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MntR DNA-binding transcriptional dual regulator

Synonyms: MntR-Mn2+, MntR-Cd2+
Summary:
MntR, "Mn2+ transport regulator", the primary sensor and transducer of manganese abundance, is a dual regulator that senses manganese and negatively or positively controls the transcription of different genes involved in manganese homeostasis [3, 4] This protein belongs to the DtxR family. The members of this family have three domains: an N-terminal domain with a helix-turn-helix motif, which binds to DNA; a central domain for dimerization and metal ion binding; and a C-terminal alpha-spectrin SH3-like domain. However, MntR lacks the SH3-like domain [3] The 3D structure of apo-MntR has been solved. The protein dimerizes via its C-terminal domain. The N-terminal and C-terminal domains are connected by a long α-helical linker [6] The N-terminal domain is expected to bind two manganese ions per monomer, in analogy to BsMntR from B. subtilis, which has been crystallized with and without bound manganese [7, 8] All residues involved in manganese binding in BsMntR ar conserved in MntR [6] MntR does not seem to be autoregulated [3] Many iron acquisition genes are derepressed in the mntR mutant [4] Read more >


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
MntR-Cd2+ Functional Allosteric Holo nd nd nd
MntR-Mn2+ Functional   Apo nd nd nd
TFBs length: 22
TFBs symmetry: inverted-repeat
Connectivity class: Local Regulator
Gene name: mntR
  Genome position: 853183-853650
  Length: 468 bp / 155 aa
Operon name: mntR-ybiR
TU(s) encoding the TF:
Transcription unit        Promoter
mntR-ybiR
mntRp


Regulon       
Regulated gene(s) dps, mntH, mntP, mntS, rybA
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
membrane (2)
incorporation of metal ions (1)
nucleoproteins, basic proteins (1)
starvation (1)
Porters (Uni-, Sym- and Antiporters) (1)
Read more >
Regulated operon(s) dps, mntH, mntP, rybA-mntS
First gene in the operon(s) dps, mntH, mntP, mntS
Simple and complex regulons Fis,H-NS,IHF,MntR,OxyR
Fur,MntR
Fur,MntR,OxyR
MntR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[MntR,+](1)
[MntR,-](4)


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
  MntR-Mn2+ repressor dpsp Sigma70 -17.5 -56.5 dps
gaatagcggaACACATAGCCGGTGCTATACTTaatctcgtta
 848957 848978 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1], [1]
  MntR-Mn2+ repressor dpsp2 Sigma38 -17.5 -56.5 dps
gaatagcggaACACATAGCCGGTGCTATACTTaatctcgtta
 848957 848978 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1], [1]
  MntR-Mn2+ repressor mntHp Sigma70 5.5 -23.5 mntH
gcatagcatgAAACATAGCAAAGGCTATGTTTtagaggcaca
 2512719 2512740 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2], [3], [3]
  MntR-Mn2+ activator mntPp Sigma70 -183.5 -412.5 mntP
aataagttatGAATTTAGCCAAAGCTATGTTTagtgtatttt
 1905265 1905286 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [4], [4]
  MntR-Mn2+ activator mntPp Sigma70 -143.5 -372.5 mntP
tttaataatcAGACATAGCTTAGGCTATATTAcctcttccct
 1905305 1905326 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [4], [4]
  MntR-Mn2+ repressor rybAp Sigma70 -19.5 -86.5 mntS, rybA
aaaaaattaaCGTTTTAGCAATAGCTATATAAtatagcctgt
 853073 853094 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ] S [4], [4], [5]
  MntR-Mn2+ repressor rybAp Sigma70 -0.5 -67.5 mntS, rybA
aatagctataTAATATAGCCTGTGCTATATCTgtatgtaatg
 853054 853075 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ] S [4], [4], [5]


Alignment and PSSM for MntR TFBSs    

Aligned TFBS of MntR   
  Sequence
  GATATAGCACAGGCTATATTATATA
  AACATAGCAAAGGCTATGTTTTAGA
  AATTTAGCCAAAGCTATGTTTAGTG
  AATATAGCCTAAGCTATGTCTGATT
  AGTATAGCACCGGCTATGTGTTCCG
  GTTTTAGCAATAGCTATATAATATA

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

Consensus    
;	consensus.strict             	aataTAGCaaagGCTATGTtttata
;	consensus.strict.rc          	TATAAAACATAGCCTTTGCTATATT
;	consensus.IUPAC              	ratwTAGCmmarGCTATRTtwtatr
;	consensus.IUPAC.rc           	YATAWAAYATAGCYTKKGCTAWATY
;	consensus.regexp             	[ag]at[at]TAGC[ac][ac]a[ag]GCTAT[AG]Tt[at]tat[ag]
;	consensus.regexp.rc          	[CT]ATA[AT]AA[CT]ATAGC[CT]T[GT][GT]GCTA[AT]AT[CT]

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    

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

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

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


Reference(s)    

 [1] Yamamoto K., Ishihama A., Busby SJ., Grainger DC., 2011, The Escherichia coli K-12 MntR miniregulon includes dps, which encodes the major stationary-phase DNA-binding protein., J Bacteriol 193(6):1477-80

 [2] Kehres DG., Janakiraman A., Slauch JM., Maguire ME., 2002, Regulation of Salmonella enterica serovar Typhimurium mntH transcription by H(2)O(2), Fe(2+), and Mn(2+)., J Bacteriol 184(12):3151-8

 [3] Patzer SI., Hantke K., 2001, Dual repression by Fe(2+)-Fur and Mn(2+)-MntR of the mntH gene, encoding an NRAMP-like Mn(2+) transporter in Escherichia coli., J Bacteriol 183(16):4806-13

 [4] Waters LS., Sandoval M., Storz G., 2011, The Escherichia coli MntR miniregulon includes genes encoding a small protein and an efflux pump required for manganese homeostasis., J Bacteriol 193(21):5887-97

 [5] 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

 [6] Tanaka T, Shinkai A, Bessho Y, Kumarevel T, Yokoyama S, 2009, Crystal structure of the manganese transport regulatory protein from Escherichia coli., Proteins, 77(3):741 10.1002/prot.22541

 [7] Glasfeld A, Guedon E, Helmann JD, Brennan RG, 2003, Structure of the manganese-bound manganese transport regulator of Bacillus subtilis., Nat Struct Biol, 10(8):652 10.1038/nsb951

 [8] DeWitt MA, Kliegman JI, Helmann JD, Brennan RG, Farrens DL, Glasfeld A, 2007, The conformations of the manganese transport regulator of Bacillus subtilis in its metal-free state., J Mol Biol, 365(5):1257 10.1016/j.jmb.2006.10.080


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