RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: malXY
Synonym(s): OP00176
Gene(s): malX, malY   Genome Browser M3D Gene expression COLOMBOS
Note(s): The malY and malX genes are defined as part of the same operon according to their chromosomal positions, their induction pattern, and the polar effect on malY caused by an insertion in malX, but it is not clear whether malY is the last gene in this operon.
In addition, the 5' portion of the malY gene contains stretches of sequences that would allow the formation of two stable stem-and-loop structures. The possible significance of these structures is unknown.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[PM] Polar mutation
Reference(s): [1] Otsuka J., et al., 1996
[2] Reidl J., et al., 1991
Promoter
Name: malXp
+1: 1699313
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 42
Sequence: tcgttgcgtaatgtgatttatgcctcactaaaatttgataaaacgttttatcttctcgcgCaatttactgaatccagattg
                            -35                  -10        +1                   
Evidence: [ICA]
[ICWHO]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[4] Lloyd GS., et al., 2008
[2] Reidl J., et al., 1991
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cAMP1 activator malXp 1699201 1699222 -101.5 tactccctgaTTATGTGACAGATAAAACGTTTTaccttttatt nd [AIBSCS], [BPP], [GEA], [SM] [4], [5]
proximal CRP-cAMP2 activator malXp 1699261 1699282 -41.5 tatcgttgcgTAATGTGATTTATGCCTCACTAAaatttgataa nd [AIBSCS], [BCE], [BPP], [GEA], [SM] [4], [6]
[MalI,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MalI repressor malXp 1699288 1699305 -16.5 cactaaaattTGATAAAACGTTTTATCTTctcgcgcaat nd [BCE], [GEA], [SM] [6]
Note(s): 1CRP site 2 (-101.5) plays little or no role in CRP-dependent activation of the malX promoter. It might function synergistically with the downstream bound CRP, site 1 (-41.5) Lloyd GS,2008
2CRP site 2 (-101.5) plays little or no role in CRP-dependent activation of the malX promoter. It might function synergistically with the downstream bound CRP, site 1 (-41.5) Lloyd GS,20081CRP site 2 (-101.5) plays little or no role in CRP-dependent activation of the malX promoter. It might function synergistically with the downstream bound CRP, site 1 (-41.5) Lloyd GS,2008
2CRP site 2 (-101.5) plays little or no role in CRP-dependent activation of the malX promoter. It might function synergistically with the downstream bound CRP, site 1 (-41.5) Lloyd GS,2008


Transcription unit       
Name: malY
Gene(s): malY   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IEP] Inferred from expression pattern
Reference(s): [7] Li Z., et al., 2019
Promoter
Name: malYp
+1: 1700840
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 117
Sequence: cgtttgtctgtgaaagatatgtcgcttgttaatgtgcaggcactgaaggacaatcgggcaAttggcgtagtacaacttaat
                          -35                    -10        +1                   
Evidence: [ICWHO]
[RS-EPT-CBR]
[RSE]
[TIM]
Reference(s): [7] Li Z., et al., 2019
[8] Salgado H, et al., 2012


Evidence    

 [ICA] Inferred by computational analysis

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [SM] Site mutation

 [BCE] Binding of cellular extracts

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

 [RSE] RNA-seq evidence


Reference(s)    

 [1] Otsuka J., Watanabe H., Mori KT., 1996, Evolution of transcriptional regulation system through promiscuous coupling of regulatory proteins with operons; suggestion from protein sequence similarities in Escherichia coli., J Theor Biol 178(2):183-204

 [2] Reidl J., Boos W., 1991, The malX malY operon of Escherichia coli encodes a novel enzyme II of the phosphotransferase system recognizing glucose and maltose and an enzyme abolishing the endogenous induction of the maltose system., J Bacteriol 173(15):4862-76

 [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] Lloyd GS., Hollands K., Godfrey RE., Busby SJ., 2008, Transcription initiation in the Escherichia coli K-12 malI-malX intergenic region and the role of the cyclic AMP receptor protein., FEMS Microbiol Lett 288(2):250-7

 [5] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [6] Lloyd GS., Godfrey RE., Busby SJ., 2010, Targets for the MalI repressor at the divergent Escherichia coli K-12 malX-malI promoters., FEMS Microbiol Lett 305(1):28-34

 [7] 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

 [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.

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