Practical 4′-Phosphopantetheine active site discovery from proteomic samples

Journal of Proteome Research

Volumn 10, Issue 1, 2011, Pages 320-329

  Meier, Jordan L ^a   Patel, Anand D ^a   Niessen, Sherry ^b   Meehan, Michael ^c   Kersten, Roland ^a   Yang, Jane Y ^a   Rothmann, Michael ^a   Cravatt, Benjamin F ^a   Dorrestein, Pieter C ^a,c   Burkart, Michael D ^a   Bafna, Vineet ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

^c UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

Carrier protein domain; InsPecT; LC MS MS; Natural products; Nonribosomal peptide synthetase; Polyketide synthase; Post translational modification; Support vector machine

Indexed keywords

NATURAL PRODUCT; NONRIBOSOMAL PEPTIDE SYNTHETASE; PANTETHEINE PHOSPHATE; PEPTIDE SYNTHASE; POLYKETIDE; POLYKETIDE SYNTHASE; PROTEOME; RECOMBINANT PROTEIN; UNCLASSIFIED DRUG; 4'-PHOSPHOPANTETHEINE; BACTERIAL PROTEIN; DRUG DERIVATIVE; NON RIBOSOMAL PEPTIDE SYNTHASE; NON-RIBOSOMAL PEPTIDE SYNTHASE; PANTETHEINE; PEPTIDE FRAGMENT;

BACILLUS SUBTILIS; BIOSYNTHESIS; CONFERENCE PAPER; ENZYME ANALYSIS; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; NONRIBOSOMAL PEPTIDE SYNTHESIS; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN PROCESSING; PROTEOMICS; SUPPORT VECTOR MACHINE; ALGORITHM; ARTICLE; ARTIFICIAL INTELLIGENCE; CHEMISTRY; ENZYME ACTIVE SITE; METABOLISM; PROTEIN TERTIARY STRUCTURE; RECEIVER OPERATING CHARACTERISTIC; REPRODUCIBILITY; TANDEM MASS SPECTROMETRY;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; BACILLUS SUBTILIS; BACTERIAL PROTEINS; CATALYTIC DOMAIN; CHROMATOGRAPHY, LIQUID; PANTETHEINE; PEPTIDE FRAGMENTS; PEPTIDE SYNTHASES; POLYKETIDE SYNTHASES; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEIN STRUCTURE, TERTIARY; PROTEOME; PROTEOMICS; REPRODUCIBILITY OF RESULTS; ROC CURVE; TANDEM MASS SPECTROMETRY;

EID: 79951522331     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr100953b     Document Type: Conference Paper

References (32)

1. Fischbach, M. A.; Walsh, C. T. Assembly-line enzymology for polyketide and nonribosomal Peptide antibiotics: logic, machinery, and mechanisms. Chem. Rev. 2006, 106 (8), 3468-96. (Pubitemid 44376945)
2. Mercer, A. C.; Burkart, M. D. The ubiquitous carrier protein-a window to metabolite biosynthesis. Nat. Prod. Rep. 2007, 24 (4), 750-73. (Pubitemid 47106915)
3. Walsh, C. T.; Fischbach, M. A. Natural products version 2.0: connecting genes to molecules. J. Am. Chem. Soc. , 132 (8), 2469-93.
4. Nguyen, T.; Ishida, K.; Jenke-Kodama, H.; Dittmann, E.; Gurgui, C.; Hochmuth, T.; Taudien, S.; Platzer, M.; Hertweck, C.; Piel, J. Exploiting the mosaic structure of trans-acyltransferase polyketide synthases for natural product discovery and pathway dissection. Nat. Biotechnol. 2008, 26 (2), 225-33. (Pubitemid 351225955)
5. Challis, G. L. Genome mining for novel natural product discovery. J. Med. Chem. 2008, 51 (9), 2618-28. (Pubitemid 351620782)
6. Meier, J. L.; Niessen, S.; Hoover, H. S.; Foley, T. L.; Cravatt, B. F.; Burkart, M. D. An orthogonal active site identification system (OASIS) for proteomic profiling of natural product biosynthesis. ACS Chem. Biol. 2009, 4 (11), 948-57.
7. Dorrestein, P. C.; Bumpus, S. B.; Calderone, C. T.; Garneau-Tsodikova, S.; Aron, Z. D.; Straight, P. D.; Kolter, R.; Walsh, C. T.; Kelleher, N. L. Facile detection of acyl and peptidyl intermediates on thiotemplate carrier domains via phosphopantetheinyl elimination reactions during tandem mass spectrometry. Biochemistry 2006, 45 (42), 12756-66. (Pubitemid 44630862)
8. Hoffert, J. D.; Knepper, M. A. Taking aim at shotgun phosphoproteomics. Anal. Biochem. 2008, 375 (1), 1-10.
9. Dorrestein, P. C.; Kelleher, N. L. Dissecting non-ribosomal and polyketide biosynthetic machineries using electrospray ionization Fourier-Transform mass spectrometry. Nat. Prod. Rep. 2006, 23 (6), 893-918. (Pubitemid 44808993)
10. Bumpus, S. B.; Evans, B. S.; Thomas, P. M.; Ntai, I.; Kelleher, N. L. A proteomics approach to discovering natural products and their biosynthetic pathways. Nat. Biotechnol. 2009, 27 (10), 951-6.
11. Meluzzi, D.; Zheng, W. H.; Hensler, M.; Nizet, V.; Dorrestein, P. C. Top-down mass spectrometry on low-resolution instruments: characterization of phosphopantetheinylated carrier domains in polyketide and non-ribosomal biosynthetic pathways. Bioorg. Med. Chem. Lett. 2008, 18 (10), 3107-11. (Pubitemid 351680379)
12. Chen, S.; Xue, Y.; Sherman, D. H.; Reynolds, K. A. Mechanisms of molecular recognition in the pikromycin polyketide synthase. Chem. Biol. 2000, 7 (12), 907-18. (Pubitemid 32050496)
13. Yin, J.; Straight, P. D.; Hrvatin, S.; Dorrestein, P. C.; Bumpus, S. B.; Jao, C.; Kelleher, N. L.; Kolter, R.; Walsh, C. T. Genome-wide highthroughput mining of natural-product biosynthetic gene clusters by phage display. Chem. Biol. 2007, 14 (3), 303-12. (Pubitemid 46428140)
14. Jessani, N.; Niessen, S.; Wei, B. Q.; Nicolau, M.; Humphrey, M.; Ji, Y.; Han, W.; Noh, D. Y.; Yates, J. R., 3rd; Jeffrey, S. S.; Cravatt, B. F. A streamlined platform for high-content functional proteomics of primary human specimens. Nat. Methods 2005, 2 (9), 691-7. (Pubitemid 41223096)
15. Tanner, S.; Shu, H.; Frank, A.; Wang, L. C.; Zandi, E.; Mumby, M.; Pevzner, P. A.; Bafna, V. InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal. Chem. 2005, 77 (14), 4626-39. (Pubitemid 41542287)
16. Payne, S. H.; Yau, M.; Smolka, M. B.; Tanner, S.; Zhou, H.; Bafna, V. Phosphorylation-specific MS-MS scoring for rapid and accurate phosphoproteome analysis. J. Proteome Res. 2008, 8 (7)), 3373-81.
17. Barbe, V.; Cruveiller, S.; Kunst, F.; Lenoble, P.; Meurice, G.; Sekowska, A.; Vallenet, D.; Wang, T.; Moszer, I.; Medigue, C.; Danchin, A. From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later. Microbiology 2009, 155 (Pt 6), 1758-75.
18. Vapnik, V. N. The Nature of Statistical Learning Theory; Springer: New York, 1995.
19. Joachims, T. Estimating the Generalization Performance of a SVM Efficiently; Morgan Kaufmann Publishers Inc.: San Francisco, 2000; pp 431-8.
20. Stein, T.; Vater, J.; Kruft, V.; Wittmann-Liebold, B.; Franke, P.; Panico, M.; Mc Dowell, R.; Morris, H. R. Detection of 4′- phosphopantetheine at the thioester binding site for L-valine of gramicidinS synthetase 2. FEBS Lett. 1994, 340 (1-2), 39-44.
21. Liu, Y.; Patricelli, M. P.; Cravatt, B. F. Activity-based protein profiling: the serine hydrolases. Proc. Natl. Acad. Sci. U.S.A. 1999, 96 (26), 14694-9. (Pubitemid 30019702)
22. Nakano, M. M.; Corbell, N.; Besson, J.; Zuber, P. Isolation and characterization of sfp: a gene that functions in the production of the lipopeptide biosurfactant, surfactin, in Bacillus subtilis. Mol. Gen. Genet. 1992, 232 (2), 313-21.
23. Meier, J. L.; Mercer, A. C.; Burkart, M. D. Fluorescent profiling of modular biosynthetic enzymes by complementary metabolic and activity based probes. J. Am. Chem. Soc. 2008, 130 (16), 5443-5. (Pubitemid 351612950)
24. Macek, B.; Mijakovic, I.; Olsen, J. V.; Gnad, F.; Kumar, C.; Jensen, P. R.; Mann, M. The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 2007, 6 (4), 697-707. (Pubitemid 46630102)
25. The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res. 2010, 38, (Database issue), D142-8.
26. Mujezinovic, N.; Schneider, G.; Wildpaner, M.; Mechtler, K.; Eisenhaber, F. Reducing the haystack to find the needle: improved protein identification after fast elimination of non-interpretable peptide MS/MS spectra and noise reduction. BMC Genomics , 11 (1), S13.
27. Geer, L. Y.; Markey, S. P.; Kowalak, J. A.; Wagner, L.; Xu, M.; Maynard, D. M.; Yang, X.; Shi, W.; Bryant, S. H. Open mass spectrometry search algorithm. J. Proteome Res. 2004, 3 (5), 958-64. (Pubitemid 39425651)
28. Swaney, D. L.; Wenger, C. D.; Thomson, J. A.; Coon, J. J. Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 2009, 106 (4), 995-1000.
29. Bandeira, N.; Olsen, J. V.; Mann, J. V.; Mann, M.; Pevzner, P. A. Multi-spectra peptide sequencing and its applications to multistage mass spectrometry. Bioinformatics 2008, 24 (13), i416-23..
30. Dancik, V.; Addona, T. A.; Clauser, K. R.; Vath, J. E.; Pevzner, P. A. De novo peptide sequencing via tandem mass spectrometry. J. Comput. Biol. 1999, 6 (3-4), 327-42.
31. Frank, A. M.; Savitski, M. M.; Nielsen, M. L.; Zubarev, R. A.; Pevzner, P. A. De novo peptide sequencing and identification with precision mass spectrometry. J. Proteome Res. 2007, 6 (1), 114-23. (Pubitemid 46173663)
32. Johnson, R. S.; Taylor, J. A. Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry. Mol. Biotechnol. 2002, 22 (3), 301-15. (Pubitemid 35252826)