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MraZ DNA-binding transcriptional repressor

Synonyms: MraZ
Summary:
MraZ is a transcriptional repressor involved in the control of cell division and cell wall genes [1]. Based on differential gene expression analysis comparing the WT to a mraZ mutant, 100 genes under the control of MraZ were identified [1]. The analysis showed that three successive TGGGN direct repeats are separated by two consecutive 5-nt spacers [1]. The MraZ protein is highly conserved in bacteria [], and MraW is more universal [1]. MraZ is similar in both structure and sequence to the DNA-binding transition-state regulator AbrB from Bacillus subtilis [2]. A preliminary analysis of the crystal structure of MraZ has been published []. It was previously suggested that MraZ is an inhibitor of the RsmH methyltransferase [], but this report has since been retracted []. A mraZ null mutation has been generated [3].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
MraZ Functional   [APPHINH], [HIFS], [IEP], [IPI] [1]
Connectivity class: Local Regulator
Gene name: mraZ
  Genome position: 89634-90092
  Length: 459 bp / 152 aa
Operon name: mraZ-rsmH-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ-lpxC
TU(s) encoding the TF:
Transcription unit        Promoter
mraZ-rsmH-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ-lpxC
mraZp


Regulon       
Regulated gene(s) ddlB, ftsA, ftsI, ftsL, ftsQ, ftsW, ftsZ, lpxC, mioC, mraY, mraZ, murC, murD, murE, murF, murG, rsmH
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
murein (peptidoglycan) (8)
murein (8)
cell division (7)
membrane (4)
drug resistance/sensitivity (1)
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Regulated operon(s) asnC-mioC-mnmG-rsmG, mraZ-rsmH-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ-lpxC
First gene in the operon(s) mioC, mraZ
Simple and complex regulons MraZ
MraZ,PdhR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[MraZ,-](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 (Confirmed, Strong, Weak) References
  MraZ repressor mioCp nd -54.0 -74.0 mioC
tggaaaagtaTGGGAttaaaaaagc
3926527 3926531 [BPP], [GEA] [1]
  MraZ repressor mioCp nd -44.0 -64.0 mioC
gatctacctgTGGAAaagtatggga
3926517 3926521 [AIBSCS], [BPP], [GEA] [1]
  MraZ repressor mioCp nd -31.0 -51.0 mioC
gtgaacgcgtTGGGAtctacctgtg
3926504 3926508 [AIBSCS], [BPP], [GEA] [1]
  MraZ repressor mraZp Sigma70 -3.0 -41.0 mraZ, rsmH, ftsL, ftsI, murE, murF, mraY, murD, ftsW, murG, murC, ddlB, ftsQ, ftsA, ftsZ, lpxC
ctcctttcagTGGGAaattgtgggg
89591 89595 [AIBSCS], [BPP], [GEA], [SM] [1]
  MraZ repressor mraZp Sigma70 8.0 -31.0 mraZ, rsmH, ftsL, ftsI, murE, murF, mraY, murD, ftsW, murG, murC, ddlB, ftsQ, ftsA, ftsZ, lpxC
tgggaaattgTGGGGcaaagtggga
89601 89605 [AIBSCS], [BPP], [GEA], [SM] [1]
  MraZ repressor mraZp Sigma70 18.0 -21.0 mraZ, rsmH, ftsL, ftsI, murE, murF, mraY, murD, ftsW, murG, murC, ddlB, ftsQ, ftsA, ftsZ, lpxC
tggggcaaagTGGGAataaggggtg
89611 89615 [AIBSCS], [BPP], [GEA], [SM] [1]


Alignment and PSSM for MraZ TFBSs    

Position weight matrix (PWM).   
A	1	0	0	0	1	4	4	3
C	0	0	0	0	0	0	1	0
G	5	0	5	6	5	2	0	0
T	0	6	1	0	0	0	1	3

PWM logo   


 


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


Evidence    

 [APPHINH] Assay of protein purified to homogeneity from its native host

 [HIFS] Human inference of function from sequence

 [IEP] Inferred from expression pattern

 [IPI] Inferred from physical interaction

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [SM] Site mutation



Reference(s)    

 [1] Eraso JM., Markillie LM., Mitchell HD., Taylor RC., Orr G., Margolin W., 2014, The Highly Conserved MraZ Protein Is a Transcriptional Regulator in Escherichia coli., J Bacteriol 196(11):2053-66

 [2] Coles M., Djuranovic S., Soding J., Frickey T., Koretke K., Truffault V., Martin J., Lupas AN., 2005, AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi beta barrels., Structure 13(6):919-28

 [3] Merlin C., McAteer S., Masters M., 2002, Tools for characterization of Escherichia coli genes of unknown function., J Bacteriol 184(16):4573-81

 [4] Skunca N., Bosnjak M., Krisko A., Panov P., Dzeroski S., Smuc T., Supek F., 2013, Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships., PLoS Comput Biol 9(1):e1002852



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