Direct proteomic mapping of Streptomyces Luteogriseus strain 103 and cnn1 and insights into antibiotic biosynthesis

Journal of Proteome Research

Volumn 4, Issue 6, 2005, Pages 1999-2006

  Wang, Yu Xia ^a   Yuan, Ying Jin ^a  

^a TIANJIN UNIVERSITY   (China)

Author keywords

2D LC MS MS; Microlide; Polyketide pathway; Proteomics; Streptomyces luteogriseus

Indexed keywords

ANTIBIOTIC AGENT; BACTERIAL ENZYME; BACTERIAL PROTEIN; MAITUOLAIMYSIN; MEMBRANE PROTEIN; POLYKETIDE; POLYKETIDE SYNTHASE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GROWTH; BIOSYNTHESIS; CELLULAR DISTRIBUTION; CONTROLLED STUDY; FERMENTATION; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN LOCALIZATION; PROTEOMICS; STRAIN DIFFERENCE; STREPTOMYCES; STREPTOMYCES LUTEOGRISEUS;

ANTI-BACTERIAL AGENTS; BACTERIAL PROTEINS; CELL CULTURE TECHNIQUES; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; CHROMATOGRAPHY, LIQUID; COMPUTATIONAL BIOLOGY; FERMENTATION; HYDROGEN-ION CONCENTRATION; MACROLIDES; MASS SPECTROMETRY; MODELS, CHEMICAL; MOLECULAR WEIGHT; POLYKETIDE SYNTHASES; PROTEOME; PROTEOMICS; STREPTOMYCES; STREPTOMYCES COELICOLOR; TIME FACTORS; TRYPSIN;

BACTERIA (MICROORGANISMS); STREPTOMYCES; STREPTOMYCES COELICOLOR; STREPTOMYCES LUTEOGRISEUS;

EID: 29144463683     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr050169h     Document Type: Article

References (40)

1. Champness, W. C.; Chater, K. F. "Regulation and integration of antibiotic production and morphological differentiation in Streptomyces." In Regulation of Bacterial Differentiation; Piggot, P. J., Moran, C. P., Youngman, P., Eds; American Society for Microbiology, Washington DC, 1994, 61-93.
2. Yuan, Y. J.; Wang, Z. P.; Wang, L.; Li, X.; Fan, J. Y. A novel macrolide antibiotic production by microbial fermentation. Chinese Patent. 2003, 148863.
3. Chang, Z.; Sun, Y.; He, J.; Vining, L. C. p-Aminobenzoic acid and chloramphenicol biosynthesis in Streptomyces venezuelae: gene sets for a key enzyme, 4-amino-4-deoxy chorismate synthase. Microbiology 2001, 147, 2113-2126.
4. Yu, J. H.; Leonard, T. J. Sterigmatocystin biosynthesis in Aspergillus nidulans requires a novel type I polyketide synthase. J. Bacteriol. 1995, 177, 4792-4800.
5. Stachelhans, T.; Schneider, A.; Marahiel, M. A. A. Engineered biosynthesis of peptide antibiotics. Biochem. Pharm. 1996, 52, 177-186.
6. Gould, S. J. Biosynthesis of the Kanamycin. Chem. Rev. 1997, 97, 2499-2510.
7. Wilding, E. I.; Brown, J. R.; Bryant, A. P.; Chalker, A. F.; Holmes, D. J.; Ingraham, K. A.; Iordanescu, S.; So, C. Y.; Rosenberg, M.; Gwynn, M. N. Identification, Evolution, and Essentiality of the Mevalonate Pathway for Isopentenyl Diphosphate Biosynthesis in Gram-Positive Cocci. J. Bacteriol. 2000, 182, 4319-4327.
8. Washburn, M. P.; Wolters, D.; Yates, J. R., III. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 2001, 19, 242-247.
9. Zhu, W. H.; Reich, C. I.; Olsen, G. J.; Giometti, C. S.; Yates, J. R., III. Shotgun Proteomics of Methanococcus jannaschii and Insights into Methanogenesis. J. Proteome Res. 2004, 3, 538-548.
10. Wang, J. Q.; Xue, Y. F.; Feng, X. L.; Li, X. L.; Wang, H.; Li, W.; Zhao, C. F.; Cheng, X. J.; Ma, Y. H.; Zhou, P. J.; Yin, J. N.; Bhatnagar, A.; Wang, R.; Liu, S. Q. An analysis of the proteomic profile for Thermoanaerobacter tengcongensis under optimal culture conditions. Proteomics 2004, 4, 136-150.
11. Orsaria, L.; Paoletti, L.; Gramajo, H. C. Characterization of stationary- phase proteins in Stryptomyces coelicolor A3(2). FEMS Microbiol. Lett. 1998, 162, 275-281.
12. Li, X. M.; Novotna, J.; Weiser, V. J. Major proteins related to chlortetracyline biosynthesis in a Stryptomyce aureofaciens production strain studied by quantitative proteomics. Appl. Microbiol. Biotechnol. 2001, 57, 717-724.
13. Hesketh, A. R.; Chandra, G.; Shaw, A. D.; Rowland, J. J.; Kell, D. B.; Bibb, M. J.; Charter, K. F. Primary and secondary metabolism, and post-translational protein modifications as potrayed by proteomic analysis of Stryptomyces coelicolor. Mol. Microbiol. 2002, 46, 917-932.
14. Hesketh, A. R.; Chater, K. F. Evidence from proteomics that some of the enzymes of actinorhodin biosynthesis have more than one form and may occupy distinctive cellular locations. J. Ind. Microbiol. Biotechnol. 2003, 30, 523-529.
15. Novotna, J.; Vohradsky, J.; Berndt, P.; Gramajo, H.; Langen, H.; Li, X. M.; Minas, W.; Orsaria, L.; Roeder, D.; Thompson, C. J. Proteomic studies of diauxic lag in the differentiating prokaryote Stryptomyces coelicolor reveal a regulatory network of stress-induced proteins and central metabolic enzymes. Mol. Microbiol. 2003, 48, 1289-1303.
16. Sarka, B. G. Proteome analysis by two-dimensional gel electrophorasis and mass spectrometry: strengths and limitations. Trends Anal. Chem. 2003, 22, 273-281.
17. Wolters, D. A.; Washburn, M. P.; Yates, J. R., III. An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 2001, 73, 5683-5690.
18. Wu, C. C.; MacCoss, M. J.; Howell, K. E.; Yates, J. R., III. A method for the comprehensive proteomic analysis of membrane proteins. Nat. Biotechnol. 2003, 21, 532-538.
19. Jiang, X. S.; Zhou, H.; Zhang, L.; Sheng, Q. H.; Li, S. J.; Li, L.; Hao, P.; Li, Y. X.; Xia, Q. C.; Wu, J. R.; Zeng, R. A High-throughput Approach for Subcellular Proteome. Mol. Cell. Proteomics 2004, 1, 441-445.
20. Blonder, J.; Rodriguez-Galan, M. C.; Chan, K. C.; Lucas, D. A.; Yu, L. R.; Conrads, T. P.; Issaq, H. J.; Young, H. A.; Veenstra, T. D. Analysis of Murine Natural Killer Cell Microsomal Proteins Using Two-Dimensional Liquid Chromatography Coupled to Tandem Electrospray Ionization Mass Spectrometry. J. Proteome Res. 2004, 3, 862-870.
21. Eng, J. K.; McCormack, A. L.; Yates, J. R., III. An approach to correlate tandem mass-spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrum. 1994, 5, 976-989.
22. Peng, J.; Elias, J. E.; Thoreen, C. C.; Licklider, L. J.; Gygi, S. P. Evaluation of Multidimensional Chromatography Coupled with Tandem Mass Spectrometry (LC/LC-MS/MS) for Large-Scale Protein Analysis: The Yeast Proteome. J. Proteome Res. 2003, 2, 43-50.
23. Wilkins, M. R.; Gasteiger, E.; Bairoch, A.; Sanchez, J. C.; Williams, K. L.; Appel, R. D.; Hochstrasser, D. F. "Protein Identification and Analysis Tools in the ExPASy Server." In 2-D Proteome Analysis Protocols; Link, A. J., Ed.; Humana Press: New Jersey, 1998.
24. Krogh, A.; Larsson, B.; Heijne, G. V.; Sonnhammer, E. L. L. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol. 2001, 305, 567-580.
25. Nakai, K.; Horton, P. PSORT: A program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem. Sci. 1999, 24, 34-35.
26. Emanuelsson, O.; Heijne, G. V. Prediction of organellar targeting signals. Biochim. Biophys. Acta 2001, 1541, 114-119.
27. Ashburner, M.; Ball, C. A.; Blake, J. A.; Botstein, D.; Butler, H.; Cherry, J. M.; Davis, A. P.; Dolinski, K.; Dwight, S. S.; Eppig, J. T.; Harris, M. A.; Hill, D. P.; Issel-Tarver, L.; Kasarskis, A.; Lewis, S.; Matese, J. C.; Richardson, J. E.; Ringwald, M.; Rubin, G. M.; Sherlock, G. Gene Ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000, 25, 25-29.
28. Anzai, Y. J.; Saito, N.; Tanaka, M.; Kinoshita, K. J.; Koyama, Y.; Kato, F. Organization of the biosynthetic gene cluster for the polyketide macrolide mycinamicin in Micromonospora griseorubida. FEMS Microbiol. Lett. 2003, 218, 135-141.
29. Lombo, F.; Brana, A. F.; Salas, J. A.; Mendez, C. Genetic organization of the biosynthetic gene cluster for the antitumor angucycline oviedomycin in Streptomyces antibioticus ATCC 11891. Chembiochem. 2004, 5, 1181-1187.
30. LopezLara, I. M.; Geiger, O. The nodulation protein NodG shows the enzymatic activity of an 3-oxoacyl-acyl carrier protein reductase. Mol. Plant Microbe Interact. 2001, 14, 349-357.
31. Fisher, M.; Kroon, J. T.; Martindale, W.; Stuitje, A. R.; Slabas, A. R.; Rafferty, J. B. The X-ray structure of Brassica napus beta-keto acyl carrier protein reductase and its implications for substrate binding and catalysis. Structure Fold Des. 2000, 8, 339-347.
32. Durr, E.; Yu, J. Y.; Krasinska, K. M.; Carver, L. A.; Yates, J. R., III.; Testa, J. E.; Oh, P.; Schnitzer, J. E. Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture. Nat. Biotechnol. 2004, 22, 985-992.
33. Liu, H.; Sadygov, R. G.; Yates, J. R., III. A Model for Random Sampling and Estimation of Relative Protein Abundance in Shotgun Proteomics. Anal. Chem. 2004, 76, 4193-4201.
34. Van, W.; Lee, H.; Deutsch, E. W.; Lazaro, C. A.; Tang, W.; Chen, E.; Fausto, N.; Katze, M. G.; Aebersold, R. A dataset of human liver proteins identified by protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry. Mol. Cell Proteomics 2004, 3, 1039-1041.
35. 18O isotopic labeling. J. Proteome Res. 2004, 3, 604-612.
36. Steffensky, M.; Li, S. M.; Vogler, B. Novobiocin biosynthesis in Streptomyces spheroids. FEMS Microb Lett. 1998, 161, 69-74.
37. Marfori, E. C.; Bamba, T.; Kajiyama, S. Biosynthetic studies of the tetramicacid antibiotic trichosetin. Tetrahedron 2002, 58, 6655-6658.
38. Gerth, K.; Steinmetz, H.; Hofle, G. Studies on the biosynthesis of epothilones: the PKS and epothilone C/D monooxygenase. J. Antibiotics 2001, 54, 144-148.
39. Nonaka, K.; Kumasaka, C.; Okamoto, Y. Bioconversion of milbemycin-related compounds: biosynthetic pathway of milbemycins. J. Antibiotics 1999, 52, 109-116.
40. Brautaset, T.; Sekurova, O. N.; Sletta, H. Biosynthesis of the polyene antifungal antibiotic nystatin in Streptomyces noursei ATCC 11455: analysis of the gene cluster and deduction of the biosynthetic pathway. Chem. Bio. 2000, 7, 395-403.