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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 [2, 3, 4], 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 [5, 6]. A preliminary analysis of the crystal structure of MraZ has been published [7]. It was previously suggested that MraZ is an inhibitor of the RsmH methyltransferase [8], but this report has since been retracted [9]. A mraZ null mutation has been generated [10].
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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
mraZW-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) mraZ, mioC
Simple and complex regulons MraZ,PdhR
MraZ,ppGpp
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
gcttttttaaTCCCAtacttttcca
3926527 3926531 [BPP], [GEA] [1]
  MraZ repressor mioCp nd -44.0 -64.0 mioC
tcccatacttTTCCAcaggtagatc
3926517 3926521 [AIBSCS], [BPP], [GEA] [1]
  MraZ repressor mioCp nd -31.0 -51.0 mioC
cacaggtagaTCCCAacgcgttcac
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    

Aligned TFBS of MraZ   
  Sequence
  AGTGGGAA
  AGTGGGAA
  TGTGGGGC
  TGTGGAAA
  TATGGGAT
  GTTGGGAT

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

Consensus   
;	consensus.strict             	tGTGGGaa
;	consensus.strict.rc          	TTCCCACA
;	consensus.IUPAC              	wGTGGGaw
;	consensus.IUPAC.rc           	WTCCCACW
;	consensus.regexp             	[at]GTGGGa[at]
;	consensus.regexp.rc          	[AT]TCCCAC[AT]

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] Chen S, Jancrick J, Yokota H, Kim R, Kim SH, 2004, Crystal structure of a protein associated with cell division from Mycoplasma pneumoniae (GI: 13508053): a novel fold with a conserved sequence motif., Proteins, 2004 Jun 1

 [3] Mingorance J, Tamames J, Vicente M, 2004, Genomic channeling in bacterial cell division., J Mol Recognit, 2004 Sep-Oct

 [4] Tamames J, González-Moreno M, Mingorance J, Valencia A, Vicente M, 2001, Bringing gene order into bacterial shape., Trends Genet, 2001 Mar

 [5] 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

 [6] Bobay BG, Andreeva A, Mueller GA, Cavanagh J, Murzin AG, 2005, Revised structure of the AbrB N-terminal domain unifies a diverse superfamily of putative DNA-binding proteins., FEBS Lett, 2005 Oct 24

 [7] Adams MA, Udell CM, Pal GP, Jia Z, 2005, MraZ from Escherichia coli: cloning, purification, crystallization and preliminary X-ray analysis., Acta Crystallogr Sect F Struct Biol Cryst Commun, 2005 Apr 1

 [8] Gu J, Ye C, 2010, Characterization of methyltransferase properties of Escherichia coli YabC protein with an enzyme-coupled colorimetric assay., J Mol Microbiol Biotechnol, 2010

 [9] Ye C, Gu J, 2010, Retraction statements. Paper by Gu and Ye [2010;19:105-116]., J Mol Microbiol Biotechnol, 2010

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

 [11] 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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