Characterization of Bacterial Membrane Proteins Using a Novel Combination of a Lipid Based Protein Immobilization Technique with Mass Spectrometry

Mass Spectrometry for Microbial Proteomics

Volumn , Issue , 2010, Pages 157-174

  Karlsson, Roger ^a   Chooneea, Darren ^b   Carlsohn, Elisabet ^c   Encheva, Vesela ^b,d   Shah, Haroun N ^b  

^a UNIVERSITY OF GOTHENBURG   (Sweden)

^b PUBLIC HEALTH ENGLAND   (United Kingdom)

^c UNIVERSITY OF GOTHENBURG   (Sweden)

^d LGC   (United Kingdom)

Author keywords

Bacterial membrane protein characterization novel combination of lipid based protein immobilization technique with mass spectrometry; Helicobacter pylori disease mechanism and outer membrane proteins; Lipid based immobilization technique elucidating outer membrane proteome of S. Typhimurium; Lipid based protein immobilization (LPI) technique by Nanoxis AB; Pathogenic bacterial proteomics; Salmonella typhimurium disease mechanism and outer membrane proteins; Structure of cell envelope of Gram positive and Gram negative bacteria; Surface proteins, outer membrane proteins (OMPs) importance for pathogenic bacteria

Indexed keywords

EID: 84860605152     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470665497.ch8     Document Type: Chapter

References (68)

1. Arrigo , K.R. Marine microorganisms and global nutrient cycles . Nature 2005 , 437: 349 - 355 .
2. Backert , S. and Selbach , M. Role of type IV secretion in Helicobacter pylori pathogenesis Cell. Microbiol. 2008 , 10 ( 8 ), 1573 - 1581 .
3. Baik, S.C., Kim, K.M., Song, S.M., Kim, D.S., Jun, J.S., Lee, S.G., Song, J.Y., Park, J.U., Kang, H.L., Lee, W.K., Cho, M.J., Youn, H.S., Ko, G.H. and Rhee, K.H. Proteomic analysis of the sarcosine - insoluble outer membrane fraction of Helicobacter pylori strain 26695 . J. Bacteriol. 2004, 186 ( 4 ), 949 - 955 .
4. Baker, S. and Dougan, G. The genome of Salmonella enterica serovar Typhi . Clin. Infect. Dis. 2007, 45, 29 - 33 .
5. Baumler, A.J., Tsolis, R.M., Ficht, T.A. and Adams, L.G. Evolution of host adaptation in Salmonella enterica . Infect. Immun. 1998, 66 ( 10 ), 4579 - 4587 .
6. Bergey, D.H., Holt, J.G., Krieg, N.R. and Sneath, P.H.A. Bergey ' s Manual of Determinative Bacteriology, 9th edn. Baltimore: Lippincott Williams &Wilkins, 1994 .
7. Beveridge, T.J. Use of the gram stain in microbiology . Biotech. Histochem. 2001, 76 ( 3 ), 111 - 118 .
8. Bopp, C.A., Brenner, F.W., Wells, J.G. and Strockbine, N.A . In: Manual of Clinical Microbiology, Murray, P.R., Baron, E.J., Jorgensen, J.H., Pfaller, M.A. and Yolken, R.H., editors. Washington, DC: ASM Press, 2003, 654 - 671 .
9. Braun, R.J., Kinkl, N., Beer, M. and Ueffing, M. Two - dimensional electrophoresis of membrane proteins . Anal. Bioanal. Chem. 2007, 389 ( 4 ), 1033 - 1045 .
10. Brown, L.M. Helicobacter pylori: epidemiology and routes of transmission . Epidemiol. Rev. 2000, 22 ( 2 ), 283 - 297 .
11. Bumann, D., Aksu, S., Wendland, M., Janek, K., Zimny - Arndt, U., Sabarth, N., Meyer, T.F. and Jungblut, P.R. Proteome analysis of secreted proteins of the gastric pathogen Helicobacter pylori . Infect. Immun. 2002a, 70 ( 7 ), 3396 - 3403 .
12. Buman, D., Holland, P., Siejak, F., Koesling, J., Sabarth, N., Lamer, S., Zimny-Arndt, U., Jungblut, P.R. and Meyer, T.F. A comparison of murina and human immunoproteomes of Helicobacter pylori validates the preclinical murine infection model for antigen screening . Infect. Immun. 2002b, 70 ( 11 ), 6494-6498 .
13. Carlsohn, E., Nyström, J., Karlsson, H., Svennerholm, A.-M. and Nilsson, C.L. Characterization of the outer membrane protein profi le from disease-related Helicobacter pylori isolates by subcellular fractionation and nano-LC FT-ICR MS analysis . J. Proteome Res. 2006a, 5, 3197-3204 .
14. Carlsohn, E., Nystr ö m, J., B ö lin, I., Nilsson, C.L. and Svennerholm, A.-M. HpaA is essential for Helicobacter pylori colonization in mice . Infect. Immun. 2006b, 74 ( 2 ), 920-926 .
15. Coldham, N.G. and Woodward, M.J. Characterization of the Salmonella Typhimurium proteome by semi-automated two-dimensional HPLC-mass spectrometry: Detection of proteins implicated in multiple antibiotic resistance . J. Proteome Res. 2004, 3, 595-603 .
16. Cole, J.N., Ramirez, R.D., Currie, B.J., Cordwell, S.J., Djordjevic, S.P. and Walker, M.J. Surface analyses and immune reactivities of major cell wall-associated proteins of group a streptococcus . Infect. Immun. 2005, 73 ( 5 ), 3137-3146 .
17. Cordwell, S.J. Sequential extraction of proteins by chemical reagents . Methods Mol. Biol. 2008, 424, 139-146 .
18. de Jonge, R., Durrani, Z., Rijpkema, S.G., Kuipers, E.J., van Vliet, A.H.M. and Kusters, J.G. Role of the Helicobacter pylori outer-membrane proteins AlpA and AlpB in colonization of the guinea pig stomach . J. Med. Microbiol. 2004, 53, 375-379 .
19. Delcour, A.H. Structure and function of pore-forming b-barrels from bacteria . J. Mol. Microbiol. Biotechnol. 2002, 4 ( 1 ), 1-10 .
20. Devol, A.H. Nitrogen cycle: Solution to a marine mystery . Nature 2003, 422, 575-576 .
21. Dossumbekova, A., Prinz, C., Mages, J., Lang, R., Kusters, J.G., van Vliet, A.H.M., Reindl, W., Backert, S., Saur, D., Schmid, R.M. and Rad, R. Helicobacter pylori HopH (OipA) and bacterial pathogenicity: genetic and functional genomic analysis of hopH gene polymorphisms . J. Infect. Dis. 2006, 194, 1346-1355 .
22. Edwards, R.A., Olsen, G.J. and Maloy, S.R. Comparative genomics of closely related salmonellae . Trends Microbiol. 2002, 10, 94-99 .
23. Fardini, Y., Chettab, K., Grepinet, O., Rochereau, S., Trotereau, J., Harvey, P., Amy, M., Bottreau, E., Bumstead, N., Barrow, P.A. and Virlogeux-Payant, I. The YfgL lipoprotein is essential for type III secretion system expression and virulence of Salmonella enterica serovar Enteritidis . Infect. Immun. 2007, 75 ( 1 ), 358-370 .
24. Ge, Y. and Rikihisa, Y. Surface-exposed proteins of Ehrlichia chaffeensis . Infect. Immun. 2007, 75 ( 8 ), 3833-3841 .
25. Gophna, U., Ron, E.Z. and Graur, D. Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events . Gene 2003, 312, 151-163 .
26. Gram, H. C. ü ber die isolierte F ä rbung der Schizomyceten in Schnitt-und Trockenpr ä paraten . Fortschr. Medizin 1884, 2, 185-189 .
27. Harding, S.V., Sarkar-Tyson, M., Smither, S.J., Atkins, T.P., Oyston, P.C., Brown, K.A., Liu, Y., Wait, R. and Titball, R.W. The identifi cation of surface proteins of Burkholderia pseudomallei . Vaccine 2007, 25 ( 14 ), 2664-2672 .
28. Huang, D.B. and DuPont, H.L. Problem pathogens: extra-intestinal complications of Salmonella enterica serotype Typhi infection . Lancet Infect. Dis. 2005, 5 ( 6 ), 341-348 .
29. Jungblut, P.R., Bumann, D., Haas, G., Zimny-Arndt, U., Holland, P., Lamer, S., Siejak, F., Aebizher, A. and Meyer, T.F. Comparative proteome analysis of Helicobacter pylori . Mol. Microbiol. 2000, 36 ( 3 ), 710-725 .
30. Karlsson, R., Karlsson, A., Bäckman, O., Johansson, B.R. and Hulth, S. Identifi cation of key proteins involved in the anammox reaction . FEMS Microbiol. Lett. 2009, 297( 1), 87-94 . Epub 2009 Jun3.
31. Kim, N., Weeks, D.L., Moo Shin, J., Scott, D.R., Young, M.K. and Sachs, G. Proteins released by Helicobacter pylori in vitro . J. Bacteriol. 2002, 184 ( 22 ), 6155-6162 .
32. Koebnik, R., Locher, K.P. and van Gelders, P. Structure and function of bacterial outer membrane proteins: barrels in a nutshell . Mol. Microbiol. 2000, 37 ( 2 ), 239-253 .
33. Krah, A., Schmidt, F., Becher, D., Schmid, M., Albrecht, D., Rack, A., Buttner, K. and Jungblut, P.R. Analysis of automatically generated peptide mass fi ngerprints of cellular proteins and antigens from Helicobacter pylori 26695 separated by two-dimensional electrophoresis . Mol. Cell. Proteomics 2003, 2 ( 12 ), 1271-1283 .
34. Kuhle, V. and Hensel, M. Cellular microbiology of intracellular Salmonella enterica: functions of the type III secretion system encoded by Salmonella pathogenicity island 2 . Cell. Mol. Life Sci. 2004, 61 ( 22 ), 2812-2826 .
35. Kusters, J.G., van Vliet, A.H. and Kuipers, E.J. Pathogenesis of Helicobacter pylori infection . Clin. Microbiol. Rev. 2006, 19 ( 3 ), 449-490 .
36. Kuypers, M.M.M., Lavik, G., Woebken, D., Schmid, M., Fuchs, B.M., Amann, R., Jørgensen, B.B. and Jetten, M.S. Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation . Proc. Natl Acad. Sci. USA 2005, 102, 6478-6483 .
37. Liu, G.Y., Nie, P., Zhang, J. and Li, N. Proteomic analysis of the sarcosine-insoluble outer membrane fraction of Flavobacterium columnare . J. Fish Dis. 2008, 31 ( 4 ), 269-276 .
38. Liu, Z.F., Chen, C.Y., Tang, W., Zhang, J.Y., Gong, Y.Q. and Jia, J.H. Gene-expression profi les in gastric epithelial cells stimulated with spiral and coccoid Helicobacter pylori . J. Med. Microbiol. 2006, 55 ( Pt 8 ), 1009-1015 .
39. Macher, B.A. and Yen, T.-Y. Proteins at membrane surfaces-a review of approaches . Mol. Biosyst. 2007, 3, 705-713 .
40. McClelland, M., Sanderson, K.E., Spieth, J., Clifton, S.W., Latreille, P., Courtney, L., Porwollik, S., Ali, J., Dante, M., Feiyu, D., Shunfang, H., Layman, D., Leonard, S., Nguyen, C., Scott, K., Holmes, A., Grewal, N., Mulvaney, E., Ryan, E., Sun, H., Florea, L., Miller, W., Stoneking, T., Nhan, M., Waterston, R. and Wilson, R.K. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2 . Nature 2001, 413, 852-856 .
41. Molloy, M.P. Isolation of bacterial cell membranes proteins using carbonate extraction . Methods Mol. Biol. 2008, 424, 397-401 .
42. Molloy, M.P., Herbert, B.R., Slade, M.B., Rabilloud, T., Nouwens, A.S., Williams, K.L. and Gooley, A.A. Proteomic analysis of the Escherichia coli outer membrane . Eur. J. Biochem. 2000, 267, 2871-2881 .
43. Monack, D.M., Mueller, A. and Falkow, S. Persistent bacterial infections: the interface of the pathogen and the host immune system . Nat. Rev. Microbiol. 2004, 2 ( 9 ), 747-765 .
44. Mujahid, S., Pechan, T. and Wang, C. Improved solubilization of surface proteins from Listeria monocytogenes for 2-DE . Electrophoresis 2007, 28 ( 21 ), 3998-4007 .
45. Nandakumar, R., Nandakumar, M.P., Marten, M.R. and Ross, J.M. Proteome analysis of membrane and cell wall associated proteins from Staphylococcus aureus . J. Proteome Res. 2005, 4 ( 2 ), 250-257 .
46. Nyblom, M.,Öberg, F., Lindkvist-Petersson, K., Hallgren, K., Findlay, H., Wikström, J., Karlsson, A., Hansson,Ö., Booth, P.J., Bill, R.M., Neutze, R. and Hedfalk, K. Exceptional overproduction of a functional human membrane protein . Prot. Exp. Purif. 2007, 56 ( 1 ), 110-120 .
47. Parkhill, J., Dougan, G., James, K.D., Thomson, N.R., Pickard, D., Wain, J., Churcher, C., Mungall, K.L., Bentley, S.D., Holden, M.T.G., Sebaihia, M., Baker, S., Basham, D., Brooks, K., Chillingworth, T., Connerton, P., Cronin, A., Davis, P., Davies, R.M., Dowd, L., White, N., Farrar, J., Feltwell, T., Hamlin, N., Haque, A., Hien, T.T., Holroyd, S., Jagels, K., Kroghk, A., Larsenk, T.S., Leather, S., Moule, S., O ' Gaora, P., Parry, C., Quail, M., Rutherford, K., Simmonds, M., Skelton, J., Stevens, K., Whitehead, S. and Barrell, B.G. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18 . Nature 2001, 413, 848-852 .
48. Peng, X., Xu, C., Ren, H., Lin, X. ; Wu, L. and Wang, S. Proteomic analysis of the sarcosine-insoluble outer membrane fraction of Pseudomonas aeruginosa responding to ampicillin, kanamysin, and tetracycline resistance . J. Proteome Res. 2005, 4 ( 6 ), 2257-2265 .
49. Popoff, M.Y., Bockemuhl, J. and Gheesling, L.L. Supplement 2001 (no. 45) to the Kauffmann-White scheme . Res. Microbiol. 2003, 154, 173-174 .
50. Prescott, L., Harley, J. and Klein D. Microbiology, 5th edn. New York: McGraw-Hill, 2002 . Rhomberg, T.A., Karlsberg, O., Mini, T., Zimny-Arndt, U., Wickenberg, U., Röttgen, M., Jungblut, P.R., Jen ö, P., Andersson, S.G. and Dehio, C. Proteomic analysis of the sarcosine-insoluble outer membrane fraction of the bacterial pathogen Bartonella henselae . Proteomics 2004, 4 ( 10 ), 3021-3033 .
51. Rivas, L., Fegan, N. and Dykes, G.A. Expression and putative roles in attachment of outer membrane proteins of Escherichia coli O157 from planktonic and sessile culture . Foodborne Pathog. Dis. 2008, 5 ( 2 ), 155-164 .
52. Sabarth, N., Hurwitz, R., Meyer, T.F. and Bumann, D. Multiparameter selection of Helicobacter pylori antigens identifi es two novel antigens with high protective effi cacy . Infect. Immun. 2002a, 70 ( 11 ), 6499-6503 .
53. Sabarth, N., Lamer, S., Zimny-Arndt, U., Jungblut, P.R., Meyer, T.F. and Bumann, D. Identifi cation of surface proteins of Helicobacter pylori by selective biotinylation, affi nity purifi cation, and two-dimensional gel electrophoresis . J. Biol. Chem. 2002b, 277 ( 31 ), 27896-27902 .
54. Schindler, J., Jung, S., Niedner-Schatteburg, G., Friauf, E. and Nothwang, H.G. Enrichment of integral membrane proteins from small amounts of brain tissue . J. Neural Transm. 2006, 113 ( 8 ), 995-1013 .
55. Schulz, G.E. The structure of bacterial outer membrane proteins . Biochim. Biophys. Acta 2002, 1565, 308-317 .
56. Sipponen, P. Helicobacter pylori gastritis-epidemiology . J Gastroenterol. 1997, 32 ( 2 ), 273-277 .
57. Smither, S.J., Hill, J., van Baar, B.L., Hulst, A.G., de Jong, A.L. and Titball, R.W. Identifi cation of outer membrane proteins of Yersinia pestis through biotinylation . J. Microbiol. Methods 2007, 68 ( 1 ), 26-31 .
58. Smoot, D.T. How does Helicobacter pylori cause mucosal damage? Direct mechanisms . Gastroenterology 1997, 113 ( 6 Suppl. ), S31-4, discussion S50.
59. Suerbaum, S. and Michetti, P. Helicobacter pylori infection . N. Engl. J. Med. 2002, 347 ( 15 ), 1175-1186 .
60. Timothy, L. Role of Helicobacter pylori outer membrane proteins in gastroduodenal disease . J. Infect. Dis. 2006, 194, 1343-1345 .
61. Washburn, M.P. and Yates, J.R. Analysis of the microbial proteome . Curr. Opin. Microbiol. 2000, 3, 292-297 .
62. Wehmhoner, D., Dietrich, G., Fisher, E., Baumgartner, M., Wehland, J. and Jansch, L. ' Lanespector ', a tool for membrane protein profi ling based on sodium dodecyl sulphate-polyacrylamide get electrophoresis/liquid chromatography-tandem mass spectrometry analysis: application to Listeria monocytogenes membrane proteins . Electrophoresis 2005, 26, 2450-2460 .
63. Xiong, Y., Chalmers, M.J., Gao, F.P., Cross, T.A. and Marshall, A.G. Identifi cation of Mycobacterium tuberculosis H37Rv integral membrane proteins by one-dimensional gel electrophoresis and liquid chromatography electrospray ionization tandem mass spectrometry . J. Proteome Res. 2005, 4, 855-861 .
64. Yamaoka, Y. Helicobacter pylori: Molecular Genetics and Cellular Biology . Norwich: Caister Academic, 2008 .
65. Yamoaka, Y., Kita, M., Kodama, T., Imamura, S., Ohno, T., Sawai, N., Ishimaru, A., Imanishi, J. and Graham, D.Y. Helicobacter pylori infection in mice: role of outer membrane proteins in colonization and inflammation . Gastroenterology 2002, 123, 1992-2004 .
66. Zahedi, R.P., Meisinger, C. and Sickmann, A. Two- dimensional benzyldimethyl- n- hexadecylammonium chloride/SDS-PAGE for membrane proteomics . Proteomics 2005, 5 ( 14 ), 3581-3588 .
67. Zoubi-Hasona, K. and Brady, L.J. Isolation and solubilization of cellular membrane proteins from bacteria . Methods Mol. Biol. 2008, 425, 287-293 .
68. Zuobi-Hasona, K., Crowley, P.J., Hasona, A., Bleiweis, A.S. and Brady, L.J. Solubilization of cellular membrane proteins from Streptococcus mutants for two-dimensional gel electrophoresis . Electrophoresis 2005, 26 ( 6 ), 1200-1205 .