A protein export pathway involving Escherichia coli porins

Structure

Volumn 20, Issue 7, 2012, Pages 1154-1166

  Prehna, Gerd ^a   Zhang, Guijin ^c   Gong, Xiandi ^d   Duszyk, Marek ^c   Okon, Mark ^a,b   McIntosh, Lawrence P ^a,b   Weiner, Joel H ^c   Strynadka, Natalie C J ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^c UNIVERSITY OF ALBERTA   (Canada)

^d INSTITUTE OF MICROELECTRONICS   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

OUTER MEMBRANE PROTEIN; OUTER MEMBRANE PROTEIN C; OUTER MEMBRANE PROTEIN F; OUTER MEMBRANE PROTEIN X; PORIN; PROTEIN; UNCLASSIFIED DRUG; YEBF PROTEIN;

AMINO ACID SUBSTITUTION; ARTICLE; CONFORMATION; ENTEROBACTERIACEAE; ESCHERICHIA COLI; GENETICS; LIPID BILAYER; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN TRANSPORT; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; BACTERIAL OUTER MEMBRANE PROTEINS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; HYDROLASES; LIPID BILAYERS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PLASMIDS; PORINS; PROTEIN STRUCTURE, SECONDARY; PROTEIN TRANSPORT; RECOMBINANT PROTEINS; SEQUENCE ALIGNMENT; STATIC ELECTRICITY; TRANSFORMATION, BACTERIAL;

ENTEROBACTERIACEAE; ESCHERICHIA COLI;

EID: 84863533501     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2012.04.014     Document Type: Article

References (56)

1. S.F. Altschul, T.L. Madden, A.A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402 (Pubitemid 27359211)
2. H. Ashkenazy, E. Erez, E. Martz, T. Pupko, and N. Ben-Tal ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids Nucleic Acids Res. 38 Web Server issue 2010 W529 W533
3. T. Baba, T. Ara, M. Hasegawa, Y. Takai, Y. Okumura, M. Baba, K.A. Datsenko, M. Tomita, B.L. Wanner, and H. Mori Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection Mol. Syst. Biol. 2 2006 2:2006.0008
4. A.J. Baldwin, and L.E. Kay NMR spectroscopy brings invisible protein states into focus Nat. Chem. Biol. 5 2009 808 814
5. B.C. Berks, F. Sargent, and T. Palmer The Tat protein export pathway Mol. Microbiol. 35 2000 260 274 (Pubitemid 30055224)
6. V.M. Bolanos-Garcia, and O.R. Davies Structural analysis and classification of native proteins from E. coli commonly co-purified by immobilised metal affinity chromatography Biochim. Biophys. Acta 1760 2006 1304 1313 (Pubitemid 44374210)
7. C.S. Bond, and A.W. Schüttelkopf ALINE: a WYSIWYG protein-sequence alignment editor for publication-quality alignments Acta Crystallogr. D Biol. Crystallogr. 65 2009 510 512
8. A.T. Brünger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, R.W. Grosse-Kunstleve, J.S. Jiang, J. Kuszewski, M. Nilges, and N.S. Pannu Crystallography & NMR system: A new software suite for macromolecular structure determination Acta Crystallogr. D Biol. Crystallogr. 54 1998 905 921
9. P.S. Choi, and H.D. Bernstein Sequential translocation of an Escherchia coli two-partner secretion pathway exoprotein across the inner and outer membranes Mol. Microbiol. 75 2010 440 451
10. B. Clantin, A.S. Delattre, P. Rucktooa, N. Saint, A.C. Méli, C. Locht, F. Jacob-Dubuisson, and V. Villeret Structure of the membrane protein FhaC: a member of the Omp85-TpsB transporter superfamily Science 317 2007 957 961 (Pubitemid 47301325)
11. C. Cole, J.D. Barber, and G.J. Barton The Jpred 3 secondary structure prediction server Nucleic Acids Res. 36 Web Server issue 2008 W197 W201
12. R.F. Collins, R.C. Ford, A. Kitmitto, R.O. Olsen, T. Tonjum, and J.P. Derrick Three-dimensional structure of the Neisseria meningitidis secretin PilQ determined from negative-stain transmission electron microscopy J. Bacteriol. 185 2003 2611 2617 (Pubitemid 36417986)
13. C. d'Enfert, C. Chapon, and A.P. Pugsley Export and secretion of the lipoprotein pullulanase by Klebsiella pneumoniae Mol. Microbiol. 1 1987 107 116
14. F. Delaglio, S. Grzesiek, G.W. Vuister, G. Zhu, J. Pfeifer, and A. Bax NMRPipe: a multidimensional spectral processing system based on UNIX pipes J. Biomol. NMR 6 1995 277 293
15. DeLano, W.L. The PyMOL Molecular Graphics System. (2002). DeLano Scientific, San Carlos, CA, USA. Available at http://www.pymol.org.
16. T.J. Dolinsky, P. Czodrowski, H. Li, J.E. Nielsen, J.H. Jensen, G. Klebe, and N.A. Baker PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations Nucleic Acids Res. 35 Web Server issue 2007 W522 W525
17. C. Dong, K. Beis, J. Nesper, A.L. Brunkan-Lamontagne, B.R. Clarke, C. Whitfield, and J.H. Naismith Wza the translocon for E. coli capsular polysaccharides defines a new class of membrane protein Nature 444 2006 226 229 (Pubitemid 44722064)
18. A.J. Driessen, P. Fekkes, and J.P. van der Wolk The Sec system Curr. Opin. Microbiol. 1 1998 216 222 (Pubitemid 128428063)
19. M. Dupont, C.E. James, J. Chevalier, and J.M. Pagès An early response to environmental stress involves regulation of OmpX and OmpF, two enterobacterial outer membrane pore-forming proteins Antimicrob. Agents Chemother. 51 2007 3190 3198 (Pubitemid 350067527)
20. H.J. Dyson, and P.E. Wright Intrinsically unstructured proteins and their functions Nat. Rev. Mol. Cell Biol. 6 2005 197 208 (Pubitemid 40314921)
21. O. Emanuelsson, S. Brunak, G. von Heijne, and H. Nielsen Locating proteins in the cell using TargetP, SignalP and related tools Nat. Protoc. 2 2007 953 971 (Pubitemid 46745592)
22. A. Filloux, G. Michel, and M. Bally GSP-dependent protein secretion in gram-negative bacteria: the Xcp system of Pseudomonas aeruginosa FEMS Microbiol. Rev. 22 1998 177 198 (Pubitemid 28493357)
23. A.C. Fisher, C.H. Haitjema, C. Guarino, E. Çelik, C.E. Endicott, C.A. Reading, J.H. Merritt, A.C. Ptak, S. Zhang, and M.P. DeLisa Production of secretory and extracellular N-linked glycoproteins in Escherichia coli Appl. Environ. Microbiol. 77 2011 871 881
24. O. Francetic, D. Belin, C. Badaut, and A.P. Pugsley Expression of the endogenous type II secretion pathway in Escherichia coli leads to chitinase secretion EMBO J. 19 2000 6697 6703 (Pubitemid 32011662)
25. K.B. Gehring, and H. Nikaido Existence and purification of porin heterotrimers of Escherichia coli K12 OmpC, OmpF, and PhoE proteins J. Biol. Chem. 264 1989 2810 2815 (Pubitemid 19057775)
26. F. Gérard, M.A. Brooks, H. Barreteau, T. Touzé, M. Graille, A. Bouhss, D. Blanot, H. van Tilbeurgh, and D. Mengin-Lecreulx X-ray structure and site-directed mutagenesis analysis of the Escherichia coli colicin M immunity protein J. Bacteriol. 193 2011 205 214
27. P. Güntert, C. Mumenthaler, and K. Wüthrich Torsion angle dynamics for NMR structure calculation with the new program DYANA J. Mol. Biol. 273 1997 283 298 (Pubitemid 27460230)
28. S.Y. He, C. Schoedel, A.K. Chatterjee, and A. Collmer Extracellular secretion of pectate lyase by the Erwinia chrysanthemi out pathway is dependent upon Sec-mediated export across the inner membrane J. Bacteriol. 173 1991 4310 4317
29. T. Herrmann, P. Güntert, and K. Wüthrich Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA J. Mol. Biol. 319 2002 209 227 (Pubitemid 34729497)
30. L. Holm, and P. Rosenström Dali server: conservation mapping in 3D Nucleic Acids Res. 38 Web Server issue 2010 W545 W549
31. N.G. Housden, J.A. Wojdyla, J. Korczynska, I. Grishkovskaya, N. Kirkpatrick, A.M. Brzozowski, and C. Kleanthous Directed epitope delivery across the Escherichia coli outer membrane through the porin OmpF Proc. Natl. Acad. Sci. USA 107 2010 21412 21417
32. R. Ieva, P. Tian, J.H. Peterson, and H.D. Bernstein Sequential and spatially restricted interactions of assembly factors with an autotransporter beta domain Proc. Natl. Acad. Sci. USA 108 2011 E383 E391
33. K. Inaba Disulfide bond formation system in Escherichia coli J. Biochem. 146 2009 591 597
34. K. Kjaergaard, H. Hasman, M.A. Schembri, and P. Klemm Antigen 43-mediated autotransporter display, a versatile bacterial cell surface presentation system J. Bacteriol. 184 2002 4197 4204 (Pubitemid 34774300)
35. C. Kleanthous Swimming against the tide: progress and challenges in our understanding of colicin translocation Nat. Rev. Microbiol. 8 2010 843 848
36. R. Koebnik, K.P. Locher, and P. Van Gelder Structure and function of bacterial outer membrane proteins: barrels in a nutshell Mol. Microbiol. 37 2000 239 253 (Pubitemid 30481009)
37. R. Koradi, M. Billeter, and K. Wuthrich MOLMOL: a program for display and analysis of macromolecular structures J. Mol. Graph. 14 1996 51 55 29-32 (Pubitemid 26152976)
38. R.A. Laskowski, M.W. Macarthur, D.S. Moss, and J.M. Thornton Procheck - a program to check the stereochemical quality of protein structures J. Appl. Cryst. 26 1993 283 291
39. J.C. Leo, I. Grin, and D. Linke Type V secretion: mechanism(s) of autotransport through the bacterial outer membrane Philos. Trans. R. Soc. Lond. B Biol. Sci. 367 2012 1088 1101
40. J.P. Linge, M.A. Williams, C.A. Spronk, A.M. Bonvin, and M. Nilges Refinement of protein structures in explicit solvent Proteins 50 2003 496 506 (Pubitemid 36158461)
41. H. Nikaido Molecular basis of bacterial outer membrane permeability revisited Microbiol. Mol. Biol. Rev. 67 2003 593 656 (Pubitemid 37549772)
42. N. Nouwen, N. Ranson, H. Saibil, B. Wolpensinger, A. Engel, A. Ghazi, and A.P. Pugsley Secretin PulD: association with pilot PulS, structure, and ion-conducting channel formation Proc. Natl. Acad. Sci. USA 96 1999 8173 8177 (Pubitemid 29328427)
43. A. Pautsch, J. Vogt, K. Model, C. Siebold, and G.E. Schulz Strategy for membrane protein crystallization exemplified with OmpA and OmpX Proteins 34 1999 167 172 (Pubitemid 29028802)
44. M. Sattler, J. Schleucher, and C. Griesinger Heteronuclear multidimensional NMRexperiments for the structure determination of proteins in solution employing pulsed field gradients Prog. Nucl. Mag. Res. Sp. 34 1999 93 158 (Pubitemid 129595216)
45. Y. Shen, F. Delaglio, G. Cornilescu, and A. Bax TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts J. Biomol. NMR 44 2009 213 223
46. N.J. Traaseth, and G. Veglia Probing excited states and activation energy for the integral membrane protein phospholamban by NMR CPMG relaxation dispersion experiments Biochim. Biophys. Acta 1798 2010 77 81
47. T.T. Tseng, B.M. Tyler, and J.C. Setubal Protein secretion systems in bacterial-host associations, and their description in the Gene Ontology BMC Microbiol. 9 Suppl 1 2009 S2
48. D. Vertommen, M. Depuydt, J. Pan, P. Leverrier, L. Knoops, J.P. Szikora, J. Messens, J.C. Bardwell, and J.F. Collet The disulphide isomerase DsbC cooperates with the oxidase DsbA in a DsbD-independent manner Mol. Microbiol. 67 2008 336 349 (Pubitemid 350295830)
49. J. Vogt, and G.E. Schulz The structure of the outer membrane protein OmpX from Escherichia coli reveals possible mechanisms of virulence Structure 7 1999 1301 1309 (Pubitemid 29482991)
50. J.J. Ward, J.S. Sodhi, L.J. McGuffin, B.F. Buxton, and D.T. Jones Prediction and functional analysis of native disorder in proteins from the three kingdoms of life J. Mol. Biol. 337 2004 635 645 (Pubitemid 38326883)
51. J.H. Weiner, P.T. Bilous, G.M. Shaw, S.P. Lubitz, L. Frost, G.H. Thomas, J.A. Cole, and R.J. Turner A novel and ubiquitous system for membrane targeting and secretion of cofactor-containing proteins Cell 93 1998 93 101 (Pubitemid 28173555)
52. E. Yamashita, M.V. Zhalnina, S.D. Zakharov, O. Sharma, and W.A. Cramer Crystal structures of the OmpF porin: function in a colicin translocon EMBO J. 27 2008 2171 2180
53. M.R. Yen, C.R. Peabody, S.M. Partovi, Y. Zhai, Y.H. Tseng, and M.H. Saier Protein-translocating outer membrane porins of Gram-negative bacteria Biochim. Biophys. Acta 1562 2002 6 31 (Pubitemid 34461941)
54. S.D. Zakharov, V.Y. Eroukova, T.I. Rokitskaya, M.V. Zhalnina, O. Sharma, P.J. Loll, H.I. Zgurskaya, Y.N. Antonenko, and W.A. Cramer Colicin occlusion of OmpF and TolC channels: outer membrane translocons for colicin import Biophys. J. 87 2004 3901 3911 (Pubitemid 39602896)
55. G. Zhang, S. Brokx, and J.H. Weiner Extracellular accumulation of recombinant proteins fused to the carrier protein YebF in Escherichia coli Nat. Biotechnol. 24 2006 100 104 (Pubitemid 43083173)
56. C. Zwahlen, P. Legault, S.J.F. Vincent, J. Greenblatt, R. Konrat, and L.E. Kay Methods for measurement of intermolecular NOEs by multinuclear NMR spectroscopy: application to a bacteriophage lambda N-peptide/boxB RNA complex J. Am. Chem. Soc. 119 1997 6711 6721 (Pubitemid 27343493)