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MalT DNA-binding transcriptional activator

Synonyms: MalT-Maltotriose-ATP, MalT-ADP-Maltotriose, MalT, MalT-Aes, MalT-MalK, MalT-MalY
Summary:
The Maltose regulator, MalT, is a transcription factor that activates transcription of several genes and operons involved in maltose catabolism and transport [17, 19, 21, 22, 23] This regulator is sensitive to catabolite control and is induced when Escherichia coli is grown on maltodextrin in the absence of glucose [24, 25, 26] MalT is a STAND transcription factor, Signal Transduction ATP bases with numerous domains [27][28]. A novel regulatory role for the MalT regulon in glycolysis-associated utilization of carbon sources has been identified [29]
MalT is monomeric in solution, but in the presence of maltodextrin and ATP it forms multiple complexes (oligomers) in its target promoters and activates transcription by overlapping the -35 box of promoters [19, 21] The binding targets of MalT consist of 10-nucleotide-long direct repeat sequences that possess conserved motifs; each monomer binds to one of these conserved sequences [21]
The gene malT is located upstream of the operon malPQ and in the opposite direction [12, 22, 30] This transcriptional activator [31]belongs to the LuxR family of activators.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
MalT Non-Functional   Apo [BPP], [IDA], [IMP], [IPI], [SM] [1], [2], [3], [4], [5], [6], [7]
MalT-ADP-Maltotriose Functional Allosteric Holo [IPI] [6]
MalT-Aes Non-Functional Allosteric Holo [IPI] [3]
MalT-MalK Non-Functional Allosteric Holo [BPP], [GEA], [IEP], [IPI], [SM] [2], [8], [9], [10]
MalT-MalY Non-Functional Allosteric Holo [BPP], [GEA], [IEP], [IPI] [7], [10]
MalT-Maltotriose-ATP Functional Allosteric Holo [BPP], [IDA], [IMP], [IPI], [SM] [1], [2], [3], [5], [6], [7], [11]
Evolutionary Family: LuxR/UhpA
Sensing class: Using internal synthesized signals
Connectivity class: Local Regulator
Gene name: malT
  Genome position: 3553085-3555790
  Length: 2706 bp / 901 aa
Operon name: malT
TU(s) encoding the TF:
Transcription unit        Promoter
malT
malTp


Regulon       
Regulated gene(s) lamB, malE, malF, malG, malK, malM, malP, malQ, malS, malZ
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (8)
polysaccharides (4)
ABC superfamily, membrane component (2)
membrane (2)
Beta barrel porins (The Outer Membrane Porin (OMP) Functional Superfamily) (1)
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Regulated operon(s) malEFG, malK-lamB-malM, malPQ, malS, malZ
First gene in the operon(s) malE, malK, malP, malS, malZ
Simple and complex regulons CRP,CreB,Fis,MalT
CRP,MalT
CRP,MalT,PhoP
FNR,MalT
MalT
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[MalT,+](5)


Transcription factor binding sites (TFBSs) arrangements       

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  MalT-Maltotriose-ATP activator malEp Sigma70 -231.5 -276.5 malE, malF, malG
tggcttaaatCCTCCACCCCctggcttttt
4246691 4246700 [BPP], [HIBSCS], [SM] [12], [13], [14], [15], [16]
  MalT-Maltotriose-ATP activator malEp Sigma70 -207.5 -252.5 malE, malF, malG
cttttttatgGGGGAGGAGGcgggaggatg
4246667 4246676 [BPP], [HIBSCS], [SM] [12], [13], [14], [15], [16]
  MalT-Maltotriose-ATP activator malEp Sigma70 -197.5 -242.5 malE, malF, malG
ggggaggaggCGGGAGGATGagaacacggc
4246657 4246666 [AIBSCS], [BPP], [SM] [12], [13], [14], [15], [16]
  MalT-Maltotriose-ATP activator malEp Sigma70 -51.5 -96.5 malE, malF, malG
aagcgacggtGGGGCGTAGGggcaaggagg
4246511 4246520 [AIBSCS], [BPP], [HIBSCS], [SM] [12], [13], [14], [15], [16]
  MalT-Maltotriose-ATP activator malEp Sigma70 -41.5 -86.5 malE, malF, malG
ggggcgtaggGGCAAGGAGGatggaaagag
4246501 4246510 [BPP], [HIBSCS], [SM] [12], [13], [14], [15], [16]
  MalT-Maltotriose-ATP activator malKp Sigma70 -230.5 -278.5 malK, lamB, malM
ctctttccatCCTCCTTGCCcctacgcccc
4246501 4246510 [BPP], [HIBSCS], [SM] [12], [13], [14], [15], [16]
  MalT-Maltotriose-ATP activator malKp Sigma70 -220.5 -268.5 malK, lamB, malM
cctccttgccCCTACGCCCCaccgtcgctt
4246511 4246520 [AIBSCS], [BPP], [HIBSCS], [SM] [12], [13], [14], [15], [16]
  MalT-Maltotriose-ATP activator malKp Sigma70 -74.5 -122.5 malK, lamB, malM
gccgtgttctCATCCTCCCGcctcctcccc
4246657 4246666 [AIBSCS], [BPP], [SM] [12], [13], [14], [15], [16]
  MalT-Maltotriose-ATP activator malKp Sigma70 -64.5 -112.5 malK, lamB, malM
catcctcccgCCTCCTCCCCcataaaaaag
4246667 4246676 [BPP], [HIBSCS], [SM] [12], [13], [14], [15], [16]
  MalT-Maltotriose-ATP activator malKp Sigma70 -40.5 -88.5 malK, lamB, malM
aaaaagccagGGGGTGGAGGatttaagcca
4246691 4246700 [BPP], [HIBSCS], [SM] [12], [13], [14], [15], [16]
  MalT-Maltotriose-ATP activator malPp Sigma70 -95.5 -132.5 malP, malQ
ctagctttaaGTGGTTGAGAtcacatttcc
3552601 3552610 [AIBSCS], [BPP] [12], [17]
  MalT-Maltotriose-ATP activator malPp Sigma70 -73.5 -110.5 malP, malQ
acatttccttGCTCATCCCCgcaactcctc
3552579 3552588 [AIBSCS], [BPP] [5], [12], [17]
  MalT-Maltotriose-ATP activator malPp Sigma70 -60.5 -97.5 malP, malQ
catccccgcaACTCCTCCCTgcctaatccc
3552566 3552575 [AIBSCS], [BPP], [SM] [5], [12], [17], [18]
  MalT-Maltotriose-ATP activator malPp Sigma70 -37.5 -74.5 malP, malQ
taatcccccgCAGGATGAGGaaggtcaaca
3552543 3552552 [AIBSCS], [BPP], [SM] [5], [12], [17], [18]
  MalT-Maltotriose-ATP activator malSp Sigma70 -74.5 -101.5 malS
gcgcgagatcGCTCACCCTTgcttctcatc
3737391 3737400 [AIBSCS] [19]
  MalT-Maltotriose-ATP activator malSp Sigma70 -61.5 -88.5 malS
cacccttgctTCTCATCCTGtggacttacc
3737404 3737413 [AIBSCS] [19]
  MalT-Maltotriose-ATP activator malSp Sigma70 -37.5 -64.5 malS
cttaccgctcAGGGATGAGTtttgtttggc
3737428 3737437 [AIBSCS], [BCE] [19], [20]
  MalT-Maltotriose-ATP activator malZp nd -73.5 -96.5 malZ
ttccgaaagtTATCCGCCCCcgtcctcctc
422417 422426 [AIBSCS] [21]
  MalT-Maltotriose-ATP activator malZp nd -60.5 -83.5 malZ
ccgcccccgtCCTCCTCCCCcaaatatcct
422430 422439 [AIBSCS] [21]
  MalT-Maltotriose-ATP activator malZp nd -37.5 -60.5 malZ
atatccttcaGATGATGAGTgatcctgcat
422453 422462 [AIBSCS] [21]


Alignment and PSSM for MalT TFBSs    

Aligned TFBS of MalT   
  Sequence
  GGGGGCGGAT
  GGGGGAGGAG
  AGATGATGAG
  GCAGGATGAG
  CAGGGAGGAG
  CGGGGATGAG
  AGTGGTTGAG
  CAAGGGTGAG
  ACAGGATGAG
  CAGGGATGAG
  CAAGGAGGAT
  CGGTGGGGCG
  GGAGGATGAG
  GGGGGAGGAG
  GGGGGTGGAG

Position weight matrix (PWM).   
A	3	4	6	0	0	10	0	0	14	0
C	6	2	0	0	0	1	0	0	1	0
G	6	9	8	13	15	2	7	15	0	13
T	0	0	1	2	0	2	8	0	0	2

PWM logo   


 


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
TF-target gene evolutionary conservation
Promoter-target gene evolutionary conservation


Evidence    

 [BPP] Binding of purified proteins

 [IDA] Inferred from direct assay

 [IMP] Inferred from mutant phenotype

 [IPI] Inferred from physical interaction

 [SM] Site mutation

 [GEA] Gene expression analysis

 [IEP] Inferred from expression pattern

 [HIBSCS] Human inference based on similarity to consensus sequences

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BCE] Binding of cellular extracts



Reference(s)    

 [1] Dardonville B, Raibaud O., 1990, Characterization of malT mutants that constitutively activate the maltose regulon of Escherichia coli., J Bacteriol.

 [2] Joly N., Bohm A., Boos W., Richet E., 2004, MalK, the ATP-binding Cassette Component of the Escherichia coli Maltodextrin Transporter, Inhibits the Transcriptional Activator MalT by Antagonizing Inducer Binding., J Biol Chem. 279(32):33123-30

 [3] Joly N., Danot O., Schlegel A., Boos W., Richet E., 2002, The Aes protein directly controls the activity of MalT, the central transcriptional activator of the Escherichia coli maltose regulon., J Biol Chem. 277(19):16606-13

 [4] Larquet E, Schreiber V, Boisset N, Richet E., 2004, Oligomeric assemblies of the Escherichia coli MalT transcriptional activator revealed by cryo-electron microscopy and image processing., J Mol Biol.

 [5] Raibaud O., Richet E., 1987, Maltotriose is the inducer of the maltose regulon of Escherichia coli., J Bacteriol. 169(7):3059-61

 [6] Schreiber V., Richet E., 1999, Self-association of the Escherichia coli transcription activator MalT in the presence of maltotriose and ATP., J Biol Chem. 274(47):33220-6

 [7] Schreiber V., Steegborn C., Clausen T., Boos W., Richet E., 2000, A new mechanism for the control of a prokaryotic transcriptional regulator: antagonistic binding of positive and negative effectors., Mol Microbiol. 35(4):765-76

 [8] Panagiotidis CH., Boos W., Shuman HA., 1998, The ATP-binding cassette subunit of the maltose transporter MalK antagonizes MalT, the activator of the Escherichia coli mal regulon., Mol Microbiol. 30(3):535-46

 [9] Richet E., Joly N., Danot O., 2005, Two domains of MalT, the activator of the Escherichia coli maltose regulon, bear determinants essential for anti-activation by MalK., J Mol Biol. 347(1):1-10

 [10] Schlegel A., Danot O., Richet E., Ferenci T., Boos W., 2002, The N terminus of the Escherichia coli transcription activator MalT is the domain of interaction with MalY., J Bacteriol. 184(11):3069-77

 [11] Richet E., Raibaud O., 1989, MalT, the regulatory protein of the Escherichia coli maltose system, is an ATP-dependent transcriptional activator., EMBO J. 8(3):981-7

 [12] Boos W., Shuman H., 1998, Maltose/maltodextrin system of Escherichia coli: transport, metabolism, and regulation., Microbiol Mol Biol Rev. 62(1):204-29

 [13] Raibaud O., 1989, Nucleoprotein structures at positively regulated bacterial promoters: homology with replication origins and some hypotheses on the quaternary structure of the activator proteins in these complexes., Mol Microbiol. 3(3):455-8

 [14] Raibaud O., Vidal-Ingigliardi D., Richet E., 1989, A complex nucleoprotein structure involved in activation of transcription of two divergent Escherichia coli promoters., J Mol Biol. 205(3):471-85

 [15] Richet E., 1996, On the role of the multiple regulatory elements involved in the activation of the Escherichia coli malEp promoter., J Mol Biol. 264(5):852-62

 [16] Richet E., Raibaud O., 1991, Supercoiling is essential for the formation and stability of the initiation complex at the divergent malEp and malKp promoters., J Mol Biol. 218(3):529-42

 [17] 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

 [18] 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

 [19] 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

 [20] 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

 [21] Tapio S., Yeh F., Shuman HA., Boos W., 1991, The malZ gene of Escherichia coli, a member of the maltose regulon, encodes a maltodextrin glucosidase., J Biol Chem. 266(29):19450-8

 [22] Boos W., Bohm A., 2000, Learning new tricks from an old dog: MalT of the Escherichia coli maltose system is part of a complex regulatory network., Trends Genet. 16(9):404-9

 [23] Chapon C., 1982, Role of the catabolite activator protein in the maltose regulon of Escherichia coli., J Bacteriol. 150(2):722-9

 [24] Chapon C., Kolb A., 1983, Action of CAP on the malT promoter in vitro., J Bacteriol. 156(3):1135-43

 [25] Eichenberger P., Dethiollaz S., Fujita N., Ishihama A., Geiselmann J., 1996, Influence of the location of the cAMP receptor protein binding site on the geometry of a transcriptional activation complex in Escherichia coli., Biochemistry. 35(48):15302-12

 [26] Dethiollaz S., Eichenberger P., Geiselmann J., 1996, Influence of DNA geometry on transcriptional activation in Escherichia coli., EMBO J. 15(19):5449-58

 [27] Danot O., 2010, The inducer maltotriose binds in the central cavity of the tetratricopeptide-like sensor domain of MalT, a bacterial STAND transcription factor., Mol Microbiol. 77(3):628-41

 [28] Liu P., Danot O., Richet E., 2013, A dual role for the inducer in signalling by MalT, a signal transduction ATPase with numerous domains (STAND)., Mol Microbiol. 90(6):1309-23

 [29] Ritzefeld M., Wollschlager K., Niemann G., Anselmetti D., Sewald N., 2011, Minor groove recognition is important for the transcription factor PhoB: a surface plasmon resonance study., Mol Biosyst. 7(11):3132-42

 [30] Schlegel A., Bohm A., Lee SJ., Peist R., Decker K., Boos W., 2002, Network regulation of the Escherichia coli maltose system., J Mol Microbiol Biotechnol. 4(3):301-7

 [31] Cole ST., Raibaud O., 1986, The nucleotide sequence of the malT gene encoding the positive regulator of the Escherichia coli maltose regulon., Gene. 42(2):201-8

 [32] Danot O., 2001, A complex signaling module governs the activity of MalT, the prototype of an emerging transactivator family., Proc Natl Acad Sci U S A. 98(2):435-40

 [33] Steegborn C., Danot O., Huber R., Clausen T., 2001, Crystal structure of transcription factor MalT domain III: a novel helix repeat fold implicated in regulated oligomerization., Structure. 9(11):1051-60

 [34] Vidal-Ingigliardi D., Richet E., Danot O., Raibaud O., 1993, A small C-terminal region of the Escherichia coli MalT protein contains the DNA-binding domain., J Biol Chem. 268(33):24527-30

 [35] Mandrich L., Caputo E., Martin BM., Rossi M., Manco G., 2002, The Aes protein and the monomeric alpha-galactosidase from Escherichia coli form a non-covalent complex. Implications for the regulation of carbohydrate metabolism., J Biol Chem. 277(50):48241-7



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