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Application of Activity-Based Protein Profiling to the Study of Microbial Pathogenesis

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Activity-Based Protein Profiling

Part of the book series: Topics in Current Chemistry ((TOPCURRCHEM,volume 324))

Abstract

Activity-based protein profiling (ABPP) is a powerful technology for the dissection of dynamic and complex enzyme interactions. The mechanisms involved in microbial pathogenesis are an example of just such a system, with a plethora of highly regulated enzymatic interactions between the infecting organism and its host. In this review we will discuss some of the cutting-edge applications of ABPP to the study of bacterial and parasitic pathogenesis and virulence, with an emphasis on Clostridium difficile, methicillin-resistant Staphylococcus aureus, quorum sensing, and malaria.

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References

  1. World Health Organization (2011) WHO, Geneva. http://www.euro.who.int/en/home

  2. Staub I, Sieber SA (2009) Beta-lactam probes as selective chemical-proteomic tools for the identification and functional characterization of resistance associated enzymes in MRSA. J Am Chem Soc 131:6271

    Article  CAS  Google Scholar 

  3. Heal WP, Dang TH, Tate EW (2011) Activity-based probes: discovering new biology and new drug targets. Chem Soc Rev 40:246

    Article  CAS  Google Scholar 

  4. Heal WP, Wickramasinghe SR, Tate EW (2008) Activity based chemical proteomics: profiling proteases as drug targets. Curr Drug Discov Technol 5:200

    Article  CAS  Google Scholar 

  5. Tang C, Holden D (1999) Pathogen virulence genes–implications for vaccines and drug therapy. Br Med Bull 55:387

    Article  CAS  Google Scholar 

  6. Miller MB, Bassler BL (2001) Quorum sensing in bacteria. Annu Rev Microbiol 55:165

    Article  CAS  Google Scholar 

  7. Masuda K, Itoh M, Kawata T (1989) Characterization and reassembly of a regular array in the cell wall of Clostridium difficile GAI 4131. Microbiol Immunol 33:287

    CAS  Google Scholar 

  8. Sleytr UB, Messner P (1983) Crystalline surface layers on bacteria. Annu Rev Microbiol 37:311

    Article  CAS  Google Scholar 

  9. Dang TH, de la Riva L, Fagan RP, Storck EM, Heal WP, Janoir C, Fairweather NF, Tate EW (2010) Chemical probes of surface layer biogenesis in Clostridium difficile. ACS Chem Biol 5:279

    Article  CAS  Google Scholar 

  10. Schirmeister T, Klockow A (2003) Cysteine protease inhibitors containing small rings. Mini Rev Med Chem 3:585

    Article  CAS  Google Scholar 

  11. Böttcher T, Sieber SA (2010) Showdomycin as a versatile chemical tool for the detection of pathogenesis-associated enzymes in bacteria. J Am Chem Soc 132:6964

    Article  Google Scholar 

  12. Uehara Y, Fisher JM, Rabinovitz M (1980) Showdomycin and its reactive moiety, maleimide. A comparison in selective toxicity and mechanism of action in vitro. Biochem Pharmacol 29:2199

    Article  CAS  Google Scholar 

  13. Rupnik M, Wilcox MH, Gerding DN (2009) Clostridium difficile infection: new developments in epidemiology and pathogenesis. Nat Rev Microbiol 7:526

    Article  CAS  Google Scholar 

  14. Lyras D, O’Connor JR, Howarth PM, Sambol SP, Carter GP, Phumoonna T, Poon R, Adams V, Vedantam G, Johnson S, Gerding DN, Rood JI (2009) Toxin B is essential for virulence of Clostridium difficile. Nature 458:1176

    Article  CAS  Google Scholar 

  15. Puri AW, Lupardus PJ, Deu E, Albrow VE, Garcia KC, Bogyo M, Shen A (2010) Rational design of inhibitors and activity-based probes targeting Clostridium difficile virulence factor TcdB. Chem Biol 17:1201

    Article  CAS  Google Scholar 

  16. Shen A, Lupardus PJ, Albrow VE, Guzzetta A, Powers JC, Garcia KC, Bogyo M (2009) Mechanistic and structural insights into the proteolytic activation of Vibrio cholerae MARTX toxin. Nat Chem Biol 5:469

    Article  CAS  Google Scholar 

  17. Greenbaum D, Medzihradszky KF, Burlingame A, Bogyo M (2000) Epoxide electrophiles as activity-dependent cysteine protease profiling and discovery tools. Chem Biol 7:569

    Article  CAS  Google Scholar 

  18. Bogyo M, Verhelst S, Bellingard-Dubouchaud V, Toba S, Greenbaum D (2000) Selective targeting of lysosomal cysteine proteases with radiolabeled electrophilic substrate analogs. Chem Biol 7:27

    Article  CAS  Google Scholar 

  19. Shen A, Lupardus PJ, Gersch MM, Puri AW, Albrow VE, Garcia KC, Bogyo M (2011) Defining an allosteric circuit in the cysteine protease domain of Clostridium difficile toxins. Nat Struct Mol Biol 18:364

    Article  CAS  Google Scholar 

  20. Kluytmans J, van Belkum A, Verbrugh H (1997) Nasal carriage of Staphylococcus aureus: epidemiology, underlying mechanisms, and associated risks. Clin Microbiol Rev 10:505

    CAS  Google Scholar 

  21. Böttcher T, Sieber SA (2008) Beta-lactones as privileged structures for the active-site labeling of versatile bacterial enzyme classes. Angew Chem Int Ed Engl 47:4600

    Article  Google Scholar 

  22. Böttcher T, Sieber SA (2008) Beta-lactones as specific inhibitors of ClpP attenuate the production of extracellular virulence factors of Staphylococcus aureus. J Am Chem Soc 130:14400

    Article  Google Scholar 

  23. Frees D, Qazi SN, Hill PJ, Ingmer H (2003) Alternative roles of ClpX and ClpP in Staphylococcus aureus stress tolerance and virulence. Mol Microbiol 48:1565

    Article  CAS  Google Scholar 

  24. Staudinger H (1907) Zur Kenntniss der Ketene. Diphenylketen. Justus Liebigs Ann Chem 356:51

    Article  CAS  Google Scholar 

  25. Chain E, Florey HW, Gardner AD, Heatley NG, Jennings MA, Orr-Ewing J, Sanders AG (1940) Penicillin as a chemotherapoutic agent. Lancet 236:226

    Article  Google Scholar 

  26. Abraham EP, Chain E (1940) An enzyme from bacteria able to destroy penicillin. Nature 46:837

    Article  Google Scholar 

  27. Breman JG (2001) The ears of the hippopotamus: manifestations, determinants, and estimates of the malaria burden. Am J Trop Med Hyg 64:1

    CAS  Google Scholar 

  28. Greenbaum DC, Baruch A, Grainger M, Bozdech Z, Medzihradszky KF, Engel J, DeRisi J, Holder AA, Bogyo M (2002) A role for the protease falcipain 1 in host cell invasion by the human malaria parasite. Science 298:2002

    Article  CAS  Google Scholar 

  29. Hastings JW, Nealson KH (1977) Bacterial bioluminescence. Annu Rev Microbiol 31:549

    Article  CAS  Google Scholar 

  30. Engebrecht J, Nealson K, Silverman M (1983) Bacterial bioluminescence: isolation and genetic analysis of functions from Vibrio fischeri. Cell 32:773

    Article  CAS  Google Scholar 

  31. Chan KG, Atkinson S, Mathee K, Sam CK, Chhabra SR, Camara M, Koh CL, Williams P (2011) Characterization of N-acylhomoserine lactone-degrading bacteria associated with the Zingiber officinale (ginger) rhizosphere: co-existence of quorum quenching and quorum sensing in Acinetobacter and Burkholderia. BMC Microbiol 11:51

    Article  CAS  Google Scholar 

  32. Ritchie AJ, Jansson A, Stallberg J, Nilsson P, Lysaght P, Cooley MA (2005) The Pseudomonas aeruginosa quorum-sensing molecule N-3-(oxododecanoyl)-L-homoserine lactone inhibits T-cell differentiation and cytokine production by a mechanism involving an early step in T-cell activation. Infect Immun 73:1648

    Article  CAS  Google Scholar 

  33. Kravchenko VV, Kaufmann GF, Mathison JC, Scott DA, Katz AZ, Grauer DC, Lehmann M, Meijler MM, Janda KD, Ulevitch RJ (2008) Modulation of gene expression via disruption of NF-kappaB signaling by a bacterial small molecule. Science 321:259

    Article  CAS  Google Scholar 

  34. Dubinsky L, Jarosz LM, Amara N, Krief P, Kravchenko VV, Krom BP, Meijler MM (2009) Synthesis and validation of a probe to identify quorum sensing receptors. Chem Commun 47:7378

    Article  Google Scholar 

  35. Blencowe A, Hayes W (2005) Development and application of diazirines in biological and synthetic macromolecular systems. Soft Matter 1:178

    Article  CAS  Google Scholar 

  36. Winson MK, Swift S, Fish L, Throup JP, Jorgensen F, Chhabra SR, Bycroft BW, Williams P, Stewart GS (1998) Construction and analysis of luxCDABE-based plasmid sensors for investigating N-acyl homoserine lactone-mediated quorum sensing. FEMS Microbiol Lett 163:185

    Article  CAS  Google Scholar 

  37. Rayo J, Amara N, Krief P, Meijler MM (2011) Live cell labeling of native intracellular bacterial receptors using aniline-catalyzed oxime ligation. J Am Chem Soc 133:7469

    Article  CAS  Google Scholar 

  38. Amara N, Mashiach R, Amar D, Krief P, Spieser SA, Bottomley MJ, Aharoni A, Meijler MM (2009) Covalent inhibition of bacterial quorum sensing. J Am Chem Soc 131:10610

    Article  CAS  Google Scholar 

  39. Garner AL, Yu J, Struss AK, Lowery CA, Zhu J, Kim SK, Park J, Mayorov AV, Kaufmann GF, Kravchenko VV, Janda KD (2011) Synthesis of 'clickable' acylhomoserine lactone quorum sensing probes: unanticipated effects on mammalian cell activation. Bioorg Med Chem Lett 21:2702

    Article  CAS  Google Scholar 

  40. Dirksen A, Hackeng TM, Dawson PE (2006) Nucleophilic catalysis of oxime ligation. Angew Chem Int Ed Engl 45:7581

    Article  CAS  Google Scholar 

  41. Ventre I, Ledgham F, Prima V, Lazdunski A, Foglino M, Sturgis JN (2003) Dimerization of the quorum sensing regulator RhlR: development of a method using EGFP fluorescence anisotropy. Mol Microbiol 48:187

    Article  CAS  Google Scholar 

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Correspondence to Edward W. Tate .

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© 2011 Springer-Verlag Berlin Heidelberg

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Heal, W.P., Tate, E.W. (2011). Application of Activity-Based Protein Profiling to the Study of Microbial Pathogenesis. In: Sieber, S. (eds) Activity-Based Protein Profiling. Topics in Current Chemistry, vol 324. Springer, Berlin, Heidelberg. https://doi.org/10.1007/128_2011_299

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