RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: mdh
Synonym(s): OP00149
Gene(s): mdh   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under nitrogen-rich growth conditions, the expression of the mdh gene increased in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, gene expression was decreased in the cyoA and cydB and Fnr mutants. It is unknown if the effects of the transcriptional regulators act directly on the gene expression; also, it is unknown which of the two promoters that transcribe the gene could be regulated by the regulators Kumar R,2011
The expression of the gene mdh is decreased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013
In a study where it was shown that the L-tryptophan eradicated persister cells, it was observed that the exogenous amino acid decreased the expression of the mdh gene Li Y, Liu B, Guo J, Cong H, He S, Zhou H, Zhu F, Wang Q, Zhang L,2019.
Evidence: [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
Reference(s): [1] Iuchi S., et al., 1990
Promoter
Name: mdhp1
+1: 3384313
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 45
Sequence: ctacacattcttgagatgtggtcattgtaaacggcaattttgtggattaaggtcgcggcaGcggagcaacatatcttagtt
                              -35                    -10    +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[3] Vogel RF., et al., 1987
[4] Yamamoto K., et al., 2008
TF binding sites (TFBSs)
[ArcA,-] 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 ArcA-phosphorylated repressor mdhp1 3384280 3384294 27.0 catatcttagTTTATCAATATAATAaggagtttag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] W [6], [7], [8]
[BtsR,-] 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 BtsR-Phosphorylated repressor mdhp1 3384357 3384368 -49.0 cgtgactacaCATTCTTGAGATgtggtcattg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-PATTERN-DISCOVERY], [EXP-GSELEX] S [5]
proximal BtsR-Phosphorylated repressor mdhp1 3384381 3384392 -73.0 ttaaatgcatAAACGCTAAACTtgcgtgacta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-PATTERN-DISCOVERY], [EXP-GSELEX] S [5]
remote BtsR-Phosphorylated repressor mdhp1 3384453 3384464 -145.0 ccacctgttgGAATGTTGCGCTaatgcataag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-PATTERN-DISCOVERY], [EXP-GSELEX] S [5]
[CRP,+] 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 CRP-cyclic-AMP activator mdhp1 3384363 3384384 -60.5 ataaacgctaAACTTGCGTGACTACACATTCTtgagatgtgg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] W [3]
[DpiA,+] 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
nd DpiA-phosphorylated activator mdhp1 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
[FlhDC,-] 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
nd FlhDC repressor mdhp1 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [9]


Transcription unit          
Name: mdh
Gene(s): mdh   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under nitrogen-rich growth conditions, the expression of the mdh gene increased in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, gene expression was decreased in the cyoA and cydB and Fnr mutants. It is unknown if the effects of the transcriptional regulators act directly on the gene expression; also, it is unknown which of the two promoters that transcribe the gene could be regulated by the regulators Kumar R,2011
The expression of the gene mdh is decreased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013
In a study where it was shown that the L-tryptophan eradicated persister cells, it was observed that the exogenous amino acid decreased the expression of the mdh gene Li Y, Liu B, Guo J, Cong H, He S, Zhou H, Zhu F, Wang Q, Zhang L,2019.
Reference(s): [4] Yamamoto K., et al., 2008
Promoter
Name: mdhp2
+1: 3384470
Distance from start of the gene: 202
Sequence: aaattaattgttatcaaattgatgttgttttggctgaacggtagggtatattgtcaccacCtgttggaatgttgcgctaat
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [4] Yamamoto K., et al., 2008
TF binding sites (TFBSs)
[DpiA,+] 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
nd DpiA-phosphorylated activator mdhp2 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

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

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts

 [COMP-AINF-PATTERN-DISCOVERY] Automated inference based on sequence pattern discovery

 [EXP-GSELEX] genomic SELEX

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


Reference(s)    

 [1] Iuchi S., Matsuda Z., Fujiwara T., Lin EC., 1990, The arcB gene of Escherichia coli encodes a sensor-regulator protein for anaerobic repression of the arc modulon., Mol Microbiol 4(5):715-27

 [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] Vogel RF., Entian KD., Mecke D., 1987, Cloning and sequence of the mdh structural gene of Escherichia coli coding for malate dehydrogenase., Arch Microbiol 149(1):36-42

 [4] Yamamoto K., Matsumoto F., Oshima T., Fujita N., Ogasawara N., Ishihama A., 2008, Anaerobic regulation of citrate fermentation by CitAB in Escherichia coli., Biosci Biotechnol Biochem 72(11):3011-4

 [5] Ogasawara H., Ishizuka T., Yamaji K., Kato Y., Shimada T., Ishihama A., 2019, Regulatory role of pyruvate-sensing BtsSR in biofilm formation by Escherichia coli K-12., FEMS Microbiol Lett 366(24)

 [6] Lynch AS., Lin EC., 1996, Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: characterization of DNA binding at target promoters., J Bacteriol 178(21):6238-49

 [7] Park SJ., Cotter PA., Gunsalus RP., 1995, Regulation of malate dehydrogenase (mdh) gene expression in Escherichia coli in response to oxygen, carbon, and heme availability., J Bacteriol 177(22):6652-6

 [8] Salmon KA., Hung SP., Steffen NR., Krupp R., Baldi P., Hatfield GW., Gunsalus RP., 2005, Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA., J Biol Chem 280(15):15084-96

 [9] Pruss BM., Liu X., Hendrickson W., Matsumura P., 2001, FlhD/FlhC-regulated promoters analyzed by gene array and lacZ gene fusions., FEMS Microbiol Lett 197(1):91-7

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