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MalI DNA-binding transcriptional repressor

Synonyms: MalI
Summary:
"Maltose inhibitor," MalI, is a repressor that controls genes related to the maltose system. It is negatively autoregulated and coordinately represses transcription of a divergent operon that encodes a maltose-glucose PTS permease and a bifunctional protein that interacts directly with the MalT transcriptional activator [4, 5] This transcription factor binds to two 12-bp-long direct repeat nucleotide sequences in tandem, overlapping the malXp and malIp simultaneously [4, 5] MalI shows high similarity to GalR (28%), CytR (21%), and LacI (24%), and homology to a fragment of 30 amino acids from MalT. Additionally, the N-terminal region has a helix-turn-helix DNA-binding domain [5] The gene encoding this protein is homologous to transcriptional repressors of the LacI/GalR family.


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
MalI Functional   nd nd nd
Evolutionary Family: GalR/LacI
TFBs length: 18
TFBs symmetry: inverted-repeat
Connectivity class: Local Regulator
Gene name: malI
  Genome position: 1698152-1699180
  Length: 1029 bp / 342 aa
Operon name: malI
TU(s) encoding the TF:
Transcription unit        Promoter
malI
malIp


Regulon       
Regulated gene(s) malI, malX, malY
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (3)
operon (2)
Transcription related (1)
repressor (1)
Phosphotransferase Systems (PEP-dependent PTS) (1)
Regulated operon(s) malI, malXY
First gene in the operon(s) malI, malX
Simple and complex regulons CRP,MalI
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[MalI,-](2)


Transcription factor regulation    


Transcription factor binding sites (TFBSs) arrangements
      

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  MalI repressor malIp Sigma70 10.5 -38.5 malI
gataaataaaAGGTAAAACGTTTTATCTgtcacataat
 1699210 1699227 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [1], [1], [2], [3], [4], [5]
  MalI repressor malXp Sigma70 -16.5 -58.5 malX, malY
cactaaaattTGATAAAACGTTTTATCTtctcgcgcaa
 1699288 1699305 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] S [1], [1], [4], [5]


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


Evidence    

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

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] 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

 [2] Baumgart LA, Lee JE, Salamov A, Dilworth DJ, Na H, Mingay M, Blow MJ, Zhang Y, Yoshinaga Y, Daum CG, O'Malley RC, 2021, Persistence and plasticity in bacterial gene regulation., Nat Methods, 18(12):1499 10.1038/s41592-021-01312-2

 [3] 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

 [4] 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

 [5] Reidl J., Romisch K., Ehrmann M., Boos W., 1989, MalI, a novel protein involved in regulation of the maltose system of Escherichia coli, is highly homologous to the repressor proteins GalR, CytR, and LacI., J Bacteriol 171(9):4888-99


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