RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: malS
Synonym(s): OP00184
Gene(s): malS   Genome Browser M3D Gene expression COLOMBOS
Note(s): The malS gene, which codes for a periplasmic α-amylase, is an isolated gene Freundlieb S,1986, and it is regulated by the maltose regulator, MalT Freundlieb S,1986, the catabolite repressor, Crp Bukau B,1986, and the Mg deprivation response cognate, PhoP Monsieurs P,2005. Genes flanking malS are encoded in opposite directions: the downstream gene,avtA, which codes for an alanine-valine transaminase Wang MD,1987, and the bax gene.
Evidence: [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
Reference(s): [1] Bukau B., et al., 1986
[2] Freundlieb S., et al., 1986
[3] Monsieurs P., et al., 2005
[4] Otsuka J., et al., 1996
[5] Schneider E., et al., 1992
[6] Wang MD., et al., 1987
Promoter
Name: malSp
+1: 3737470
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 27
Sequence: cctgtggacttaccgctcagggatgagttttgtttggcttatcgctggcaaactgtctgaAatcgcagcaataaggactca
                       -35                       -10        +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [7] Huerta AM., et al., 2003
[5] Schneider E., et al., 1992
Terminator(s)
Type: rho-independent
Sequence: aacagtaactTTTCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGCCGCCAAccaggataaa
Reference(s): [5] Schneider E., et al., 1992
Type: rho-independent
Sequence: cagccctaatCAGCGTTGCAGGATAAAGCACCGCTCactcttcaac
Reference(s): [5] Schneider E., et al., 1992
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
remote CRP-cyclic-AMP activator malSp 3737228 3737250 -231.5 tttttcacaaATTTGAGAGTTGAATCTCAAATCatatcaaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [8]
[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 malSp 3737391 3737400 -74.5 gcgcgagatcGCTCACCCTTgcttctcatc nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd nd
proximal MalT-maltotriose-ATP activator malSp 3737404 3737413 -61.5 cacccttgctTCTCATCCTGtggacttacc nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd nd
proximal MalT-maltotriose-ATP activator malSp 3737428 3737437 -37.5 cttaccgctcAGGGATGAGTtttgtttggc nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] nd nd
[PhoP,+] 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 PhoP-phosphorylated activator malSp 3737301 3737317 -161.0 caaatctgaaACTATGTCACGTGTTAAcgattcagat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -14.5 3737405 3737444 cccttgcttcTCATCCTGTGGACTTACCGCTCAGGGATGAGTTTTGTTTggcttatcgc
  anti-terminator -6.3 3737378 3737417 cagccgttttTTGCGCGAGATCGCTCACCCTTGCTTCTCATCCTGTGGActtaccgctc
  anti-anti-terminator -13.8 3737349 3737396 gcagaaaatgTGGGGGTTATCGCAAAATTCAGCCGTTTTTTGCGCGAGATCGCTCACccttgcttct
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [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

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


Reference(s)    

 [1] Bukau B., Ehrmann M., Boos W., 1986, Osmoregulation of the maltose regulon in Escherichia coli., J Bacteriol 166(3):884-91

 [2] Freundlieb S., Boos W., 1986, Alpha-amylase of Escherichia coli, mapping and cloning of the structural gene, malS, and identification of its product as a periplasmic protein., J Biol Chem 261(6):2946-53

 [3] Monsieurs P., De Keersmaecker S., Navarre WW., Bader MW., De Smet F., McClelland M., Fang FC., De Moor B., Vanderleyden J., Marchal K., 2005, Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium., J Mol Evol 60(4):462-74

 [4] 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

 [5] Schneider E., Freundlieb S., Tapio S., Boos W., 1992, Molecular characterization of the MalT-dependent periplasmic alpha-amylase of Escherichia coli encoded by malS., J Biol Chem 267(8):5148-54

 [6] Wang MD., Liu L., Wang BM., Berg CM., 1987, Cloning and characterization of the Escherichia coli K-12 alanine-valine transaminase (avtA) gene., J Bacteriol 169(9):4228-34

 [7] 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

 [8] 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

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