RegulonDB RegulonDB 10.7: Operon Form
   

dmsABC operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: dmsABC
Synonym(s): OP00026, dms
Gene(s): dmsA, dmsB, dmsC   Genome Browser M3D Gene expression COLOMBOS
Note(s): The regulatory effect of FlhDC in dmsABC operon transcription has been proved only by microarray analysis by |CITS: [11287152]|
dmsABC was significantly upregulated in response to quinonas anthraquinone-2-sulfonate (AQSim) reduction and azo dye acid red 18 (AR 18) decolorization under anaerobic conditions |CITS: [23820558]|.
Reference(s): [1] Bilous PT., et al., 1988
[2] Tseng CP., et al., 1996
[3] Tseng CP., et al., 1994
Promoter
Name: dmsAp1
+1: 940823
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 136
Sequence: ttttgtctccctttgataccgaacaataattactcctcacttacacgtaatactactttcGagtgaaaatctacctatctc
                          -35                   -10         +1                   
Evidence: [NAS]
[RS-EPT-CBR]
[TIM]
Reference(s): [4] Bearson SM., et al., 2002
[5] Salgado H, et al., 2012
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR1 activator dmsAp1 940775 940788 -41.5 ttgtctccctTTGATACCGAACAAtaattactcc nd [BCE], [BPP], [GEA], [SM] [4], [6], [7], [8]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis repressor dmsAp1 940783 940797 -33.0 ctttgataccGAACAATAATTACTCctcacttaca nd [AIBSCS], [GEA] [9]
proximal Fis repressor dmsAp1 940821 940840 8.0 aatactacttTCGAGTGAAAATCTACCTATctctttgatt nd [AIBSCS], [GEA] [9]
remote Fis repressor dmsAp1 940874 940888 59.0 atgtatacaaGCCTATATAGCGAACtgctatagaa nd [AIBSCS], [GEA] [9]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarL-Phosphorylated1 repressor dmsAp1 940788 940803 -27.0 ataccgaacaATAATTACTCCTCACTtacacgtaat nd [BCE], [BPP] [4], [8]
proximal NarL-Phosphorylated2 repressor dmsAp1 940808 940823 -7.0 ctcacttacaCGTAATACTACTTTCGagtgaaaatc nd [BCE], [BPP] [4], [8]
proximal NarL-Phosphorylated3 repressor dmsAp1 940829 940844 15.0 tttcgagtgaAAATCTACCTATCTCTttgattttca nd [APIORCISFBSCS], [BPP] [4], [8]
Note(s): 1The spacing between the FNR site and the RNA polymerase site is critical in the expression of dmsA .
FNR activates dmsA expression under anaerobic environmental conditions Bearson SM,2002and under mock ionizing radiation conditions Bruckbauer ST, Trimarco JD, Henry C, Wood EA, Battista JR, Cox MM,2019.1There are several putative NarL-binding sites, but only three of them have a NarL consensus with only one
mismatch Bearson SM,2002
2There are several putative NarL-binding sites, but only three of them have a NarL consensus with only one
mismatch Bearson SM,2002
3There are several putative NarL-binding sites, but only three of them have a NarL consensus with only one
mismatch Bearson SM,20021The spacing between the FNR site and the RNA polymerase site is critical in the expression of dmsA .
FNR activates dmsA expression under anaerobic environmental conditions Bearson SM,2002and under mock ionizing radiation conditions Bruckbauer ST, Trimarco JD, Henry C, Wood EA, Battista JR, Cox MM,2019.
3There are several putative NarL-binding sites, but only three of them have a NarL consensus with only one
mismatch Bearson SM,2002
4There are several putative NarL-binding sites, but only three of them have a NarL consensus with only one
mismatch Bearson SM,2002
6There are several putative NarL-binding sites, but only three of them have a NarL consensus with only one
mismatch Bearson SM,2002


Transcription unit          
Name: dmsABC
Gene(s): dmsA, dmsB, dmsC   Genome Browser M3D Gene expression COLOMBOS
Note(s): The regulatory effect of FlhDC in dmsABC operon transcription has been proved only by microarray analysis by |CITS: [11287152]|
Reference(s): [1] Bilous PT., et al., 1988
[2] Tseng CP., et al., 1996
[3] Tseng CP., et al., 1994
Promoter
Name: dmsAp2
+1: 940878
Distance from start of the gene: 81
Sequence: ctttcgagtgaaaatctacctatctctttgattttcaaattattcgatgtatacaagcctAtatagcgaactgctatagaa
Evidence: [HIPP]
Reference(s): [10] McNicholas PM., et al., 1998
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF repressor dmsAp2 940850 940862 -22.0 tctctttgatTTTCAAATTATTCgatgtataca nd [APIORCISFBSCS], [BPP], [GEA] [10]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal ModE-MoO42- repressor dmsAp2 940861 940884 -5.0 ttcaaattatTCGATGTATACAAGCCTATATAGCgaactgctat nd [APIORCISFBSCS], [BPP], [GEA], [SM] [10]


Transcription unit       
Name: dmsC
Gene(s): dmsC   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IEP] Inferred from expression pattern
Reference(s): [11] Li Z., et al., 2019
Promoter
Name: dmsCp
+1: 943957
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 76
Sequence: catggcgatctggcggccgttgcgccgttgccgcgagctcactttaccaaaccgaatattGtgatcaaacccaatgccaat
                         -35                        -10     +1                   
Evidence: [RE]
[TIM]
Reference(s): [11] Li Z., et al., 2019




Reference(s)    

 [1] Bilous PT., Cole ST., Anderson WF., Weiner JH., 1988, Nucleotide sequence of the dmsABC operon encoding the anaerobic dimethylsulphoxide reductase of Escherichia coli., Mol Microbiol 2(6):785-95

 [2] Tseng CP., Albrecht J., Gunsalus RP., 1996, Effect of microaerophilic cell growth conditions on expression of the aerobic (cyoABCDE and cydAB) and anaerobic (narGHJI, frdABCD, and dmsABC) respiratory pathway genes in Escherichia coli., J Bacteriol 178(4):1094-8

 [3] Tseng CP., Hansen AK., Cotter P., Gunsalus RP., 1994, Effect of cell growth rate on expression of the anaerobic respiratory pathway operons frdABCD, dmsABC, and narGHJI of Escherichia coli., J Bacteriol 176(21):6599-605

 [4] Bearson SM., Albrecht JA., Gunsalus RP., 2002, Oxygen and nitrate-dependent regulation of dmsABC operon expression in Escherichia coli: sites for Fnr and NarL protein interactions., BMC Microbiol 2(1):13

 [5] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [6] Lamberg KE., Kiley PJ., 2000, FNR-dependent activation of the class II dmsA and narG promoters of Escherichia coli requires FNR-activating regions 1 and 3., Mol Microbiol 38(4):817-27

 [7] Melville SB., Gunsalus RP., 1996, Isolation of an oxygen-sensitive FNR protein of Escherichia coli: interaction at activator and repressor sites of FNR-controlled genes., Proc Natl Acad Sci U S A 93(3):1226-31

 [8] Tyson KL., Bell AI., Cole JA., Busby SJ., 1993, Definition of nitrite and nitrate response elements at the anaerobically inducible Escherichia coli nirB promoter: interactions between FNR and NarL., Mol Microbiol 7(1):151-7

 [9] Bradley MD., Beach MB., de Koning AP., Pratt TS., Osuna R., 2007, Effects of Fis on Escherichia coli gene expression during different growth stages., Microbiology 153(Pt 9):2922-40

 [10] McNicholas PM., Chiang RC., Gunsalus RP., 1998, Anaerobic regulation of the Escherichia coli dmsABC operon requires the molybdate-responsive regulator ModE., Mol Microbiol 27(1):197-208

 [11] Li Z., Pan Q., Xiao Y., Fang X., Shi R., Fu C., Danchin A., You C., 2019, Deciphering global gene expression and regulation strategy in Escherichia coli during carbon limitation., Microb Biotechnol 12(2):360-376


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