A proteomic view of the host-pathogen interaction: The host perspective

Proteomics

Volumn 11, Issue 15, 2011, Pages 3212-3220

  Hartlova, Anetta ^a   Krocova, Zuzana ^b   Cerveny, Lukas ^a   Stulik, Jiri ^b  

^a UNIVERSITY OF DEFENCE   (Czech Republic)

^b UNIVERSITY OF DEFENCE   (Czech Republic)

Author keywords

Host response; Host pathogen interaction; Microbiology; MS

Indexed keywords

PROTEOME;

BACTERIAL INFECTION; BACTERIAL STRAIN; BACTERIUM; BIOINFORMATICS; CELL MIGRATION; FUNCTIONAL GENOMICS; HOST; HOST PATHOGEN INTERACTION; MASS SPECTROMETRY; MOLECULAR DYNAMICS; MUTANT; NONHUMAN; PRIORITY JOURNAL; PROTEOMICS; REVIEW; WILD TYPE;

BACTERIAL INFECTIONS; HOST-PATHOGEN INTERACTIONS; HUMANS; PROTEINS; PROTEOME; PROTEOMICS;

BACTERIA (MICROORGANISMS);

EID: 79960416662     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201000767     Document Type: Review

References (53)

1. Jones, K. E., Patel, N. G., Levy, M. A., Storeygard, A., et al., Global trends in emerging infectious diseases. Nature 2008, 451, 990-993.
2. Jain, A., Mondal, R., Extensively drug-resistant tuberculosis: current challenges and threats. FEMS Immunol. Med. Microbiol. 2008, 53, 145-150.
3. Huang, S. H., Triche, T., Jong, A. Y., Infectomics: genomics and proteomics of microbial infections. Funct. Integr. Genomics 2002, 1, 331-344.
4. Schwegmann, A., Brombacher, F., Host-directed drug targeting of factors hijacked by pathogens. Sci. Signal. 2008, 1, re8.
5. Cossart, P., Bacterial invasion: a new strategy to dominate cytoskeleton plasticity. Dev. Cell 2004, 3, 314-315.
6. Jenner, R. G., Young, R. A., Insights into host responses against pathogens from transcriptional profiling. Nat. Rev. Microbiol. 2005, 3, 281-294.
7. Brodsky, I. E., Medzhitov, R., Targeting of immune signalling networks by bacterial pathogens. Nat. Cell Biol. 2009, 11, 521-526.
8. Aebersold, R., Mann, M., Mass spectrometry-based proteomics. Nature 2003, 422, 198-207.
9. O'Farrell, P. H., High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 1975, 250, 4007-4021.
10. Jungblut, P., Thiede, B., Protein identification from 2-DE gels by MALDI mass spectrometry. Mass Spectrom. Rev. 1997, 16, 145-162.
11. Link, A. J., Eng, J., Schieltz, D. M., Carmack, E. et al., Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 1999, 17, 676-682.
12. McCormack, A. L., Schieltz, D. M., Goode, B., Yang, S. et al., Direct analysis and identification of proteins in mixtures by LC/MS/MS and database searching at the low-femtomole level. Anal. Chem. 1997, 69, 767-776.
13. Yates, J. R., 3rd, Schieltz, D., Carmack, E., Link, A. J., Direct analysis of protein mixtures by tandem mass spectrometr. J. Protein Chem. 1997, 16, 495-497.
14. McDonald, W. H., Yates, J. R., 3rd, Shotgun proteomics and biomarker discovery. Dis. Markers 2002, 18, 99-105.
15. Kislinger, T., Emili, A., Going global: protein expression profiling using shotgun mass spectrometry. Curr. Opin. Mol. Ther. 2003, 5, 285-293.
16. Ong, S. E., Foster, L. J., Mann, M., Mass spectrometric-based approaches in quantitative proteomics. Methods 2003, 29, 124-130.
17. Oda, Y., Huang, K., Cross, F. R., Cowburn, D., Chait, B. T., Accurate quantitation of protein expression and site-specific phosphorylation. Proc. Natl. Acad. Sci. USA 1999, 96, 6591-6596.
18. Unwin, R. D., Evans, C. A., Whetton, A. D., Relative quantification in proteomics: new approaches for biochemistry. Trends Biochem. Sci. 2006, 31, 473-484.
19. Kirkpatrick, D. S., Gerber, S. A., Gygi, S. P., The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. Methods 2005, 35, 265-273.
20. Blondeau, F., Ritter, B., Allaire, P. D., Wasiak, S. et al., Tandem MS analysis of brain clathrin-coated vesicles reveals their critical involvement in synaptic vesicle recycling. Proc. Natl. Acad. Sci. USA 2004, 101, 3833-3838.
21. Silva, J. C., Gorenstein, M. V., Li, G. Z., Vissers, J. P. et al., Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Mol. Cell. Proteomics 2006, 5, 144-156.
22. Gilchrist, A., Au, C. E., Hiding, J., Bell, A. W. et al., Quantitative proteomics analysis of the secretory pathway. Cell 2006. 127, 1265-1281.
23. Mann, M., Jensen, O. N., Proteomic analysis of post-translational modifications. Nat. Biotechnol. 2003, 21, 255-261.
24. Stasyk, T., Huber, L. A., Zooming in: fractionation strategies in proteomics. Proteomics 2004, 4, 3704-3716.
25. Salomon, A. R., Ficarro, S. B., Brill, L. M., Brinker, A. et al., Profiling of tyrosine phosphorylation pathways in human cells using mass spectrometry. Proc. Natl. Acad. Sci. USA 2003, 100, 443-448.
26. Zhang, H., Yan, W., Aebersold, R., Chemical probes and tandem mass spectrometry: a strategy for the quantitative analysis of proteomes and subproteomes. Curr. Opin. Chem. Biol. 2004, 8, 66-75.
27. Gevaert, K., Ghesquière, B., Staes, A., Martens, L. et al., Reversible labeling of cysteine-containing peptides allows their specific chromatographic isolation for non-gel proteome studies. Proteomics 2004, 4, 897-908.
28. Cossart, P., Sansonetti, P. J., Bacterial invasion: the paradigms of enteroinvasive pathogens. Science 2004, 304, 242-248.
29. Dhungana, S., Merrick, B. A., Tomer, K. B., Fessler, M. B., Quantitative proteomics analysis of macrophage rafts reveals compartmentalized activation of the proteasome and of proteasome-mediated ERK activation in response to lipopolysaccharide. Mol. Cell. Proteomics 2009, 8, 201-213.
30. Simons, K., Ikonen, E., Functional rafts in cell membranes. Nature 1997, 387, 569-572.
31. Gu, S., Wang, T., Chen, X., Quantitative proteomic analysis of LPS-induced differential immune response associated with TLR4 Polymorphisms by multiplex amino acid coded mass tagging. Proteomics 2008, 8, 3061-3070.
32. Akira, S., Mammalian Toll-like receptors. Curr. Opin. Immunol. 2003, 15, 5-11.
33. Du, R., Subcellular quantitative proteomics reveals multiple pathway cross-talk that coordinates specific signaling and transcriptional regulation for the early host response to LPS. J. Proteome Res. 2010, 9, 1805-1821.
34. Olsen, J. V., Blagoev, B., Gnad, F., Macek, B. et al., Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006, 127, 635-648.
35. Sharma, K., Kumar, C., Kéri, G., Breitkopf, S. B. et al., Quantitative Analysis of Kinase-proximal Signaling in Lipopolysaccharide-induced Innate Immune Response. J Proteome Res. 2010, 9, 2539-2549.
36. Shui, W., Gilmore, S. A., Sheu, L., Liu, J. et al., Quantitative proteomic profiling of host-pathogen interactions: the macrophage response to Mycobacterium tuberculosis lipids. J. Proteome Res. 2009, 8, 282-289.
37. Urban, C. F., Ermert, D., Schmid, M., Abu-Abed, U. et al., Neutrophil extracellular traps contain calprotectin, a cytosolic protein complex involved in host defense against Candida albicans. PLoS Pathog. 2009, 5, e1000639.
38. Cardoso, C. M., Ordaol, J., Vieira, O. V., Rab10 regulates phagosome maturation and its overexpression rescues Mycobacterium-containing phagosomes maturation. Traffic 2010, 11, 221-235.
39. Lee, B. Y., Jethwaney, D., Schilling, B., Clemens, D. L. et al., The Mycobacterium bovis bacille Calmette-Guerin phagosome proteome. Mol. Cell. Proteomics 2010, 9, 32-53.
40. Reinl, T., Nimtz, M., Hundertmark, C., Johl, T. et al., Quantitative phosphokinome analysis of the Met pathway activated by the invasin internalin B from Listeria monocytogenes. Mol. Cell. Proteomics 2009, 8, 2778-2795.
41. Kuhn, M., The microtubule depolymerizing drugs nocodazole and colchicine inhibit the uptake of Listeria monocytogenes by P388D1 macrophages. FEMS Microbiol. Lett. 1998, 160, 87-90.
42. Selbach, M., Paul, F. E., Brandt, S., Guye, P. et al., Host cell interactome of tyrosine-phosphorylated bacterial proteins. Cell Host Microbe 2009, 5, 397-403.
43. Roy, K., Hilliard, G. M., Hamilton, D. J., Luo, J. et al., Enterotoxigenic Escherichia coli EtpA mediates adhesion between flagella and host cells. Nature 2009, 457, 594-598.
44. Upritchard, H. G., Cordwell, S. J., Lamont, I. L., Immunoproteomics to examine cystic fibrosis host interactions with extracellular Pseudomonas aeruginosa proteins. Infect. Immun. 2008, 76, 4624-4632.
45. Greub, G., Kebbi-Beghdadi, C., Bertelli, C., Collyn, F. et al., High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach. PLoS One 2009, 4, e8423.
46. Karunakaran, K. P., Rey-Ladino, J., Stoynov, N., Berg, K. et al., Immunoproteomic discovery of novel T cell antigens from the obligate intracellular pathogen Chlamydia. J. Immunol. 2008, 180, 2459-2465.
47. Hardwidge, P. R., Rodriguez-Escudero, I., Goode, D., Donohoe, S. et al., Proteomic analysis of the intestinal epithelial cell response to enteropathogenic Escherichia coli. J. Biol. Chem. 2004, 279, 20127-20136.
48. Backert, S., Gressmann, H., Kwok, T., Zimny-Arndt, U. et al., Gene expression and protein profiling of AGS gastric epithelial cells upon infection with Helicobacter pylori. Proteomics 2005, 5, 3902-3918.
49. Dyer, M. D., Murali, T. M., Sobral, B. W., The landscape of human proteins interacting with viruses and other pathogens. PLoS Pathog. 2008, 4, e32.
50. Finlay, B. B., McFadden, G., Anti-immunology: evasion of the host immune system by bacterial and viral pathogens. Cell 2006, 124, 767-782.
51. Hancock, R. E., Sahl, H. G., Antimicrobial and host-defense peptides as new anti-infective therapeutic strategies. Nat. Biotechnol. 2006, 24, 1551-1557.
52. Yu, H. B., Kielczewska, A., Rozek, A., Takenaka, S. et al., Sequestosome-1/p62 is the key intracellular target of innate defense regulator peptide. J. Biol. Chem. 2009, 284, 36007-36011.
53. Kumar, C., Mann, M., Bioinformatics analysis of mass spectrometry-based proteomics data sets. FEBS Lett. 2009, 583, 1703-1712.