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MetR DNA-binding transcriptional dual regulator

Synonyms: MetR-L-homocysteine, MetR


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
MetR Non-Functional   Apo [BPP], [GEA], [SM] [1], [2]
MetR-L-homocysteine Functional Allosteric Holo [BPP], [GEA], [SM] [1], [2]
Evolutionary Family: LysR
Sensing class: Using internal synthesized signals
Connectivity class: Local Regulator
Gene name: metR
  Genome position: 4011863-4012816
  Length: 954 bp / 317 aa
Operon name: metR
TU(s) encoding the TF:
Transcription unit        Promoter
metR
metRp1
metR
metRp2


Regulon       
Regulated gene(s) glyA, hmp, metE, metH, metR
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
methionine (3)
amino acids (1)
glycine (1)
formyl-THF biosynthesis (1)
unassigned reversible reactions (1)
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Regulated operon(s) glyA, hmp, metE, metH, metR
First gene in the operon(s) glyA, hmp, metE, metH, metR, metR
Simple and complex regulons FNR,Fur,MetR,NsrR
Fur,MetR
MetJ,MetR
MetR,PurR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[MetR,+-](1)
[MetR,+](4)
[MetR,-](2)


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
  MetR-L-homocysteine dual glyAp Sigma70 -143.0 -210.0 glyA
atgtgatgaaGTGAAAAATTTGCATcacaaacctg
2685710 2685724 [BPP], [GEA], [HIBSCS], [IMP], [SM] [3], [4], [5], [6], [7]
  MetR-L-homocysteine activator glyAp Sigma70 -121.0 -188.0 glyA
catcacaaacCTGAAAAGAAATCCGtttccggttg
2685688 2685702 [BPP], [GEA], [HIBSCS], [SM] [3], [4], [5], [6]
  MetR activator hmpAp Sigma38 -80.0 -118.0 hmp
caggtttgtgATGCAAATTTTTCACttcatcacat
2685710 2685724 [BPP], [GEA], [HIBSCS], [IMP], [SM] [3], [4], [5], [6], [7]
  MetR-L-homocysteine activator metEp nd -62.0 -231.0 metE
tacttcgatcATGAAAGTCCTTCACttcggcatga
4012815 4012829 [BPP], [GEA], [HIBSCS] [2], [8], [9], [10], [11]
  MetR-L-homocysteine activator metEp nd -41.0 -210.0 metE
tcacttcggcATGAATAATTTGCGCttgaggaata
4012836 4012850 [BPP], [GEA] [8], [9], [10], [11]
  MetR activator metHp Sigma70 -57.0 -102.0 metH
tgagttaatgTTGAACAAATCTCATgttgcgtggt
4223719 4223733 [GEA], [HIBSCS] [8], [9], [10], [12]
  MetR-L-homocysteine repressor metRp1 nd 13.0 -27.0 metR
tattcctcaaGCGCAAATTATTCATgccgaagtga
4012836 4012850 [BPP], [GEA] [8], [9], [10], [11]
  MetR-L-homocysteine repressor metRp1 nd 34.0 -6.0 metR
tcatgccgaaGTGAAGGACTTTCATgatcgaagta
4012815 4012829 [BPP], [GEA], [HIBSCS] [2], [8], [9], [10], [11]
  MetR-L-homocysteine repressor metRp2 nd -6.0 -27.0 metR
tattcctcaaGCGCAAATTATTCATgccgaagtga
4012836 4012850 [BPP], [GEA] [8], [9], [10], [11]
  MetR-L-homocysteine repressor metRp2 nd 16.0 -6.0 metR
tcatgccgaaGTGAAGGACTTTCATgatcgaagta
4012815 4012829 [BPP], [GEA], [HIBSCS] [2], [8], [9], [10], [11]


Alignment and PSSM for MetR TFBSs    

Aligned TFBS of MetR   
  Sequence
  GAAAAGAAATCCGTTT
  GAAGTGAAAAATTTGC
  GAAGTGAAGGACTTTC
  GGCATGAATAATTTGC
  AACATGAGATTTGTTC

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

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

 [GEA] Gene expression analysis

 [SM] Site mutation

 [HIBSCS] Human inference based on similarity to consensus sequences

 [IMP] Inferred from mutant phenotype



Reference(s)    

 [1] Maxon ME., Wigboldus J., Brot N., Weissbach H., 1990, Structure-function studies on Escherichia coli MetR protein, a putative prokaryotic leucine zipper protein., Proc Natl Acad Sci U S A. 87(18):7076-9

 [2] Weissbach H., Brot N., 1991, Regulation of methionine synthesis in Escherichia coli., Mol Microbiol. 5(7):1593-7

 [3] Lorenz E., Stauffer GV., 1995, Characterization of the MetR binding sites for the glyA gene of Escherichia coli., J Bacteriol. 177(14):4113-20

 [4] Lorenz E., Stauffer GV., 1996, RNA polymerase, PurR and MetR interactions at the glyA promoter of Escherichia coli., Microbiology. 142 ( Pt 7):1819-24

 [5] Lorenz E., Stauffer GV., 1996, MetR-mediated repression of the glyA gene in Escherichia coli., FEMS Microbiol Lett. 144(2-3):229-33

 [6] Lorenz E., Stauffer GV., 1996, Cooperative MetR binding in the Escherichia coli glyA control region., FEMS Microbiol Lett. 137(2-3):147-52

 [7] Membrillo-Hernandez J., Coopamah MD., Channa A., Hughes MN., Poole RK., 1998, A novel mechanism for upregulation of the Escherichia coli K-12 hmp (flavohaemoglobin) gene by the 'NO releaser', S-nitrosoglutathione: nitrosation of homocysteine and modulation of MetR binding to the glyA-hmp intergenic region., Mol Microbiol. 29(4):1101-12

 [8] Cai XY., Maxon ME., Redfield B., Glass R., Brot N., Weissbach H., 1989, Methionine synthesis in Escherichia coli: effect of the MetR protein on metE and metH expression., Proc Natl Acad Sci U S A. 86(12):4407-11

 [9] Cai XY., Redfield B., Maxon M., Weissbach H., Brot N., 1989, The effect of homocysteine on MetR regulation of metE, metR and metH expression in vitro., Biochem Biophys Res Commun. 163(1):79-83

 [10] Jafri S., Urbanowski ML., Stauffer GV., 1995, A mutation in the rpoA gene encoding the alpha subunit of RNA polymerase that affects metE-metR transcription in Escherichia coli., J Bacteriol. 177(3):524-9

 [11] Maxon ME., Redfield B., Cai XY., Shoeman R., Fujita K., Fisher W., Stauffer G., Weissbach H., Brot N., 1989, Regulation of methionine synthesis in Escherichia coli: effect of the MetR protein on the expression of the metE and metR genes., Proc Natl Acad Sci U S A. 86(1):85-9

 [12] Old IG., Margarita D., Glass RE., Saint Girons I., 1990, Nucleotide sequence of the metH gene of Escherichia coli K-12 and comparison with that of Salmonella typhimurium LT2., Gene. 87(1):15-21



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