Activity-based protein profiling of microbes

Current Opinion in Chemical Biology

Volumn 24, Issue , 2015, Pages 139-144

  Sadler, Natalie C ^a   Wright, Aaron T ^a  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; ANTIBIOTIC AGENT; CELL EXTRACT; FATTY ACID SYNTHASE; GLYCOSIDASE; PHOSPHOTRANSFERASE; REGULATOR PROTEIN; SERINE PROTEINASE; BACTERIAL PROTEIN; FUNGAL PROTEIN;

ACTIVITY BASED PROTEIN PROFILING; CYANOBACTERIUM; ENZYMOLOGY; HUMAN; MICROORGANISM; MOLECULAR BIOLOGY; MYCOBACTERIUM; NONHUMAN; PHOTOAUTOTROPH; PROTEIN INTERACTION; PROTEIN STRUCTURE, FUNCTION AND VARIABILITY; REVIEW; SIGNAL TRANSDUCTION; BACTERIUM; CHEMISTRY; FUNGUS; METABOLISM; PROCEDURES; PROTEOMICS;

CORYNEBACTERINEAE; CYANOBACTERIA;

BACTERIA; BACTERIAL PROTEINS; FUNGAL PROTEINS; FUNGI; PROTEOMICS;

EID: 84919363162     PISSN: 13675931     EISSN: 18790402     Source Type: Journal    
DOI: 10.1016/j.cbpa.2014.10.022     Document Type: Review

References (33)

1. Rostovtsev V.V., Green L.G., Fokin V.V., Sharpless K.B. A stepwise huisgen cycloaddition process: copper(I)-catalyzed regioselective "ligation" of azides and terminal alkynes. Angew Chem Int Ed Engl 2002, 41:2596-2599.
2. Speers A.E., Cravatt B.F. Profiling enzyme activities in vivo using click chemistry methods. Chem Biol 2004, 11:535-546.
3. Jeffery D.A., Bogyo M. Chemical proteomics and its application to drug discovery. Curr Opin Biotechnol 2003, 14:87-95.
4. Kozarich J.W. Activity-based proteomics: enzyme chemistry redux. Curr Opin Chem Biol 2003, 7:78-83.
5. Chan E.W., Chattopadhaya S., Panicker R.C., Huang X., Yao S.Q. Developing photoactive affinity probes for proteomic profiling: hydroxamate-based probes for metalloproteases. J Am Chem Soc 2004, 126:14435-14446.
6. Staub I., Sieber S.A. Beta-lactams as selective chemical probes for the in vivo labeling of bacterial enzymes involved in cell wall biosynthesis, antibiotic resistance, and virulence. J Am Chem Soc 2008, 130:13400-13409.
7. Bottcher T., Sieber S.A. Showdomycin as a versatile chemical tool for the detection of pathogenesis-associated enzymes in bacteria. J Am Chem Soc 2010, 132:6964-6972.
8. Eirich J., Orth R., Sieber S.A. Unraveling the protein targets of vancomycin in living S. aureus and E. faecalis cells. J Am Chem Soc 2011, 133:12144-12153.
9. Kocaoglu O., Calvo R.A., Sham L.T., Cozy L.M., Lanning B.R., Francis S., Winkler M.E., Kearns D.B., Carlson E.E. Selective penicillin-binding protein imaging probes reveal substructure in bacterial cell division. ACS Chem Biol 2012, 7:1746-1753.
10. Battenberg O.A., Yang Y., Verhelst S.H., Sieber S.A. Target profiling of 4-hydroxyderricin in S. aureus reveals seryl-tRNA synthetase binding and inhibition by covalent modification. Mol Biosyst 2013, 9:343-351.
11. Liu Y., Patricelli M.P., Cravatt B.F. Activity-based protein profiling: the serine hydrolases. Proc Natl Acad Sci USA 1999, 96:14694-14699.
12. Wiedner S.D., Burnum K.E., Pederson L.M., Anderson L.N., Fortuin S., Chauvigne-Hines L.M., Shukla A.K., Ansong C., Panisko E.A., Smith R.D., et al. Multiplexed activity-based protein profiling of the human pathogen Aspergillus fumigatus reveals large functional changes upon exposure to human serum. J Biol Chem 2012, 287:33447-33459.
13. Wiedner S.D., Ansong C., Webb-Robertson B.J., Pederson L.M., Fortuin S., Hofstad B.A., Shukla A.K., Panisko E.A., Smith R.D., Wright A.T. Disparate proteome responses of pathogenic and nonpathogenic aspergilli to human serum measured by activity-based protein profiling (ABPP). Mol Cell Proteomics 2013, 12:1791-1805.
14. Sherratt A.R., Blais D.R., Ghasriani H., Pezacki J.P., Goto N.K. Activity-based protein profiling of the Escherichia coli GlpG rhomboid protein delineates the catalytic core. Biochemistry 2012, 51:7794-7803.
15. Patricelli M.P., Szardenings A.K., Liyanage M., Nomanbhoy T.K., Wu M., Weissig H., Aban A., Chun D., Tanner S., Kozarich J.W. Functional interrogation of the kinome using nucleotide acyl phosphates. Biochemistry 2007, 46:350-358.
16. Ansong C., Ortega C., Payne S.H., Haft D.H., Chauvigne-Hines L.M., Lewis M.P., Ollodart A.R., Purvine S.O., Shukla A.K., Fortuin S., et al. Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis. Chem Biol 2013, 20:123-133.
17. Wolfe L.M., Veeraraghavan U., Idicula-Thomas S., Schurer S., Wennerberg K., Reynolds R., Besra G.S., Dobos K.M. A chemical proteomics approach to profiling the ATP-binding proteome of Mycobacterium tuberculosis. Mol Cell Proteomics 2013, 12:1644-1660.
18. Ortega C., Liao R., Anderson L.N., Rustad T., Ollodart A.R., Wright A.T., Sherman D.R., Grundner C. Mycobacterium tuberculosis Ser/Thr protein kinase B mediates an oxygen-dependent replication switch. PLoS Biol 2014, 12:e1001746.
19. Nishino M., Choy J.W., Gushwa N.N., Oses-Prieto J.A., Koupparis K., Burlingame A.L., Renslo A.R., McKerrow J.H., Taunton J. Hypothemycin, a fungal natural product, identifies therapeutic targets in Trypanosoma brucei. Elife 2013, 2:e00712.
20. Yestrepsky B.D., Kretz C.A., Xu Y., Holmes A., Sun H., Ginsburg D., Larsen S.D. Development of tag-free photoprobes for studies aimed at identifying the target of novel Group A Streptococcus antivirulence agents. Bioorg Med Chem Lett 2014, 24:1538-1544.
21. Clarke K.M., Mercer A.C., La Clair J.J., Burkart M.D. In vivo reporter labeling of proteins via metabolic delivery of coenzyme A analogues. J Am Chem Soc 2005, 127:11234-11235.
22. Meier J.L., Mercer A.C., Rivera H., Burkart M.D. Synthesis and evaluation of bioorthogonal pantetheine analogues for in vivo protein modification. J Am Chem Soc 2006, 128:12174-12184.
23. Mercer A.C., Meier J.L., Torpey J.W., Burkart M.D. In vivo modification of native carrier protein domains. Chembiochem 2009, 10:1091-1100.
24. Chauvigne-Hines L.M., Anderson L.N., Weaver H.M., Brown J.N., Koech P.K., Nicora C.D., Hofstad B.A., Smith R.D., Wilkins M.J., Callister S.J., et al. Suite of activity-based probes for cellulose-degrading enzymes. J Am Chem Soc 2012, 134:20521-20532.
25. Anderson L.N., Culley D.E., Hofstad B.A., Chauvigne-Hines L.M., Zink E.M., Purvine S.O., Smith R.D., Callister S.J., Magnuson J.M., Wright A.T. Activity-based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30. Mol Biosyst 2013, 9:2992-3000.
26. Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 1999, 17:994-999.
27. Shiio Y., Aebersold R. Quantitative proteome analysis using isotope-coded affinity tags and mass spectrometry. Nat Protoc 2006, 1:139-145.
28. Weerapana E., Wang C., Simon G.M., Richter F., Khare S., Dillon M.B., Bachovchin D.A., Mowen K., Baker D., Cravatt B.F. Quantitative reactivity profiling predicts functional cysteines in proteomes. Nature 2010, 468:790-795.
29. Deng X., Weerapana E., Ulanovskaya O., Sun F., Liang H., Ji Q., Ye Y., Fu Y., Zhou L., Li J., et al. Proteome-wide quantification and characterization of oxidation-sensitive cysteines in pathogenic bacteria. Cell Host Microbe 2013, 13:358-370.
30. Leichert L.I., Jakob U. Protein thiol modifications visualized in vivo. PLoS Biol 2004, 2:e333.
31. Leichert L.I., Gehrke F., Gudiseva H.V., Blackwell T., Ilbert M., Walker A.K., Strahler J.R., Andrews P.C., Jakob U. Quantifying changes in the thiol redox proteome upon oxidative stress in vivo. Proc Natl Acad Sci USA 2008, 105:8197-8202.
32. Sadler N.C., Melnicki M.R., Serres M.H., Merkley E.D., Chrisler W.B., Hill E.A., Romine M.F., Kim S., Zink E.M., Datta S., et al. Live cell chemical profiling of temporal redox dynamics in a photoautotrophic cyanobacterium. ACS Chem Biol 2014, 9:291-300.
33. Ansong C., Sadler N.C., Hill E.A., Lewis M.P., Zink E.M., Smith R.D., Beliaev A.S., Konopka A.E., Wright A.T. Characterization of protein redox dynamics induced during light-to-dark transitions and nutrient limitation in cyanobacteria. Front Microbiol 2014, 5:325.