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Escherichia coli K-12 substr. MG1655 Protein: outer membrane protein; export and assembly of type 1 fimbriae



Gene: fimD Accession Numbers: EG10311 (EcoCyc), b4317, ECK4308

Synonyms: fimD_1, fimD_2, FimD usher

Regulation Summary Diagram: ?

Subunit composition of outer membrane protein; export and assembly of type 1 fimbriae = [FimD]2
         FimD monomer = FimD

Summary:
FimD is a member of the Fimbrial Usher Porin (FUP) family [Zhai02]. FimD is the usher constituent in the type 1 pilus (fimbrial) chaperone-usher pathway in Escherichia coli. During type 1 pilus assembly, the chaperone-subunit complex composed of the FimC chaperone and the FimA, FimF, FimG or FimH subunit is targeted to the FimD usher which facilitates assembly of the pilus and subsequent translocation across the outer membrane [Barnhart03]. Type 1 pili mediate recognition of and adhesion to, host tissues and much of our knowledge regarding type 1 pili in E. coli is derived from studies using uropathogenic strains.

FimD consists of 5 functional domains: an N-terminal domain, a pore domain that, in the resting state, is occluded by a plug domain and two carboxy-terminal domains [Capitani06, Nishiyama03, Remaut08]. The purified N-terminal 139 residues of FimD bind chaperone(FimC)-FimH and FimC-FimF complexes in vitro [Nishiyama03]. Cryo-electron microscopy of the FimD usher bound to translocating FimC-FimF-FimF-FimH suggests that the functional usher consists of a twinned-pore structure [Remaut08].

Deletion of fimD results in cells that either lack fimbrial structures or the occasional presence of a singular abnormal fimbrium [Klemm90]. Following pre-incubation with the FimC-FimH (chaperone-adhesin) complex, purified FimD from the E. coli K-12 strain W3110, assembles native-like pili from purified FimC-FimA proteins in vitro [Nishiyama08]. In vitro assembly of pili from purified proteins proceeds independently of cellular energy [Nishiyama08].

Subunit polymerisation at FimD occurs via a mechanism known as donor strand exchange (DSE) whereby the N-terminal extension of an incoming subunit replaces the FimC chaperone strand that transiently occupies a groove in the previously assembled subunit [Sauer02]. Crystal structures of a pilus biogenesis initiation complex (FimD-FimC-FimH) [Sauer02] and a post initiation elongation complex (FimD-FimC-FimF-FimG-FimH) [Geibel13] have been obtained. In the first case FimH is captured inside the FimD pore and the usher plug is displaced from the barrel to the periplasm. The chaperone (FimC)-FimH complex is held in place by interactions with the two periplasmic carboxy terminal domains of FimD. The crystal structure reported by [Geibel13] captures secretion of the pilus tip consisting of FimF-FimG-FimH through the usher pore. In this structure FimH is on the extracellular side of the pore, FimG is in the lumen of the pore and FimF is at the pore entry and remains in complex with the chaperone FimC.

FimD is homologous with the PapC protein of the P pili usher protein of uropathogenic E. coli [Thanassi98]. High-resolution electron microscopy revealed that PapC assembles into a 2nm diameter oligomeric pore complex [Thanassi98a].

Reviews: [Waksman09, Geibel11, Busch12, Allen12]

Gene Citations: [Schwan94, Dove97]

Locations: outer membrane

Map Position: [4,543,119 -> 4,545,755] (97.92 centisomes)
Length: 2637 bp / 878 aa

Molecular Weight of Polypeptide: 96.482 kD (from nucleotide sequence), 89.0 kD (experimental) [Klemm85 ]

Unification Links: ASAP:ABE-0014151 , CGSC:18349 , DIP:DIP-9612N , EchoBASE:EB0307 , EcoGene:EG10311 , EcoliWiki:b4317 , Mint:MINT-1292016 , OU-Microarray:b4317 , PortEco:fimD , PR:PRO_000022619 , Protein Model Portal:P30130 , RefSeq:NP_418737 , RegulonDB:EG10311 , SMR:P30130 , String:511145.b4317 , UniProt:P30130

Relationship Links: InterPro:IN-FAMILY:IPR000015 , InterPro:IN-FAMILY:IPR018030 , InterPro:IN-FAMILY:IPR025885 , InterPro:IN-FAMILY:IPR025949 , PDB:Structure:1ZDV , PDB:Structure:1ZDX , PDB:Structure:1ZE3 , PDB:Structure:3BWU , PDB:Structure:3OHN , PDB:Structure:3RFZ , PDB:Structure:4J3O , Pfam:IN-FAMILY:PF00577 , Pfam:IN-FAMILY:PF13953 , Pfam:IN-FAMILY:PF13954 , Prosite:IN-FAMILY:PS01151

In Paralogous Gene Group: 43 (37 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009297 - pilus assembly Inferred from experiment [Nishiyama08]
GO:0055085 - transmembrane transport Inferred from experiment [Nishiyama08]
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0015473 - fimbrial usher porin activity Inferred from experiment [Nishiyama08]
GO:0005215 - transporter activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0009279 - cell outer membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Klemm90]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure pilus

Essentiality data for fimD knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Credits:
Last-Curated ? 13-May-2013 by Mackie A , Macquarie University
Revised 13-May-2013 by Mackie A , Macquarie University


Sequence Features

Feature Class Location Citations Comment
Signal-Sequence 1 -> 45
[Nishiyama03, UniProt12a]
Chain 46 -> 878
[UniProt09]
UniProt: Outer membrane usher protein fimD;
Sequence-Conflict 143 -> 148
[Klemm90, UniProt10]
Alternate sequence: QDATAH → RTLLRT; UniProt: (in Ref. 1; CAA35968);
Sequence-Conflict 352 -> 402
[Klemm90, UniProt10]
Alternate sequence: DGSTQIFTVPYSSVPLLQREGHTRYSITAGEYRSGNAQQEKTRFFQSTLLH → VLAARRFLPYPIRTFPLLNVKAYSLFHYGRRIPYESRSRKKPAFSRVHYSN; UniProt: (in Ref. 1);
Sequence-Conflict 658 -> 670
[Klemm90, UniProt10]
Alternate sequence: GGDGNSGSTGYAT → EAMEIAEVQATP; UniProt: (in Ref. 1);
Sequence-Conflict 723 -> 742
[Klemm90, UniProt10]
Alternate sequence: APGAKDAKVENQTGVRTDWR → RLAQKMQKSKTRRGAYRLA; UniProt: (in Ref. 1; CAA35968);
Disulfide-Bond-Site 877, 855
[UniProt10a]
UniProt: Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b4317 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10311; confirmed by SwissProt match.


References

Allen12: Allen WJ, Phan G, Waksman G (2012). "Pilus biogenesis at the outer membrane of Gram-negative bacterial pathogens." Curr Opin Struct Biol 22(4);500-6. PMID: 22402496

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Barnhart03: Barnhart MM, Sauer FG, Pinkner JS, Hultgren SJ (2003). "Chaperone-subunit-usher interactions required for donor strand exchange during bacterial pilus assembly." J Bacteriol 185(9);2723-30. PMID: 12700251

Busch12: Busch A, Waksman G (2012). "Chaperone-usher pathways: diversity and pilus assembly mechanism." Philos Trans R Soc Lond B Biol Sci 367(1592);1112-22. PMID: 22411982

Capitani06: Capitani G, Eidam O, Grutter MG (2006). "Evidence for a novel domain of bacterial outer membrane ushers." Proteins 65(4);816-23. PMID: 17066380

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Dove97: 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. PMID: 9108285

Geibel11: Geibel S, Waksman G (2011). "Crystallography and electron microscopy of chaperone/usher pilus systems." Adv Exp Med Biol 715;159-74. PMID: 21557063

Geibel13: Geibel S, Procko E, Hultgren SJ, Baker D, Waksman G (2013). "Structural and energetic basis of folded-protein transport by the FimD usher." Nature 496(7444);243-6. PMID: 23579681

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Klemm85: Klemm P, Jorgensen BJ, van Die I, de Ree H, Bergmans H (1985). "The fim genes responsible for synthesis of type 1 fimbriae in Escherichia coli, cloning and genetic organization." Mol Gen Genet 199(3);410-4. PMID: 2863734

Klemm90: Klemm P, Christiansen G (1990). "The fimD gene required for cell surface localization of Escherichia coli type 1 fimbriae." Mol Gen Genet 1990;220(2);334-8. PMID: 1970114

Nishiyama03: Nishiyama M, Vetsch M, Puorger C, Jelesarov I, Glockshuber R (2003). "Identification and characterization of the chaperone-subunit complex-binding domain from the type 1 pilus assembly platform FimD." J Mol Biol 330(3);513-25. PMID: 12842468

Nishiyama08: Nishiyama M, Ishikawa T, Rechsteiner H, Glockshuber R (2008). "Reconstitution of pilus assembly reveals a bacterial outer membrane catalyst." Science 320(5874);376-9. PMID: 18369105

Remaut08: Remaut H, Tang C, Henderson NS, Pinkner JS, Wang T, Hultgren SJ, Thanassi DG, Waksman G, Li H (2008). "Fiber formation across the bacterial outer membrane by the chaperone/usher pathway." Cell 133(4);640-52. PMID: 18485872

Sauer02: Sauer FG, Pinkner JS, Waksman G, Hultgren SJ (2002). "Chaperone priming of pilus subunits facilitates a topological transition that drives fiber formation." Cell 111(4);543-51. PMID: 12437927

Schwan94: Schwan WR, Seifert HS, Duncan JL (1994). "Analysis of the fimB promoter region involved in type 1 pilus phase variation in Escherichia coli." Mol Gen Genet 1994;242(5);623-30. PMID: 8121417

Thanassi98: Thanassi DG, Saulino ET, Hultgren SJ (1998). "The chaperone/usher pathway: a major terminal branch of the general secretory pathway." Curr Opin Microbiol 1(2);223-31. PMID: 10066482

Thanassi98a: Thanassi DG, Saulino ET, Lombardo MJ, Roth R, Heuser J, Hultgren SJ (1998). "The PapC usher forms an oligomeric channel: implications for pilus biogenesis across the outer membrane." Proc Natl Acad Sci U S A 95(6);3146-51. PMID: 9501230

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt12a: UniProt Consortium (2012). "UniProt version 2012-11 released on 2012-11-26 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

Waksman09: Waksman G, Hultgren SJ (2009). "Structural biology of the chaperone-usher pathway of pilus biogenesis." Nat Rev Microbiol 7(11);765-74. PMID: 19820722

Zhai02: Zhai Y, Saier MH (2002). "The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes." Protein Sci 11(9);2196-207. PMID: 12192075

Other References Related to Gene Regulation

Abraham85: Abraham JM, Freitag CS, Clements JR, Eisenstein BI (1985). "An invertible element of DNA controls phase variation of type 1 fimbriae of Escherichia coli." Proc Natl Acad Sci U S A 82(17);5724-7. PMID: 2863818

Blomfield97: Blomfield IC, Kulasekara DH, Eisenstein BI (1997). "Integration host factor stimulates both FimB- and FimE-mediated site-specific DNA inversion that controls phase variation of type 1 fimbriae expression in Escherichia coli." Mol Microbiol 23(4);705-17. PMID: 9157242

Blumer05: Blumer C, Kleefeld A, Lehnen D, Heintz M, Dobrindt U, Nagy G, Michaelis K, Emody L, Polen T, Rachel R, Wendisch VF, Unden G (2005). "Regulation of type 1 fimbriae synthesis and biofilm formation by the transcriptional regulator LrhA of Escherichia coli." Microbiology 151(Pt 10);3287-98. PMID: 16207912

Dorman87: Dorman CJ, Higgins CF (1987). "Fimbrial phase variation in Escherichia coli: dependence on integration host factor and homologies with other site-specific recombinases." J Bacteriol 169(8);3840-3. PMID: 2886490

Dove96: Dove SL, Dorman CJ (1996). "Multicopy fimB gene expression in Escherichia coli: binding to inverted repeats in vivo, effect on fimA gene transcription and DNA inversion." Mol Microbiol 21(6);1161-73. PMID: 8898385

Gally94: Gally DL, Rucker TJ, Blomfield IC (1994). "The leucine-responsive regulatory protein binds to the fim switch to control phase variation of type 1 fimbrial expression in Escherichia coli K-12." J Bacteriol 1994;176(18);5665-72. PMID: 7916011

Gally96: 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. PMID: 8878036

Kawula91: Kawula TH, Orndorff PE (1991). "Rapid site-specific DNA inversion in Escherichia coli mutants lacking the histonelike protein H-NS." J Bacteriol 173(13);4116-23. PMID: 1648076

Kulasekara99: Kulasekara HD, Blomfield IC (1999). "The molecular basis for the specificity of fimE in the phase variation of type 1 fimbriae of Escherichia coli K-12." Mol Microbiol 31(4);1171-81. PMID: 10096084

McClain93: McClain MS, Blomfield IC, Eberhardt KJ, Eisenstein BI (1993). "Inversion-independent phase variation of type 1 fimbriae in Escherichia coli." J Bacteriol 175(14);4335-44. PMID: 8101185

Olsen94: Olsen PB, Klemm P (1994). "Localization of promoters in the fim gene cluster and the effect of H-NS on the transcription of fimB and fimE." FEMS Microbiol Lett 1994;116(1);95-100. PMID: 7510658

Roesch98: Roesch PL, Blomfield IC (1998). "Leucine alters the interaction of the leucine-responsive regulatory protein (Lrp) with the fim switch to stimulate site-specific recombination in Escherichia coli." Mol Microbiol 1998;27(4);751-61. PMID: 9515701

Schembri98: Schembri MA, Olsen PB, Klemm P (1998). "Orientation-dependent enhancement by H-NS of the activity of the type 1 fimbrial phase switch promoter in Escherichia coli." Mol Gen Genet 1998;259(3);336-44. PMID: 9749677


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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