttaacccaaaatgggtagactccctctAttgttagcgcgctaaatatt
                        -35                      -10        +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF]
[EXP-IDA-RNA-POLYMERASE-FOOTPRINTING]
Reference(s): [2] Huerta AM., et al., 2003
[3] Kang Y., et al., 2005
[4] Maciag A., et al., 2011
[5] Xu M., et al., 2009
TF binding sites (TFBSs)
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR activator ynfEp 1657956 1657970 -40.5 tacccttctaTTGATATGGATTAATaattcttaac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3], [5], [6]
[NarL,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarL-phosphorylated repressor ynfEp 1657977 1657983 -23.0 taataattctTAACCCAaaatgggtag nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [5]
proximal NarL-phosphorylated repressor ynfEp 1657986 1657992 -14.0 ttaacccaaaATGGGTAgactccctct nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [5]


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: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Lubitz SP., et al., 2003
Promoter
Name: ynfEp2
+1: 1658003
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 66
Sequence: tcatacccttctattgatatggattaataattcttaacccaaaatgggtagactccctctAttgttagcgcgctaaatatt
                        -35                 -10             +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF]
[EXP-IDA-RNA-POLYMERASE-FOOTPRINTING]
Reference(s): [2] Huerta AM., et al., 2003
[3] Kang Y., et al., 2005
[4] Maciag A., et al., 2011
[5] Xu M., et al., 2009
TF binding sites (TFBSs)
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR activator ynfEp2 1657956 1657970 -40.5 tacccttctaTTGATATGGATTAATaattcttaac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3], [5], [6]
[NarL,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarL-phosphorylated repressor ynfEp2 1657977 1657983 -23.0 taataattctTAACCCAaaatgggtag nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [5]
proximal NarL-phosphorylated repressor ynfEp2 1657986 1657992 -14.0 ttaacccaaaATGGGTAgactccctct nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [5]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

 [COMP-HINF] Inferred by a human based on computational evidence

 [EXP-IDA-RNA-POLYMERASE-FOOTPRINTING] RNA polymerase footprinting

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

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

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

 [EXP-IMP-SITE-MUTATION] 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] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [3] 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

 [4] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

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

 [6] 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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