RegulonDB RegulonDB 11.1: Operon Form
   

mlc-bidA operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: mlc-ynfK
Gene(s): bidA, mlc   Genome Browser M3D Gene expression COLOMBOS
Note(s): mlc expression is enhanced under anaerobic conditions Jiang GR,2001
The expression of the gene mlc is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013 but it is not known which promoter, of two transcribing mlc, is affected by PhoB.
Evidence: [COMP-AINF] Inferred computationally without human oversight
[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Nonaka G., et al., 2006
Promoter
Name: mlcp2
+1: 1668591
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 27
Sequence: cctaagtaaaaatttgacgacacgtattgaagtgcttcaccatagcctacagattatttcGgagcgcgaaaatatagggag
                                -35                      -10+1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Decker K., et al., 1998
[3] Huerta AM., et al., 2003
[1] Nonaka G., et al., 2006
[4] Shin D., et al., 2001
TF binding sites (TFBSs)
[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 mlcp2 1668651 1668673 -70.5 aaaagcccgaAAAATGTGCTGTTAATCACATGCctaagtaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [4], [5]
[Mlc,-] 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 Mlc repressor mlcp2 1668577 1668599 4.0 tagcctacagATTATTTCGGAGCGCGAAAATATagggagtatg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [2], [4]


Transcription unit          
Name: mlc-ynfK
Gene(s): bidA, mlc   Genome Browser M3D Gene expression COLOMBOS
Note(s): mlc expression is enhanced under anaerobic conditions Jiang GR,2001
The expression of the gene mlc is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013 but it is not known which promoter, of two transcribing mlc, is affected by PhoB.
Evidence: [COMP-AINF] Inferred computationally without human oversight
[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Nonaka G., et al., 2006
Promoter
Name: mlcp
+1: 1668591
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 27
Sequence: cctaagtaaaaatttgacgacacgtattgaagtgcttcaccatagcctacagattatttcGgagcgcgaaaatatagggag
                                -35                 -10     +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Decker K., et al., 1998
[3] Huerta AM., et al., 2003
[1] Nonaka G., et al., 2006
[4] Shin D., et al., 2001
TF binding sites (TFBSs)
[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 mlcp 1668651 1668673 -70.5 aaaagcccgaAAAATGTGCTGTTAATCACATGCctaagtaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [4], [5]
[Mlc,-] 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 Mlc repressor mlcp 1668577 1668599 4.0 tagcctacagATTATTTCGGAGCGCGAAAATATagggagtatg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [2], [4]


Transcription unit          
Name: mlc
Gene(s): mlc   Genome Browser M3D Gene expression COLOMBOS
Note(s): mlc expression is enhanced under anaerobic conditions Jiang GR,2001
Under nitrogen-rich growth conditions, the expression of the dgsA gene was decreased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, 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 mlc is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013 but it is not known which promoter, of two transcribing mlc, is affected by PhoB.
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: mlcp1
+1: 1668603
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 39
Sequence: gttaatcacatgcctaagtaaaaatttgacgacacgtattgaagtgcttcaccatagcctAcagattatttcggagcgcga
                                   -35                      +10                  
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [6] Cho S., et al., 2005
[2] Decker K., et al., 1998
[3] Huerta AM., et al., 2003
[4] Shin D., et al., 2001
TF binding sites (TFBSs)
[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 repressor mlcp1 1668651 1668673 -58.5 aaaagcccgaAAAATGTGCTGTTAATCACATGCctaagtaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [4], [5]
[Mlc,-] 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 Mlc repressor mlcp1 1668577 1668599 16.0 tagcctacagATTATTTCGGAGCGCGAAAATATagggagtatg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [2], [4]


Transcription unit       
Name: ynfK
Gene(s): bidA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [EXP-IDA] Inferred from direct assay

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

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

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

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

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

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

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position


Reference(s)    

 [1] Nonaka G., Blankschien M., Herman C., Gross CA., Rhodius VA., 2006, Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress., Genes Dev 20(13):1776-89

 [2] Decker K., Plumbridge J., Boos W., 1998, Negative transcriptional regulation of a positive regulator: the expression of malT, encoding the transcriptional activator of the maltose regulon of Escherichia coli, is negatively controlled by Mlc., Mol Microbiol 27(2):381-90

 [3] 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

 [4] Shin D., Lim S., Seok YJ., Ryu S., 2001, Heat shock RNA polymerase (E sigma(32)) is involved in the transcription of mlc and crucial for induction of the Mlc regulon by glucose in Escherichia coli., J Biol Chem 276(28):25871-5

 [5] Tsai MJ., Wang JR., Yang CD., Kao KC., Huang WL., Huang HY., Tseng CP., Huang HD., Ho SY., 2018, PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli., Sci Rep 8(1):951

 [6] Cho S., Shin D., Ji GE., Heu S., Ryu S., 2005, High-level recombinant protein production by overexpression of Mlc in Escherichia coli., J Biotechnol 119(2):197-203

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