RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit       
Name: malQ
Gene(s): malQ   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Promoter
Name: malQp
+1: 3550399
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 329
Sequence: aaaatatctttatttttggtcataccgtggaacaagtgaaggcaattctggccaaaggctAcgacccggtgaaatggcgga
                                   -35                 -10  +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-AINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Huerta AM., et al., 2003
[2] Rhodius VA., et al., 2005


Transcription unit          
Name: malPQ
Synonym(s): OP00049
Gene(s): malQ, malP   Genome Browser M3D Gene expression COLOMBOS
Note(s): Through DNase footprinting analyses, Danot and Raibaud (1994) showed that CRP binds at the promoter region of malPQ, centered at -93.5 upstream of the transcription start site of malPp Danot O,1994 However, the destruction of the CRP site has no effect on the transcription of the operon malPQ. In this way, the effect of CRP on the expression of malPQ might be indirect and mediated by MalT as a direct regulator Danot O,1994. Camakaris H,1982. Chapon C,1982
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for malP . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Reference(s): [3] Chao J., et al., 1974
[4] Danot O., et al., 1994
[5] Foglino M., et al., 1987
Promoter
Name: malPp
+1: 3552510
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 37
Sequence: tccctgcctaatcccccgcaggatgaggaaggtcaacatcgagcctggcaaactagcgatAacgttgtgttgaaaatctaa
                            -35                       -10   +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[EXP-IMP]
[RS-EPT-CBR]
Reference(s): [6] Debarbouille M., et al., 1982
[7] Gutierrez C., et al., 1984
[1] Huerta AM., et al., 2003
[8] Salgado H, et al., 2012
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
remote FNR activator malPp 3552631 3552644 -127.5 ttgcattgatTTGATGCTAATCCTgtggtttgca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [9]
[MalT,+] 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 MalT-maltotriose-ATP activator malPp 3552543 3552553 -37.5 ctaatcccccGCAGGATGAGGaaggtcaaca nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4]
proximal MalT-maltotriose-ATP activator malPp 3552566 3552576 -60.5 tcatccccgcAACTCCTCCCTgcctaatccc nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4]
proximal MalT-maltotriose-ATP activator malPp 3552579 3552589 -73.5 cacatttcctTGCTCATCCCCgcaactcctc nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4]
remote MalT-maltotriose-ATP activator malPp 3552601 3552611 -95.5 actagctttaAGTGGTTGAGAtcacatttcc nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd nd


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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

 [EXP-IMP] Inferred from mutant phenotype

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] 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

 [2] Rhodius VA., Suh WC., Nonaka G., West J., Gross CA., 2005, Conserved and variable functions of the sigmaE stress response in related genomes., PLoS Biol 4(1):e2

 [3] Chao J., Weathersbee CJ., 1974, Regulation of maltodextrin phosphorylase synthesis in Escherichia coli by cyclic adenosine 3', 5'-monophosphate and glucose., J Bacteriol 117(1):181-8

 [4] Danot O., Raibaud O., 1994, Multiple protein-DNA and protein-protein interactions are involved in transcriptional activation by MalT., Mol Microbiol 14(2):335-46

 [5] Foglino M., Lazdunski A., 1987, Deletion analysis of the promoter region of the Escherichia coli pepN gene, a gene subject in vivo to multiple global controls., Mol Gen Genet 210(3):523-7

 [6] Debarbouille M., Cossart P., Raibaud O., 1982, A DNA sequence containing the control sites for gene malT and for the malPQ operon., Mol Gen Genet 185(1):88-92

 [7] Gutierrez C., Raibaud O., 1984, Point mutations that reduce the expression of malPQ, a positively controlled operon of Escherichia coli., J Mol Biol 177(1):69-86

 [8] 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.

 [9] 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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