Proteomics of bacterial pathogens

Expert Opinion on Drug Discovery

Volumn 3, Issue 5, 2008, Pages 461-473

  Cash, Phillip ^a  

^a UNIVERSITY OF ABERDEEN   (United Kingdom)

Author keywords

Bacteria; Pathogenesis; Protein; Proteomics; Vaccine and antibiotic development

Indexed keywords

AMOXICILLIN; AMPICILLIN; BACTERIAL GHOST VACCINE; BACTERIAL PROTEIN; BACTERIAL VACCINE; CHLORTETRACYCLINE; ENROFLOXACIN; HELICOBACTER PYLORI VACCINE; METRONIDAZOLE; OUTER MEMBRANE PROTEIN; OXACILLIN; PERIPLASMIC BINDING PROTEIN; PERIPLASMIC PROTEIN; PROTEIN ACE1569; PROTEIN ACE961; PROTEIN HP0231; PROTEIN HP0410; PROTEOME; QUINOLINE DERIVED ANTIINFECTIVE AGENT;

ANTIBIOTIC RESISTANCE; BACTERIAL GENETICS; BACTERIAL INFECTION; CAMPYLOBACTER JEJUNI; COMPARATIVE STUDY; CORRELATION ANALYSIS; DRUG SCREENING; DRUG TARGETING; GENE EXPRESSION; GENE SEQUENCE; HELICOBACTER INFECTION; HELICOBACTER PYLORI; HUMAN; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEOMICS; REVIEW; SURFACE ENHANCED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; TWO DIMENSIONAL GEL ELECTROPHORESIS;

EID: 44649147111     PISSN: 17460441     EISSN: None     Source Type: Journal    
DOI: 10.1517/17460441.3.5.461     Document Type: Review

References (110)

1. Wilkins MR, Pasquali C, Appel RD, et al. From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Biotechnology 1996;14:61-5
2. O'Farrell PH. High resolution two-dimensional electrophoresis of proteins. J Biol Chem 1975;250:4007-21
3. Cash P. Protein mutations revealed by two-dimensional electrophoresis. J Chromatogr A 1995;698:203-24
4. Cash P. Characterisation of bacterial proteomes by two-dimensional electrophoresis. Analytica Chimica Acta 1998;372:121-46
5. O'Connor CD, Adams P, Alefounder P, et al. The analysis of microbial proteomes: strategies and data exploitation. Electrophoresis 2000;21:1178-86
6. Washburn MP, Yates JR 3rd. Analysis of the microbial proteome. Curr Opin Microbiol 2000;3:292-7
7. Cash P. Bacterial proteomics. In: Bull AT, editor, Microbial diversity and bioprospecting. Washington DC: ASM Press; 2004. p. 260-79
8. Phillips CI, Bogyo M. Proteomics meets microbiology: technical advances in the global mapping of protein expression and function. Cell Microbiol 2005;7:1061-76
9. Cash P. Proteomics in medical microbiology. Electrophoresis 2000;21:1187-201
10. Cordwell SJ, Nouwens AS, Walsh BJ. Comparative proteomics of bacterial pathogens. Proteomics 2001;1:461-72
11. Jungblut PR. Proteome analysis of bacterial pathogens. Microbes Infect 2001;3:831-40
12. Cash P. Proteomics of bacterial pathogens. Adv Biochem Eng Biotechnol 2003;83:93-115
13. Macarthur DJ, Jacques NA. Proteome analysis of oral pathogens. J Dent Res 2003;82:870-6
14. Cash P. Analyzing bacterial pathogenesis at level of proteome. Methods Biocheml Anal 2006;49:211-35
15. Weissinger EM, Mischak H. Application of proteomics to posttransplantational Follow-up. Methods Mol Med 2007;134:217-28
16. Tonella L, Hoogland C, Binz PA, et al. New perspectives in the Escherichia coli proteome investigation. Proteomics 2001;1:409-23
17. Lock RA, Cordwell SJ, Coombs GW, et al. Proteome analysis of Helicobacter pylori: major proteins of type strain NCTC 11637. Pathology 2001;33:365-74
18. Mashego MR, Rumbold K, De May M, et al. Microbial metabolomics: past, present and future methodologies. Biotechnol Lett 2007;29:1-16
19. Gygi SP, Rochon Y, Franza BR, et al. Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 1999;19:1720-30
20. Freiberg C, Brotz-Oesterhelt H, Labischinski H. The impact of transcriptome and proteome analyses on antibiotic drug discovery [review] [57 refs]. Curr Opin Microbiol 2004;7:451-9
21. Moxon R, Tang C. Challenge of investigating biologically relevant functions of virulence factors in bacterial pathogens [review] [104 refs]. Philosophical Transactions of the Royal Society of London - Series B. Biol Sci 2000;355:643-56
22. Available from: http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi
23. Hayashi T, Makino K, Ohnishi M, et al. Complete genome sequence of enterohemorrhagic Escherichia coli O157: H7 and genomic comparison with laboratory strain K-12. DNA Res 2001;8:11-22
24. Eppinger M, Baar C, Raddatz G, et al. Comparative analysis of four Campylobacterales. Nat Rev Microbiol 2004;2:872-85
25. Holden M, Crossman L, Cerdeno-Tarraga A, et al. Pathogenomics of non-pathogens. Nat Rev Microbiol 2004;2:91-2
26. VanBogelen RA. Probing the molecular physiology of the microbial organism, Escherichia coli using proteomics. Adv Biochem Eng Biotechnol 2003;83:27-55
27. VanBogelen RA, Abshire KZ, Pertsemlidis A, et al. Gene-Protein database of Escherichia coli K-12. In: Neidhardt FC, Curtiss R, Ingraham JL, et al., editors, Escherichia coli and salmonella: cellular and molecular biology. 6th edition. Washington DC: ASM Press; 1996. p. 2067-117
28. Hecker M, Volker U. Towards a comprehensive understanding of Bacillus subtilis cell physiology by physiological proteomics [review] [122 refs]. Proteomics 2004;4:3727-50
29. Jungblut PR, Bumann D. Haas G, et al. Comparative proteome analysis of Helicobacter pylori. Mol Microbiol 2000;36:710-25
30. Bumann D, Meyer TF, Jungblut PR. Proteome analysis of the common human pathogen Helicobacter pylori. Proteomics 2001;1:473-9
31. Cho MJ, Jeon BS, Park JW, et al. Identifying the major proteome components of Helicobacter pylori strain 26695. Electrophoresis 2002;23:1161-73
32. Jungblut PR, Schaible UE, Mallenkopf HJ, et al. Comparative proteome analysis of Mycobacterium tuberculosis and Mycobacterium bovis BCG strains: towards functional genomics of microbial pathogens. Mol Microbiol 1999;33:1103-17
33. Rosenkrands I, King A, Weldingh K, et al. Towards the proteome of Mycobacterium tuberculosis. Electrophoresis 2000;21:3740-56
34. Rosenkrands I, Weldingh K, Jacobsen S, et al. Mapping and identification of Mycobacterium tuberculosis proteins by two-dimensional gel electrophoresis, microsequencing and immunodetection. Electrophoresis 2000;21:935-48
35. Bernardini G, Braconi D, Santucci A. The analysis of Neisseria meningitidis proteomes: reference maps and their applications. Proteomics 2007;7:2933-46
36. Jungblut PR, Muller EC, Mattow J, et al. Proteomics reveals open reading frames in Mycobacterium tuberculosis H37Rv not predicted by genomics. Infect Immun 2001;69:5905-7
37. Urquhart BL, Atsalos TE, Roach D, et al. 'Proteomic contigs' of Mycobacterium tuberculosis and Mycobacterium bovis (BCG) using novel immobilised pH gradients. Electrophoresis 1997;18:1384-92
38. Mollenkopf HJ, Jungblut PR, Raupach B, et al. A dynamic two-dimensional polyacrylamide gel electrophoresis database: the mycobacterial proteome via internet. Electrophoresis 1999;20:2172-80
39. Mahairas GG, Sabo PJ, Hickey MJ, et al. Molecular analysis of genetic differences between Mycobacterium bovis BCG and virulent M. bovis. J Bacteriol 1996;178:1274-82
40. Pym AS, Brodin P, Brosch R, et al. Loss of RD1 contributed to the attenuation of the live tuberculosis vaccines Mycobacterium bovis BCG and Mycobacterium microti. Mol Microbiol 2002;46:709-17
41. Brusasca PN, Colangeli R, Lyashchenko KP, et al. Immunological characterization of antigens encoded by the RD1 region of the Mycobacterium tuberculosis genome. Scand J Immunol 2001;54:448-52
42. Agger EM, Brock I, Okkels LM, et al. Human T-cell responses to the RD1-encoded protein TB27.4 (Rv3878) from Mycobacterium tuberculosis. Immunology 2003;110:507-12
43. Amoudy HA, Ahmad S, Thole JE, et al. Demonstration of in vivo expression of a hypothetical Open Reading Frame (ORF-14) encoded by the RD1 region of Mycobacterium tuberculosis. Scand J Immunol 2007;66:422-5
44. Schmidt F, Donahoe S, Hagens K, et al. Complementary analysis of the Mycobacterium tuberculosis proteome by two-dimensional electrophoresis and isotope-coded affinity tag technology. Mol Cell Proteomics 2004;3:24-42
45. Bjellqvist B, Sanchez JC, Pasquali C, et al. Micropreparative two-dimensional electrophoresis allowing the separation of samples containing milligram amounts of proteins. Electrophoresis 1993;14:1375-8
46. Westbrook JA, Yan JX, Wait R, et al. Zooming-in on the proteome: very narrow-range immobilised pH gradients reveal more protein species and isoforms [review] [19 refs]. Electrophoresis 2001;22:2865-71
47. Birch RM, O'Byrne C, Booth IR, et al. Enrichment of Escherichia coli proteins by column chromatography on reactive dye columns. Proteomics 2003;3:764-76
48. McGee DJ, Mobley HL. Mechanisms of Helicobacter pylori infection: bacterial factors. Curr Top Microbiol Immunol 1999;241:155-80
49. Cordwell SJ. Technologies for bacterial surface proteomics. Curr Opin Microbiol 2006;9:320-9
50. Sabarth N, Lamer S, Zimmy-Arndt U, et al. Identification of surface proteins of Helicobacter pylroi by selective biotinylation, affinity purification and two-dimensional gel electrophoresis. J Biol Chem 2002;31:27896-902
51. Nouwens AS, Cordwell SJ, Larsen MR, et al. Complementing genomics with proteomics: the membrane subproteome of Pseudomonas aeruginosa PAO1. Electrophoresis 2000;21:3797-809
52. Nouwens AS, Willcox MD, Walsh BJ, et al. Proteomic comparison of membrane and extracellular proteins from invasive (PAO1) and cytotoxic 6206; strains of Pseudomonas aeruginosa. Proteomics 2002;2:1325-46
53. Wehmhoner D, Haussler S, Tummler B, et al. Inter- and intraclonal diversity of the Pseudomonas aeruginosa proteome manifests within the secretome. J Bacteriol 2003;185:5807-14
54. Blonder J, Goshe MB, Xiao W, et al. Global analysis of the membrane subproteome of Pseudomonas aeruginosa using liquid chromatography-tandem mass spectrometry. J Proteome Res 2004;3:434-44
55. Cardwell SJ, Len AC, Touma RG, et al. Identification of membrane-associated proteins from Campylobacter jejuni strains using complementary proteomics technologies. Proteomics 2008;8:122-39
56. Rodwell AW, Rodwell ES. Relationships between strains of Mycoplasma mycoides subspp mycoides and capri studied by two-dimensional gel electrophoresis of cell proteins. J Gen Microbiol 1978;109:259-63
57. Jackson P, Thornley MJ, Thompson RJ. A study by high resolution two-dimensional polyacrylamide gel electrophoresis of relationships between Neisseria gonorrhoeae and other bacteria. J Gen Microbiol 1984;130:3189-201
58. Gormon T, Phan-Thanh L. Identification and classification of Listeria by two-dimensional protein mapping. Res Microbiol 1995;146:143-54
59. Schmid O, Ball G, Lancashire L, et al. New approaches to identification of bacterial pathogens by surface enhanced laser desorption/ionization time of flight mass spectrometry in concert with artificial neural networks, with special reference to Neisseria gonorrhoeae. J Med Microbiol 2005;54:1205-11
60. Conway GC, Smole SC, Sarracino DA, et al. Phyloproteomics: species identification of Enterobacteriaceae using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Mol Microbiol Biotechnol 2001;3:103-12
61. Edwards-Jones V, Claydon MA, Evason DJ, et al. Rapid discrimination between methicillin-sensitive and methicillin-resistant Staphylococcus aureus by intact cell mass spectrometry. J Med Microbiol 2000;49:295-300
62. Walker J, Fox AJ, Edwards-Jones V, et al. Intact cell mass spectrometry (ICMS) used to type methicillin-resistant Staphylococcus aureus: media effects and inter-laboratory reproducibility. J Microbiol Methods 2002;48:117-26
63. Jackson KA, Edwards-Jones V, Sutton CW, et al. Optimisation of intact cell MALDI method for fingerprinting of methicillin-resistant Staphylococcus aureus. J Microbiol Methods 2005;62:273-84
64. Hettick JM, Kashon ML, Simpson JP, et al. Proteomic profiling of intact mycobacteria by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, Anal Chem 2004;76:5769-76
65. Hettick JM, Kashon ML, Slaven JE, et al. Discrimination of intact mycobacteria at the strain level: a combined MALDI-TOF MS and biostatistical analysis. Proteomics 2006;6:6416-25
66. Demirev PA, Lin JS, Puneda FJ, et al. Bioinformatics and mass spectrometry for microorganism identification: proteome-wide post-translational modifications and database search algorithms for characterization of intact H. pylori [see comment]. Anal Chem 2001;73:4566-73
67. Enroth H, Akerlund T, Sille A, et al. Clustering of clinical strains of Helicobacter pylori analyzed by two-dimensional gel electrophoresis. Clin Diag Lab Immunol 2000;7:301-6
68. Hazell SL, Andrews RH, Mitchell HM, et al. Variability of gene order in different Helicobacter pylori strains contributes to genome diversity. FEMS Microbiol Lett 1996;20:833-42
69. Park SA, Lee HW, Hong MH, et al. Comparative proteomic analysis of Helicobacter pylori strains associated with iron deficiency anemia. Proteomics 2006;6:1319-28
70. Mattow J, Siejak F, Hagens K, et al. Proteins unique to intraphagosomally grown Mycobacterium tuberculosis. Proteomics 2006;6:2485-94
71. Hagan EC, Mobley HL. Uropathogenic Escherichia coli outer membrane antigens expressed during urinary tract infection. Infect Immun 2007;75:3941-9
72. Alteri CJ, Mobley HL. Quantitative profile of the uropathogenic Escherichia coli outer membrane proteome during growth in human urine. Infect Immun 2007;75:2679-88
73. Hughes V, Smith S, Garcia-Sanchez A, et al. Proteomic comparison of Mycobacterium avium subspecies paratuberculosis grown in vitro and isolated from clinical cases of ovine paratuberculosis. Microbiology 2007;153:196-205
74. Boyce JD, Cullen PA, Nguyen V, et al. Analysis of the Pasteurella multocida outer membrane sub-proteome and its response to the in vivo environment of the natural host. Proteomics 2006;6:870-80
75. Becker D, Selbach M, Rollenhagen C, et al. Robust Salmonella metabolism limits possibilities for new antimicrobials. Nature 2006;440:303-7
76. Twine SM, Mykytczuk NC, Petit MD, et al. In vivo proteomic analysis of the intracellular bacterial pathogen, Francisella tularensis, isolated from mouse spleen. Biochem Biophys Res Commun 2006;345:1621-33
77. Johri AK, Paoletti LC, Glaser P, et al. Group B Streptococcus: global incidence and vaccine development. Nat Rev Microbiol 2006;4:932-42
78. Johnson PD, MacInnes SJ, Gilbert GL. Antibodies to Haemophilus influenzae type b outer membrane proteins in children with epiglottitis or meningitis and in healthy controls. Infect Immun 1993;61:1531-7
79. Jungblut PR, Grabher G, Stoffler G. Comprehensive detection of immunorelevant Borrelia garinii antigens by two-dimensional electrophoresis. Electrophoresis 1999;20:3611-22
80. Lemos JA, Giambiagi-Demarval M, Castro AC. Expression of heat-shock proteins in Streptococcus pyogenes and their immunoreactivity with sera from patients with streptococcal diseases. J Med Microbiol 1998;47:711-5
81. Teixeira-Gomes AP, Cloeckaert A, Bezard G, et al. Identification and characterization of Brucella ovis immunogenic proteins using two-dimensional electrophoresis and immunoblottung. Electrophoresis 1997;18:1491-7
82. Covert BA, Spencer JS, Orme IM, et al. The application of proteomics in defining the T cell antigens of Mycobacterium tuberculosis. Proteomics 2001;1:574-86
83. McAtee CP, Fry KE, Berg DE. Identification of potential diagnostic and vaccine candidates of Helicobacter pylori by "proteome" technologies. Helicobacter 1998;3:163-9
84. McAtee CP, Lim MY, Fung K, et al. Identification of potential diagnostic and vaccine candidates of Helicobacter pylori by two-dimensional gel electrophoresis, sequence analysis, and serum profiling. Clin Diagn Lab Immunol 1998;5:537-42
85. McAtee CP, Lim MY, Fung K, et al. Characterization of a Helicobacter pylori vaccine candidate by proteome techniques. J Chromatogr 1998;325-33
86. Pathak SK, Basu S, Bhattacharyya A, et al. TLR4-dependent NF-kappaB activation and mitogen- and stress-activated protein kinase 1-triggered phosphorylation events are central to Helicobacter pylori peptidyl prolyl cis-, trans-isomerase (HP0175)-mediated induction of IL-6 release from macrophages. J Immunol 2006;177:7950-8
87. Khan AS, Mujer CV, Alefantis TG, et al. Proteomics and bioinformatics strategies to design countermeasures against infectious threat agents. J Chem Inf Model 2006;46:111-5
88. Bumann D, Jungblut PR, Meyer TF. Helicobacter pylori vaccine development based on combined subproteome analysis. Proteomics 2004;4:2843-8
89. Sabarth N, Hurwitz R, Meyer TF, et al. Multiparameter selection of Helicobacter pylori antigens identifies two novel antigens with high protective efficacy. Infect Immun 2002;70:6499-503
90. Vurma-Rapp U, Kayser FH, Hadorn K, et al. Mechanism of imipenem resistance acquired by three Pseudomonas aeruginosa strains during imipenem therapy. Eur J Clin Microbiol Infect Dis 1990;9:580-7
91. Michea-Hamzehpour M, Sanchez JC, Epp SF, et al. Two-dimensional polyacrylamide gel electrophoresis isolation and microsequencing of Pseudomonas aeruginosa proteins. Enzyme Protein 1993;47:1-8
92. Al-Haroni M, Skaug N, Bakken V, et al. Proteomic analysis of ampicillin-resistant oral Fusobacterium nucleatum. Oral Microbiol Immunol 2008;23:36-42
93. Wilson M, DeRisi J, Kristensen H, et al. Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization. Proc Natl Acad Sci USA 1999;96:12833-4
94. Singh VK, Jayaswal RK, Wilkinson BJ. Cell wall-active antibiotic induced proteins of Staphylococcus aureus identified using a proteomic approach. FEMS Microbiol Lett 2001;199:79-84
95. Coldham NG, Randall LP, Piddock LJ, et al. Effect of fluoroquinolone exposure on the proteome of Salmonella enterica serovar Typhimurium. J Antimicrob Chemother 2006;58:1145-53
96. Nanduri B, Lawrence ML, Boyle CR, et al. Effects of subminimum inhibitory concentrations of antibiotics on the Pasteurella multocida proteome. J Proteome Res 2006;5:572-80
97. McAtee CP, Hoffman PS, Berg DE. Identification of differentially regulated proteins in metronidozole resistant Helicobacter pylori by proteome techniques. Proteomics 2001;1:516-21
98. Pang JX, Ginanni N, Dongre AR, et al. Biomarker discovery in urine by proteomics. J Proteome Res 2002;1:161-9
99. Rain JC, Selig L, De Reuse H, et al. The protein-protein interaction map of Helicobacter pylori. Nature 2001;409:211-5
100. Bock JR, Gough DA. Whole-proteome interaction mining. Bioinformatics 2003;19:125-34
101. Noirot P, Noirot-Gros MF, Noirot P, et al. Protein interaction networks in bacteria. Curr Opin Microbiol 2004;7:505-12
102. Cahill DJ. Protein and antibody arrays and their medical applications. J Immunol Methods 2001;250:81-91
103. Fung ET, Thulasiraman V, Weinberger SR, et al. Protein biochips for differential profiling. Curr Opin Biotechnol 2001;12:65-9
104. Figeys D. Adapting arrays and lab-on-a-chip technology for proteomics. Proteomics 2002;2:373-82
105. Rabilloud T. Two-dimensional gel electrophoresis in proteomics: old, old fashioned, but it still climbs up the mountains. Proteomics 2002;2:3-10
106. Chen C-S, Korobkova E, Chen H, et al. A proteome chip approach reveals new DNA damage recognition activities in Escherichia coli. Nat Methods 2008;5:69-74
107. Matte A, Jia Z, Sunita S, et al. Insights into the biology of Escherichia coli through structural proteomics. J Struct Funct Genomics 2007;8:45-55
108. Plikat U, Voshol H, Dangendorf Y, et al. From proteomics to systems biology of bacterial pathogens: approaches, tools, and applications. Proteomics 2007;7:992-1003
109. Hooper LV. Laser microdissection: exploring host-bacterial encounters at the front lines. Curr Opin Microbiol 2004;7:290-5
110. Wright ME, Han DK, Aebersold R. Mass spectrometry-based expression profiling of clinical prostate cancer. Mol Cell Proteomics 2005;4:545-54