RegulonDB RegulonDB 10.6.3: Gene Form
   

fimB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

nanC fimB fimE fimA3\' BasR NagC IHF NagC CRP NanR NanR NanR DksA DksA-ppGpp DksA-ppGpp ppGpp terminator anti-terminator anti-anti-terminator fimEp fimEp fimBp1 fimBp1 TSS_5131 TSS_5131 fimBp2 fimBp2 nanCp nanCp

Gene      
Name: fimB    Texpresso search in the literature
Synonym(s): ECK4303, EG10309, b4312, pil
Genome position(nucleotides): 4540957 --> 4541559 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
43.45
Note(s):
fimB transcription is regulated by growth phase and its repression require the alternative sigma factor, RpoS during enter stationary phase. Although the mechanism by which RpoS achieves negative control is unknown it is possible that the effect on fimB is exerted indirectly Dove SL,1997
By making use of microarray analysis, Constantinidou et al Constantinidou C,2006 concluded that FNR represses fimB gene expression, but it is not know which of the three promoters (fimBp1, fimBp2, fimBp3) is affected. They also identified a putative FNR binding site upstream of the gene, but the sequence was not shown.
Reference(s): [1] Dove SL., et al., 1997
External database links:  
ASAP:
ABE-0014141
CGSC:
18355
ECHOBASE:
EB0305
ECOCYC:
EG10309
ECOLIHUB:
fimB
OU-MICROARRAY:
b4312
REGULONDB:
b4312
STRING:
511145.b4312
M3D: fimB
COLOMBOS: fimB
PortEco: b4312


Shine dalgarno      
Sequence: tctgtaattaTAAGGGaaaaacgATG


Product      
Name: regulator for fimA
Synonym(s): FimB, Pil
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 22.993
Isoelectric point: 10.687
Motif(s):
 
Type Positions Sequence
85 -> 85 E
12 -> 180 FLTHSEIESLLKAANTGPHAARNYCLTLLCFIHGFRASEICRLRISDIDLKAKCIYIHRLKKGFSTTHPLLNKEVQALKNWLSIRTSYPHAESEWVFLSRKGNPLSRQQFYHIISTSGGNAGLSLEIHPHMLRHSCGFALANMGIDTRLIQDYLGHRNIRHTVWYTASN
13 -> 13 L
32 -> 32 A

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.6 - biosynthesis of macromolecules (cellular constituents) --> 1.6.13 - fimbri, pili
  2 - information transfer --> 2.1 - DNA related --> 2.1.3 - DNA recombination
  3 - regulation --> 3.1 - type of regulation --> 3.1.1 - DNA structure level
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.1 - operon
  6 - cell structure --> 6.5 - pilus
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
biological_process GO:0006310 - DNA recombination
GO:0006974 - cellular response to DNA damage stimulus
GO:0015074 - DNA integration
Note(s): Note(s): ...[more].
Evidence: [AUP] Assay of unpurified protein
Reference(s): [2] Burns LS., et al., 2000
[3] Gally DL., et al., 1996
[4] Hasman H., et al., 2000
[5] Teng CH., et al., 2006
[6] Wolf DM., et al., 2002
External database links:  
DIP:
DIP-47842N
ECOCYC:
EG10309-MONOMER
ECOLIWIKI:
b4312
INTERPRO:
IPR002104
INTERPRO:
IPR013762
INTERPRO:
IPR011010
MINT:
MINT-1221137
MODBASE:
P0ADH5
PFAM:
PF00589
PRIDE:
P0ADH5
PRODB:
PRO_000022617
PROTEINMODELPORTAL:
P0ADH5
REFSEQ:
NP_418732
SMR:
P0ADH5
UNIPROT:
P0ADH5


Operon      
Name: fimB         
Operon arrangement:
Transcription unit        Promoter
fimB
fimB
fimB


Transcriptional Regulation      
Display Regulation             
Activated by: NagC, IHF, BasR, NanR
Repressed by: H-NS


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_5131 4540686 forward nd [RS-EPT-CBR] [7]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates



Reference(s)    

 [1] Dove SL., Smith SG., Dorman CJ., 1997, Control of Escherichia coli type 1 fimbrial gene expression in stationary phase: a negative role for RpoS., Mol Gen Genet 254(1):13-20

 [2] Burns LS., Smith SG., Dorman CJ., 2000, Interaction of the FimB integrase with the fimS invertible DNA element in Escherichia coli in vivo and in vitro., J Bacteriol 182(10):2953-9

 [3] Gally DL., Leathart J., Blomfield IC., 1996, Interaction of FimB and FimE with the fim switch that controls the phase variation of type 1 fimbriae in Escherichia coli K-12., Mol Microbiol 21(4):725-38

 [4] Hasman H., Schembri MA., Klemm P., 2000, Antigen 43 and type 1 fimbriae determine colony morphology of Escherichia coli K-12., J Bacteriol 182(4):1089-95

 [5] Teng CH., Xie Y., Shin S., Di Cello F., Paul-Satyaseela M., Cai M., Kim KS., 2006, Effects of ompA deletion on expression of type 1 fimbriae in Escherichia coli K1 strain RS218 and on the association of E. coli with human brain microvascular endothelial cells., Infect Immun 74(10):5609-16

 [6] Wolf DM., Arkin AP., 2002, Fifteen minutes of fim: control of type 1 pili expression in E. coli., OMICS 6(1):91-114

 [7] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Mu¿¿iz-Rascado L, Garc¿¿a-Sotelo JS, Weiss V, Solano-Lira H, Mart¿¿nez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hern¿¿ndez S, Alquicira-Hern¿¿ndez K, L¿¿pez-Fuentes A, Porr¿¿n-Sotelo L, Huerta AM, Bonavides-Mart¿¿nez C, Balderas-Mart¿¿nez YI, Pannier L, Olvera M, Labastida A, Jim¿¿nez-Jacinto V, Vega-Alvarado L, Del Moral-Ch¿¿vez V, Hern¿¿ndez-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.


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