Protein & Cell

, Volume 3, Issue 5, pp 346–363 | Cite as

Two-dimensional gel electrophoresis in bacterial proteomics

  • Shirly O. T. Curreem
  • Rory M. Watt
  • Susanna K. P. LauEmail author
  • Patrick C. Y. WooEmail author


Two-dimensional gel electrophoresis (2-DE) is a gel-based technique widely used for analyzing the protein composition of biological samples. It is capable of resolving complex mixtures containing more than a thousand protein components into individual protein spots through the coupling of two orthogonal biophysical separation techniques: isoelectric focusing (first dimension) and polyacrylamide gel electrophoresis (second dimension). 2-DE is ideally suited for analyzing the entire expressed protein complement of a bacterial cell: its proteome. Its relative simplicity and good reproducibility have led to 2-DE being widely used for exploring proteomics within a wide range of environmental and medically-relevant bacteria. Here we give a broad overview of the basic principles and historical development of gel-based proteomics, and how this powerful approach can be applied for studying bacterial biology and physiology. We highlight specific 2-DE applications that can be used to analyze when, where and how much proteins are expressed. The links between proteomics, genomics and mass spectrometry are discussed. We explore how proteomics involving tandem mass spectrometry can be used to analyze (post-translational) protein modifications or to identify proteins of unknown origin by de novo peptide sequencing. The use of proteome fractionation techniques and non-gel-based proteomic approaches are also discussed. We highlight how the analysis of proteins secreted by bacterial cells (secretomes or exoproteomes) can be used to study infection processes or the immune response. This review is aimed at non-specialists who wish to gain a concise, comprehensive and contemporary overview of the nature and applications of bacterial proteomics.


two-dimensional gel electrophoresis bacteria proteomics 


  1. Aebersold, R., and Goodlett, D.R. (2001). Mass spectrometry in proteomics. Chem Rev 101, 269–295.Google Scholar
  2. Aebersold, R., and Mann, M. (2003). Mass spectrometry-based proteomics. Nature 422, 198–207.Google Scholar
  3. Al Dahouk, S., Jubier-Maurin, V., Scholz, H.C., Tomaso, H., Karges, W., Neubauer, H., and Köhler, S. (2008). Quantitative analysis of the intramacrophagic Brucella suis proteome reveals metabolic adaptation to late stage of cellular infection. Proteomics 8, 3862–3870.Google Scholar
  4. Altarriba, M., Merino, S., Gavín, R., Canals, R., Rabaan, A., Shaw, J.G., and Tomás, J.M. (2003). A polar flagella operon (flg) of Aeromonas hydrophila contains genes required for lateral flagella expression. Microb Pathog 34, 249–259.Google Scholar
  5. Alteri, C.J., Smith, S.N., and Mobley, H.L. (2009). Fitness of Escherichia coli during urinary tract infection requires gluconeogenesis and the TCA cycle. PLoS Pathog 5, e1000448.Google Scholar
  6. Anglade, P., Demey, E., Labas, V., Le Caer, J.P., and Chich, J.F. (2000). Towards a proteomic map of Lactococcus lactis NCDO 763. Electrophoresis 21, 2546–2549.Google Scholar
  7. Antelmann, H., Tjalsma, H., Voigt, B., Ohlmeier, S., Bron, S., van Dijl, J.M., and Hecker, M. (2001). A proteomic view on genome-based signal peptide predictions. Genome Res 11, 1484–1502.Google Scholar
  8. Appel, R.D., Hochstrasser, D.F., Funk, M., Vargas, J.R., Pellegrini, C., Muller, A.F., and Scherrer, J.R. (1991). The MELANIE project: from a biopsy to automatic protein map interpretation by computer. Electrophoresis 12, 722–735.Google Scholar
  9. Appel, R.D., Sanchez, J.C., Bairoch, A., Golaz, O., Miu, M., Vargas, J.R., and Hochstrasser, D.F. (1993). SWISS-2DPAGE: a database of two-dimensional gel electrophoresis images. Electrophoresis 14, 1232–1238.Google Scholar
  10. Bendt, A.K., Burkovski, A., Schaffer, S., Bott, M., Farwick, M., Hermann, T., Farwick, M., and Hermann, T. (2003). Towards a phosphoproteome map of Corynebacterium glutamicum. Proteomics 3, 1637–1646.Google Scholar
  11. Bendtsen, J.D., Kiemer, L., Fausbøll, A., and Brunak, S. (2005). Non-classical protein secretion in bacteria. BMC Microbiol 5, 58.Google Scholar
  12. Bernardini, G., Laschi, M., Serchi, T., Arena, S., D’Ambrosio, C., Braconi, D., Scaloni, A., and Santucci, A. (2011). Mapping phosphoproteins in Neisseria meningitidis serogroup A. Proteomics 11, 1351–1358.Google Scholar
  13. Bjellqvist, B., Ek, K., Righetti, P.G., Gianazza, E., Görg, A., Westermeier, R., and Postel, W. (1982). Isoelectric focusing in immobilized pH gradients: principle, methodology and some applications. J Biochem Biophys Methods 6, 317–339.Google Scholar
  14. Blomberg, A., Blomberg, L., Norbeck, J., Fey, S.J., Larsen, P.M., Larsen, M., Roepstorff, P., Degand, H., Boutry, M., Posch, A., et al. (1995). Interlaboratory reproducibility of yeast protein patterns analyzed by immobilized pH gradient two-dimensional gel electrophoresis. Electrophoresis 16, 1935–1945.Google Scholar
  15. Breen, E.J., Hopwood, F.G., Williams, K.L., and Wilkins, M.R. (2000). Automatic poisson peak harvesting for high throughput protein identification. Electrophoresis 21, 2243–2251.Google Scholar
  16. Bumann, D. (2010). Pathogen proteomes during infection: A basis for infection research and novel control strategies. J Proteomics 73, 2267–2276.Google Scholar
  17. Bumann, D., Aksu, S., Wendland, M., Janek, K., Zimny-Arndt, U., Sabarth, N., Meyer, T.F., and Jungblut, P.R. (2002). Proteome analysis of secreted proteins of the gastric pathogen Helicobacter pylori. Infect Immun 70, 3396–3403.Google Scholar
  18. Bumann, D., Jungblut, P.R., and Meyer, T.F. (2004). Helicobacter pylori vaccine development based on combined subproteome analysis. Proteomics 4, 2843–2848.Google Scholar
  19. Bunai, K., and Yamane, K. (2005). Effectiveness and limitation of two-dimensional gel electrophoresis in bacterial membrane protein proteomics and perspectives. J Chromatogr B Analyt Technol Biomed Life Sci 815, 227–236.Google Scholar
  20. Cash, P. (2011). Investigating pathogen biology at the level of the proteome. Proteomics 11, 3190–3202.Google Scholar
  21. Chevalier, F. (2010). Highlights on the capacities of “Gel-based” proteomics. Proteome Sci 8, 23.Google Scholar
  22. Chitlaru, T., Gat, O., Gozlan, Y., Ariel, N., and Shafferman, A. (2006). Differential proteomic analysis of the Bacillus anthracis secretome: distinct plasmid and chromosome CO2-dependent cross talk mechanisms modulate extracellular proteolytic activities. J Bacteriol 188, 3551–3571.Google Scholar
  23. Clauser, K.R., Baker, P., and Burlingame, A.L. (1999). Role of accurate mass measurement (+/− 10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal Chem 71, 2871–2882.Google Scholar
  24. Coelho, A., de Oliveira Santos, E., Faria, M.L., de Carvalho, D.P., Soares, M.R., von Kruger, W.M., and Bisch, P.M. (2004). A pro teome reference map for Vibrio cholerae El Tor. Proteomics 4, 1491–1504.Google Scholar
  25. Coote, J.G. (2001). Environmental sensing mechanisms in Bordetella. Adv Microb Physiol 44, 141–181.Google Scholar
  26. Coquet, L., Cosette, P., Dé, E., Galas, L., Vaudry, H., Rihouey, C., Lerouge, P., Junter, G.A., and Jouenne, T. (2005). Immobilization induces alterations in the outer membrane protein pattern of Yersinia ruckeri. J Proteome Res 4, 1988–1998.Google Scholar
  27. Corbett, J.M., Dunn, M.J., Posch, A., and Görg, A. (1994). Positional reproducibility of protein spots in two-dimensional polyacrylamide gel electrophoresis using immobilised pH gradient isoelectric focusing in the first dimension: an interlaboratory comparison. Electrophoresis 15, 1205–1211.Google Scholar
  28. Cordwell, S.J., Larsen, M.R., Cole, R.T., and Walsh, B.J. (2002). Comparative proteomics of Staphylococcus aureus and the response of methicillin-resistant and methicillin-sensitive strains to Triton X-100. Microbiology 148, 2765–2781.Google Scholar
  29. Cordwell, S.J., Nouwens, A.S., Verrills, N.M., Basseal, D.J., and Walsh, B.J. (2000). Subproteomics based upon protein cellular location and relative solubilities in conjunction with composite two-dimensional electrophoresis gels. Electrophoresis 21, 1094–1103.Google Scholar
  30. Cortay, J.C., Rieul, C., Duclos, B., and Cozzone, A.J. (1986). Characterization of the phosphoproteins of Escherichia coli cells by electrophoretic analysis. Eur J Biochem 159, 227–237.Google Scholar
  31. Corthals, G.L., Wasinger, V.C., Hochstrasser, D.F., and Sanchez, J.C. (2000). The dynamic range of protein expression: a challenge for proteomic research. Electrophoresis 21, 1104–1115.Google Scholar
  32. de Koning-Ward, T.F., and Robins-Browne, R.M. (1997). A novel mechanism of urease regulation in Yersinia enterocolitica. FEMS Microbiol Lett 147, 221–226.Google Scholar
  33. DebRoy, S., Dao, J., Söderberg, M., Rossier, O., and Cianciotto, N.P. (2006). Legionella pneumophila type II secretome reveals unique exoproteins and a chitinase that promotes bacterial persistence in the lung. Proc Natl Acad Sci U S A 103, 19146–19151.Google Scholar
  34. Desvaux, M., Dumas, E., Chafsey, I., Chambon, C., and Hébraud, M. (2010). Comprehensive appraisal of the extracellular proteins from a monoderm bacterium: theoretical and empirical exoproteomes of Listeria monocytogenes EGD-e by secretomics. J Proteome Res 9, 5076–5092.Google Scholar
  35. Desvaux, M., Hébraud, M., Talon, R., and Henderson, I.R. (2009). Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue. Trends Microbiol 17, 139–145.Google Scholar
  36. Deutscher, J., and Saier, M.H. Jr. (2005). Ser/Thr/Tyr protein phosphorylation in bacteria — for long time neglected, now well established. J Mol Microbiol Biotechnol 9, 125–131.Google Scholar
  37. Dowell, J.A., Frost, D.C., Zhang, J., and Li, L. (2008). Comparison of two-dimensional fractionation techniques for shotgun proteomics. Anal Chem 80, 6715–6723.Google Scholar
  38. Edman, P. (1950). Method for determination of the amino acid sequence in peptides. Acta Chem Scand 4, 283–293.Google Scholar
  39. Edman, P., and Begg, G. (1967). A protein sequenator. Eur J Biochem 1, 80–91.Google Scholar
  40. El-Sharoud, W.M., and Rowbury, R.J. (2006). Recent insights into microbial physiology. Sci Prog 89, 141–149.Google Scholar
  41. Encheva, V., Gharbia, S.E., Wait, R., Begum, S., and Shah, H.N. (2006). Comparison of extraction procedures for proteome analysis of Streptococcus pneumoniae and a basic reference map. Proteomics 6, 3306–3317.Google Scholar
  42. Encheva, V., Wait, R., Gharbia, S.E., Begum, S., and Shah, H.N. (2005). Proteome analysis of serovars Typhimurium and Pullorum of Salmonella enterica subspecies I. BMC Microbiol 5, 42.Google Scholar
  43. Eng, J.K., McCormack, A.L., and Yates, J.R. (1994). An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 5, 976–989.Google Scholar
  44. Eymann, C., Dreisbach, A., Albrecht, D., Bernhardt, J., Becher, D., Gentner, S., Tam, T., Büttner, K., Buurman, G., Scharf, C., et al. (2004). A comprehensive proteome map of growing Bacillus subtilis cells. Proteomics 4, 2849–2876.Google Scholar
  45. Fenn, J.B., Mann, M., Meng, C.K., Wong, S.F., and Whitehouse, C.M. (1989). Electrospray ionization for mass spectrometry of large biomolecules. Science 246, 64–71.Google Scholar
  46. Fleischmann, R.D., Adams, M.D., White, O., Clayton, R.A., Kirkness, E.F., Kerlavage, A.R., Bult, C.J., Tomb, J.F., Dougherty, B.A., Merrick, J.M., et al. (1995). Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496–512.Google Scholar
  47. Folio, P., Chavant, P., Chafsey, I., Belkorchia, A., Chambon, C., and Hébraud, M. (2004). Two-dimensional electrophoresis database of Listeria monocytogenes EGDe proteome and proteomic analysis of mid-log and stationary growth phase cells. Proteomics 4, 3187–3201.Google Scholar
  48. Fountoulakis, M., and Gasser, R. (2003). Proteomic analysis of the cell envelope fraction of Escherichia coli. Amino Acids 24, 19–41.Google Scholar
  49. Franco, A.T., Friedman, D.B., Nagy, T.A., Romero-Gallo, J., Krishna, U., Kendall, A., Israel, D.A., Tegtmeyer, N., Washington, M.K., and Peek, R.M. Jr. (2009). Delineation of a carcinogenic Helicobacter pylori proteome. Mol Cell Proteomics 8, 1947–1958.Google Scholar
  50. Gade, D., Gobom, J., and Rabus, R. (2005). Proteomic analysis of carbohydrate catabolism and regulation in the marine bacterium Rhodopirellula baltica. Proteomics 5, 3672–3683.Google Scholar
  51. Gao, H., Yang, Z.K., Wu, L., Thompson, D.K., and Zhou, J. (2006). Global transcriptome analysis of the cold shock response of Shewanella oneidensis MR-1 and mutational analysis of its classical cold shock proteins. J Bacteriol 188, 4560–4569.Google Scholar
  52. Gardy, J.L., and Brinkman, F.S. (2006). Methods for predicting bacterial protein subcellular localization. Nat Rev Microbiol 4, 741–751.Google Scholar
  53. Garrels, J.I. (1989). The QUEST system for quantitative analysis of two-dimensional gels. J Biol Chem 264, 5269–5282.Google Scholar
  54. Gatlin, C.L., Pieper, R., Huang, S.T., Mongodin, E., Gebregeorgis, E., Parmar, P.P., Clark, D.J., Alami, H., Papazisi, L., Fleischmann, R.D., et al. (2006). Proteomic profiling of cell envelope-associated proteins from Staphylococcus aureus. Proteomics 6, 1530–1549.Google Scholar
  55. Gevaert, K., Van Damme, P., Ghesquière, B., Impens, F., Martens, L., Helsens, K., and Vandekerckhove, J. (2007). A la carte proteomics with an emphasis on gel-free techniques. Proteomics 7, 2698–2718.Google Scholar
  56. Görg, A., Obermaier, C., Boguth, G., Harder, A., Scheibe, B., Wildgruber, R., and Weiss, W. (2000). The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 21, 1037–1053.Google Scholar
  57. Greenough, C., Jenkins, R.E., Kitteringham, N.R., Pirmohamed, M., Park, B.K., and Pennington, S.R. (2004). A method for the rapid depletion of albumin and immunoglobulin from human plasma. Proteomics 4, 3107–3111.Google Scholar
  58. Guerrera, I.C., and Kleiner, O. (2005). Application of mass spectrometry in proteomics. Biosci Rep 25, 71–93.Google Scholar
  59. Gupta, M.K., Subramanian, V., and Yadav, J.S. (2009). Immunoproteomic identification of secretory and subcellular protein antigens and functional evaluation of the secretome fraction of Mycobacterium immunogenum, a newly recognized species of the Mycobacterium chelonae-Mycobacterium abscessus group. J Proteome Res 8, 2319–2330.Google Scholar
  60. Haas, G., Karaali, G., Ebermayer, K., Metzger, W.G., Lamer, S., Zimny-Arndt, U., Diescher, S., Goebel, U.B., Vogt, K., Roznowski, A.B., et al. (2002). Immunoproteomics of Helicobacter pylori infection and relation to gastric disease. Proteomics 2, 313–324.Google Scholar
  61. Han, M.J., and Lee, S.Y. (2006). The Escherichia coli proteome: past, present, and future prospects. Microbiol Mol Biol Rev 70, 362–439.Google Scholar
  62. Hecker, M., Antelmann, H., Büttner, K., and Bernhardt, J. (2008). Gel-based proteomics of Gram-positive bacteria: a powerful tool to address physiological questions. Proteomics 8, 4958–4975.Google Scholar
  63. Hecker, M., and Völker, U. (2004). Towards a comprehensive understanding of Bacillus subtilis cell physiology by physiological proteomics. Proteomics 4, 3727–3750.Google Scholar
  64. Henderson, B., and Martin, A. (2011). Bacterial virulence in the moonlight: multitasking bacterial moonlighting proteins are virulence determinants in infectious disease. Infect Immun 79, 3476–3491.Google Scholar
  65. Henzel, W.J., Watanabe, C., and Stults, J.T. (2003). Protein identification: the origins of peptide mass fingerprinting. J Am Soc Mass Spectrom 14, 931–942.Google Scholar
  66. Houthaeve, T., Gausepohl, H., Ashman, K., Nillson, T., and Mann, M. (1997). Automated protein preparation techniques using a digest robot. J Protein Chem 16, 343–348.Google Scholar
  67. Hueck, C.J. (1998). Type III protein secretion systems in bacterial pathogens of animals and plants. Microbiol Mol Biol Rev 62, 379–433.Google Scholar
  68. Ishihama, Y., Schmidt, T., Rappsilber, J., Mann, M., Hartl, F.U., Kerner, M.J., and Frishman, D. (2008). Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics 9, 102.Google Scholar
  69. James, P., Quadroni, M., Carafoli, E., and Gonnet, G. (1994). Protein identification in DNA databases by peptide mass fingerprinting. Protein Sci 3, 1347–1350.Google Scholar
  70. Jeffery, C.J. (2009). Moonlighting proteins—an update. Mol Biosyst 5, 345–350.Google Scholar
  71. Jongbloed, J.D., Martin, U., Antelmann, H., Hecker, M., Tjalsma, H., Venema, G., Bron, S., van Dijl, J.M., and Müller, J. (2000). TatC is a specificity determinant for protein secretion via the twin-arginine translocation pathway. J Biol Chem 275, 41350–41357.Google Scholar
  72. Jungblut, P.R. (2001). Proteome analysis of bacterial pathogens. Microbes Infect 3, 831–840.Google Scholar
  73. Jungblut, P.R., Bumann, D., Haas, G., Zimny-Arndt, U., Holland, P., Lamer, S., Siejak, F., Aebischer, A., and Meyer, T.F. (2000). Comparative proteome analysis of Helicobacter pylori. Mol Microbiol 36, 710–725.Google Scholar
  74. Kalia, A., and Gupta, R.P. (2005). Proteomics: a paradigm shift. Crit Rev Biotechnol 25, 173–198.Google Scholar
  75. Karas, M., and Hillenkamp, F. (1988). Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal Chem 60, 2299–2301.Google Scholar
  76. Klose, J. (1975). Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik 26, 231–243.Google Scholar
  77. Klose, J. (2009). From 2-D electrophoresis to proteomics. Electrophoresis 30, S142–S149.Google Scholar
  78. Konkel, M.E., and Tilly, K. (2000). Temperature-regulated expression of bacterial virulence genes. Microbes Infect 2, 157–166.Google Scholar
  79. Lau, S.K., Fan, R.Y., Ho, T.C., Wong, G.K., Tsang, A.K., Teng, J.L., Chen, W., Watt, R.M., Curreem, S.O., Tse, H., et al. (2011). Environmental adaptability and stress tolerance of Laribacter hongkongensis: a genome-wide analysis. Cell Biosci 1, 22.Google Scholar
  80. Lau, S.K., Woo, P.C., Fan, R.Y., Ma, S.S., Hui, W.T., Au, S.Y., Chan, L.L., Chan, J.Y., Lau, A.T., Leung, K.Y., et al. (2007). Isolation of Laribacter hongkongensis, a novel bacterium associated with gastroenteritis, from drinking water reservoirs in Hong Kong. J Appl Microbiol 103, 507–515.Google Scholar
  81. Lau, S.K.P., Lee, L.C.K., Fan, R.Y.Y., Teng, J.L.L., Tse, C.W.S., Woo, P.C.Y., and Yuen, K.-Y. (2009). Isolation of Laribacter hongkongensis, a novel bacterium associated with gastroenteritis, from Chinese tiger frog. Int J Food Microbiol 129, 78–82.Google Scholar
  82. Lescuyer, P., Hochstrasser, D.F., and Sanchez, J.C. (2004). Comprehensive proteome analysis by chromatographic protein prefractionation. Electrophoresis 25, 1125–1135.Google Scholar
  83. Liao, X., Ying, T., Wang, H., Wang, J., Shi, Z., Feng, E., Wei, K., Wang, Y., Zhang, X., Huang, L., et al. (2003). A two-dimensional proteome map of Shigella flexneri. Electrophoresis 24, 2864–2882.Google Scholar
  84. Link, A.J., Eng, J., Schieltz, D.M., Carmack, E., Mize, G.J., Morris, D.R., Garvik, B.M., and Yates, J.R. 3rd. (1999). Direct analysis of protein complexes using mass spectrometry. Nat Biotechnol 17, 676–682.Google Scholar
  85. Lopez-Campistrous, A., Semchuk, P., Burke, L., Palmer-Stone, T., Brokx, S.J., Broderick, G., Bottorff, D., Bolch, S., Weiner, J.H., and Ellison, M.J. (2005). Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth. Mol Cell Proteomics 4, 1205–1209.Google Scholar
  86. Macek, B., Mijakovic, I., Olsen, J.V., Gnad, F., Kumar, C., Jensen, P.R., and Mann, M. (2007). The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol Cell Proteomics 6, 697–707.Google Scholar
  87. Marceau, M. (2005). Transcriptional regulation in Yersinia: an update. Curr Issues Mol Biol 7, 151–177.Google Scholar
  88. Markert, S., Arndt, C., Felbeck, H., Becher, D., Sievert, S.M., Hügler, M., Albrecht, D., Robidart, J., Bench, S., Feldman, R.A., et al. (2007). Physiological proteomics of the uncultured endosymbiont of Riftia pachyptila. Science 315, 247–250.Google Scholar
  89. Marouga, R., David, S., and Hawkins, E. (2005). The development of the DIGE system: 2D fluorescence difference gel analysis technology. Anal Bioanal Chem 382, 669–678.Google Scholar
  90. McHugh, L., and Arthur, J.W. (2008). Computational methods for protein identification from mass spectrometry data. PLoS Comput Biol 4, e12.Google Scholar
  91. Medberry, S., Gallagher, S., and Moomaw, B. (2005). Overview of digital electrophoresis analysis. Curr Protoc Protein Sci Chapter 10, Unit 10 12.Google Scholar
  92. Miesel, L., Greene, J., and Black, T.A. (2003). Genetic strategies for antibacterial drug discovery. Nat Rev Genet 4, 442–456.Google Scholar
  93. Molloy, M.P., Herbert, B.R., Slade, M.B., Rabilloud, T., Nouwens, A.S., Williams, K.L., and Gooley, A.A. (2000). Proteomic analysis of the Escherichia coli outer membrane. Eur J Biochem 267, 2871–2881.Google Scholar
  94. Mora, M., Donati, C., Medini, D., Covacci, A., and Rappuoli, R. (2006). Microbial genomes and vaccine design: refinements to the classical reverse vaccinology approach. Curr Opin Microbiol 9, 532–536.Google Scholar
  95. Morris, H.R., Panico, M., Barber, M., Bordoli, R.S., Sedgwick, R.D., and Tyler, A. (1981). Fast atom bombardment: a new mass spectrometric method for peptide sequence analysis. Biochem Biophys Res Commun 101, 623–631.Google Scholar
  96. Ni, X.P., Ren, S.H., Sun, J.R., Xiang, H.Q., Gao, Y., Kong, Q.X., Cha, J., Pan, J.C., Yu, H., and Li, H.M. (2007). Laribacter hongkongensis isolated from a patient with community-acquired gastroenteritis in Hangzhou City. J Clin Microbiol 45, 255–256.Google Scholar
  97. Nouwens, A.S., Willcox, M.D., Walsh, B.J., and Cordwell, S.J. (2002). Proteomic comparison of membrane and extracellular proteins from invasive (PAO1) and cytotoxic (6206) strains of Pseudomonas aeruginosa. Proteomics 2, 1325–1346.Google Scholar
  98. O’Connor, C.D., Farris, M., Fowler, R., and Qi, S.Y. (1997). The proteome of Salmonella enterica serovar typhimurium: current progress on its determination and some applications. Electrophoresis 18, 1483–1490.Google Scholar
  99. O’Farrell, P.H. (1975). High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250, 4007–4021.Google Scholar
  100. Pancholi, V., and Fischetti, V.A. (1992). A major surface protein on group A streptococci is a glyceraldehyde-3-phosphate-dehydrogenase with multiple binding activity. J Exp Med 176, 415–426.Google Scholar
  101. Parkhill, J., and Wren, B.W. (2011). Bacterial epidemiology and biology — lessons from genome sequencing. Genome Biol 12, 230.Google Scholar
  102. Patton, W.F. (2002). Detection technologies in proteome analysis. J Chromatogr B Analyt Technol Biomed Life Sci 771, 3–31.Google Scholar
  103. Pemberton, J.M., Kidd, S.P., and Schmidt, R. (1997). Secreted enzymes of Aeromonas. FEMS Microbiol Lett 152, 1–10.Google Scholar
  104. Perkins, D.N., Pappin, D.J.C., Creasy, D.M., and Cottrell, J.S. (1999). Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551–3567.Google Scholar
  105. Perrin, C., González-Márquez, H., Gaillard, J.L., Bracquart, P., and Guimont, C. (2000). Reference map of soluble proteins from Streptococcus thermophilus by two-dimensional electrophoresis. Electrophoresis 21, 949–955.Google Scholar
  106. Phadtare, S., Alsina, J., and Inouye, M. (1999). Cold-shock response and cold-shock proteins. Curr Opin Microbiol 2, 175–180.Google Scholar
  107. Phillips, C.I., and Bogyo, M. (2005). Proteomics meets microbiology: technical advances in the global mapping of protein expression and function. Cell Microbiol 7, 1061–1076.Google Scholar
  108. Poetsch, A., and Wolters, D. (2008). Bacterial membrane proteomics. Proteomics 8, 4100–4122.Google Scholar
  109. Poland, T., Rabilloud, T., and Sinha, P. (2005). Silver Staining of 2-D Gels. In: The Proteomics Protocols Handbook., Walker J.M., ed. Totowa, NJ: Human Press, 177–184.Google Scholar
  110. Qian, W.J., Jacobs, J.M., Liu, T., Camp, D.G. 2nd, and Smith, R.D. (2006). Advances and challenges in liquid chromatography-mass spectrometry-based proteomics profiling for clinical applications. Mol Cell Proteomics 5, 1727–1744.Google Scholar
  111. Rabilloud, T. (2009). Membrane proteins and proteomics: love is possible, but so difficult. Electrophoresis 30, S174–S180.Google Scholar
  112. Rabilloud, T., Chevallet, M., Luche, S., and Lelong, C. (2010). Two-dimensional gel electrophoresis in proteomics: Past, present and future. J Proteomics 73, 2064–2077.Google Scholar
  113. Rabilloud, T., Heller, M., Gasnier, F., Luche, S., Rey, C., Aebersold, R., Benahmed, M., Louisot, P., and Lunardi, J. (2002). Proteomics analysis of cellular response to oxidative stress. Evidence for in vivo overoxidation of peroxiredoxins at their active site. J Biol Chem 277, 19396–19401.Google Scholar
  114. Rabilloud, T., Vaezzadeh, A.R., Potier, N., Lelong, C., Leize-Wagner, E., and Chevallet, M. (2009). Power and limitations of electrophoretic separations in proteomics strategies. Mass Spectrom Rev 28, 816–843.Google Scholar
  115. Rappuoli, R. (2001). Reverse vaccinology, a genome-based approach to vaccine development. Vaccine 19, 2688–2691.Google Scholar
  116. Regula, J.T., Ueberle, B., Boguth, G., Görg, A., Schnölzer, M., Herrmann, R., and Frank, R. (2000). Towards a two-dimensional proteome map of Mycoplasma pneumoniae. Electrophoresis 21, 3765–3780.Google Scholar
  117. Renzone, G., D’Ambrosio, C., Arena, S., Rullo, R., Ledda, L., Ferrara, L., and Scaloni, A. (2005). Differential proteomic analysis in the study of prokaryotes stress resistance. Ann Ist Super Sanita 41, 459–468.Google Scholar
  118. Roe, M.R., and Griffin, T.J. (2006). Gel-free mass spectrometry-based high throughput proteomics: tools for studying biological response of proteins and proteomes. Proteomics 6, 4678–4687.Google Scholar
  119. Rosen, R., Sacher, A., Shechter, N., Becher, D., Büttner, K., Biran, D., Hecker, M., and Ron, E.Z. (2004). Two-dimensional reference map of Agrobacterium tumefaciens proteins. Proteomics 4, 1061–1073.Google Scholar
  120. Rosengren, A.T., Salmi, J.M., Aittokallio, T., Westerholm, J., Lahesmaa, R., Nyman, T.A., and Nevalainen, O.S. (2003). Comparison of PDQuest and Progenesis software packages in the analysis of two-dimensional electrophoresis gels. Proteomics 3, 1936–1946.Google Scholar
  121. Sabarth, N., Hurwitz, R., Meyer, T.F., and Bumann, D. (2002). Multiparameter selection of Helicobacter pylori antigens identifies two novel antigens with high protective efficacy. Infect Immun 70, 6499–6503.Google Scholar
  122. Santoni, V., Molloy, M., and Rabilloud, T. (2000). Membrane proteins and proteomics: un amour impossible? Electrophoresis 21, 1054–1070.Google Scholar
  123. Sarioglu, H., Lottspeich, F., Walk, T., Jung, G., and Eckerskorn, C. (2000). Deamidation as a widespread phenomenon in two-dimensional polyacrylamide gel electrophoresis of human blood plasma proteins. Electrophoresis 21, 2209–2218.Google Scholar
  124. Scheele, G.A. (1975). Two-dimensional gel analysis of soluble proteins. Charaterization of guinea pig exocrine pancreatic proteins. J Biol Chem 250, 5375–5385.Google Scholar
  125. Sibbald, M.J., Ziebandt, A.K., Engelmann, S., Hecker, M., de Jong, A., Harmsen, H.J., Raangs, G.C., Stokroos, I., Arends, J.P., Dubois, J.Y., et al. (2006). Mapping the pathways to staphylococcal pathogenesis by comparative secretomics. Microbiol Mol Biol Rev 70, 755–788.Google Scholar
  126. Skurnik, M., Venho, R., Bengoechea, J.A., and Moriyón, I. (1999). The lipopolysaccharide outer core of Yersinia enterocolitica serotype O:3 is required for virulence and plays a role in outer membrane integrity. Mol Microbiol 31, 1443–1462.Google Scholar
  127. Swanson, R.V., Alex, L.A., and Simon, M.I. (1994). Histidine and aspartate phosphorylation: two-component systems and the limits of homology. Trends Biochem Sci 19, 485–490.Google Scholar
  128. Teng, J.L., Woo, P.C., Ma, S.S., Sit, T.H., Ng, L.T., Hui, W.T., Lau, S.K., and Yuen, K.Y. (2005). Ecoepidemiology of Laribacter hongkongensis, a novel bacterium associated with gastroenteritis. J Clin Microbiol 43, 919–922.Google Scholar
  129. Thein, M., Sauer, G., Paramasivam, N., Grin, I., and Linke, D. (2010). Efficient subfractionation of gram-negative bacteria for proteomics studies. J Proteome Res 9, 6135–6147.Google Scholar
  130. Thieringer, H.A., Jones, P.G., and Inouye, M. (1998). Cold shock and adaptation. Bioessays 20, 49–57.Google Scholar
  131. Tjalsma, H., Antelmann, H., Jongbloed, J.D., Braun, P.G., Darmon, E., Dorenbos, R., Dubois, J.Y., Westers, H., Zanen, G., Quax, W.J., et al. (2004). Proteomics of protein secretion by Bacillus subtilis: separating the “secrets” of the secretome. Microbiol Mol Biol Rev 68, 207–233.Google Scholar
  132. Traini, M., Gooley, A.A., Ou, K., Wilkins, M.R., Tonella, L., Sanchez, J.C., Hochstrasser, D.F., and Williams, K.L. (1998). Towards an automated approach for protein identification in proteome projects. Electrophoresis 19, 1941–1949.Google Scholar
  133. Trost, M., Wehmhöner, D., Kärst, U., Dieterich, G., Wehland, J., and Jänsch, L. (2005). Comparative proteome analysis of secretory proteins from pathogenic and nonpathogenic Listeria species. Proteomics 5, 1544–1557.Google Scholar
  134. Trülzsch, K., Roggenkamp, A., Aepfelbacher, M., Wilharm, G., Ruckdeschel, K., and Heesemann, J. (2003). Analysis of chaperone-dependent Yop secretion/translocation and effector function using a mini-virulence plasmid of Yersinia enterocolitica. Int J Med Microbiol 293, 167–177.Google Scholar
  135. Unlü, M., Morgan, M.E., and Minden, J.S. (1997). Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18, 2071–2077.Google Scholar
  136. Völker, U., and Hecker, M. (2005). From genomics via proteomics to cellular physiology of the Gram-positive model organism Bacillus subtilis. Cell Microbiol 7, 1077–1085.Google Scholar
  137. Wang, J., Ying, T., Wang, H., Shi, Z., Li, M., He, K., Feng, E., Wang, J., Yuan, J., Li, T., et al. (2005). 2-D reference map of Bacillus anthracis vaccine strain A16R proteins. Proteomics 5, 4488–4495.Google Scholar
  138. Wang, Y., Xu, A., Knight, C., Xu, L.Y., and Cooper, G.J. (2002). Hydroxylation and glycosylation of the four conserved lysine residues in the collagenous domain of adiponectin. Potential role in the modulation of its insulin-sensitizing activity. J Biol Chem 277, 19521–19529.Google Scholar
  139. Washburn, M.P., Wolters, D., and Yates, J.R. 3rd. (2001). Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19, 242–247.Google Scholar
  140. Wilkins, M.R., Gasteiger, E., Sanchez, J.C., Bairoch, A., and Hochstrasser, D.F. (1998). Two-dimensional gel electrophoresis for proteome projects: the effects of protein hydrophobicity and copy number. Electrophoresis 19, 1501–1505.Google Scholar
  141. Wilkins, M.R., Pasquali, C., Appel, R.D., Ou, K., Golaz, O., Sanchez, J.C., Yan, J.X., Gooley, A.A., Hughes, G., Humphery-Smith, I., et al. (1996). From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Biotechnology (N Y) 14, 61–65.Google Scholar
  142. Woo, P.C., Lau, S.K., Teng, J.L., Que, T.L., Yung, R.W., Luk, W.K., Lai, R.W., Hui, W.T., Wong, S.S., Yau, H.H., et al., and the L Hongkongensis study group. (2004). Association of Laribacter hongkongensis in community-acquired gastroenteritis with travel and eating fish: a multicentre case-control study. Lancet 363, 1941–1947.Google Scholar
  143. Woo, P.C., Lau, S.K., Teng, J.L., and Yuen, K.Y. (2005). Current status and future directions for Laribacter hongkongensis, a novel bacterium associated with gastroenteritis and traveller’s diarrhoea. Curr Opin Infect Dis 18, 413–419.Google Scholar
  144. Woo, P.C., Lau, S.K., Tse, H., Teng, J.L., Curreem, S.O., Tsang, A.K., Fan, R.Y., Wong, G.K., Huang, Y., Loman, N.J., et al. (2009). The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats. PLoS Genet 5, e1000416.Google Scholar
  145. Yan, J.X., Devenish, A.T., Wait, R., Stone, T., Lewis, S., and Fowler, S. (2002). Fluorescence two-dimensional difference gel electrophoresis and mass spectrometry based proteomic analysis of Escherichia coli. Proteomics 2, 1682–1698.Google Scholar
  146. Yates, J.R. 3rd, Speicher, S., Griffin, P.R., and Hunkapiller, T. (1993). Peptide mass maps: a highly informative approach to protein identification. Anal Biochem 214, 397–408.Google Scholar
  147. Yu, H.B., Kaur, R., Lim, S., Wang, X.H., and Leung, K.Y. (2007). Characterization of extracellular proteins produced by Aeromonas hydrophila AH-1. Proteomics 7, 436–449.Google Scholar
  148. Yuen, K.Y., Woo, P.C., Teng, J.L., Leung, K.W., Wong, M.K., and Lau, S.K. (2001). Laribacter hongkongensis gen. nov., sp. nov., a novel gram-negative bacterium isolated from a cirrhotic patient with bacteremia and empyema. J Clin Microbiol 39, 4227–4232.Google Scholar

Copyright information

© Higher Education Press and Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  1. 1.Department of MicrobiologyThe University of Hong Kong, Queen Mary HospitalHong KongChina
  2. 2.Oral Biosciences, Faculty of DentistryThe University of Hong Kong, Queen Mary HospitalHong KongChina
  3. 3.State Key Laboratory of Emerging Infectious Diseases, Department of MicrobiologyThe University of Hong Kong, Queen Mary HospitalHong KongChina
  4. 4.Research Centre of Infection and ImmunologyThe University of Hong Kong, Queen Mary HospitalHong KongChina
  5. 5.Carol Yu Centre of InfectionThe University of Hong KongHong KongChina

Personalised recommendations