Abstract
The use of proteomics for direct detection of expressed pathways producing natural products has yielded many new compounds, even when used in a screening mode without a bacterial genome sequence available. Here we quantify the advantages of having draft DNA-sequence available for strain-specific proteomics using the latest in ultrahigh-resolution mass spectrometry for both proteins and the small molecules they generate. Using the draft sequence of Streptomyces lilacinus NRRL B-1968, we show a >tenfold increase in the number of peptide identifications vs. using publicly available databases. Detected in this strain were six expressed gene clusters with varying homology to those known. To date, we have identified three of these clusters as encoding for the production of griseobactin (known), rakicidin D (an orphan NRPS/PKS hybrid cluster), and a putative thr and DHB-containing siderophore produced by a new non-ribosomal peptide sythetase gene cluster. The remaining three clusters show lower homology to those known, and likely encode enzymes for production of novel compounds. Using an interpreted strain-specific DNA sequence enables deep proteomics for the detection of multiple pathways and their encoded natural products in a single cultured bacterium.
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References
Antibase: the natural compound identifier (2011) Wiley VCH, Weinheim
Bumpus SB, Evans BS, Thomas PM, Ntai I, Kelleher NL (2009) A proteomics approach to discovering natural products and their biosynthetic pathways. Nat Biotechnol 27(10):951–956
Caboche S, Pupin M, Leclere V, Fontaine A, Jacques P, Kucherov G (2008) NORINE: a database of nonribosomal peptides. Nucleic Acids Res 36:D326–D331
Carr G, Poulsen M, Klassen JL, Hou Y, Wyche TP, Bugni TS, Currie CR, Clardy J (2012) Microtermolides A and B from termite-associated Streptomyces sp. and structural revision of vinylamycin. Org Lett 14(11):2822–2825
Challis GL (2008) Genome mining for novel natural product discovery. J Med Chem 51(9):2618–2628
Chen Y, McClure RA, Zheng Y, Thomson RJ, Kelleher NL (2013) Proteomics guided discovery of flavopeptins: anti-proliferative aldehydes synthesized by a reductase domain-containing non-ribosomal peptide synthetase. J Am Chem Soc 135(28):10449–10456
Chen Y, Ntai I, Ju KS, Unger M, Zamdborg L, Robinson SJ, Doroghazi JR, Labeda DP, Metcalf WW, Kelleher NL (2012) A proteomic survey of nonribosomal peptide and polyketide biosynthesis in Actinobacteria. J Proteome Res 11(1):85–94
Chen Y, Unger M, Ntai I, McClure RA, Albright JC, Thomson RJ, Kelleher NL (2013) Gobichelin A and B: mixed-ligand siderophores discovered using proteomics. Med Chem Comm 4(1):233–238
Dictionary of natural products (2013) CRC Press, Boca Raton
Doroghazi JR, Ju KS, Brown DW, Labeda DP, Deng Z, Metcalf WW, Chen W, Price NP (2011) Genome sequences of three tunicamycin-producing Streptomyces strains, S. chartreusis NRRL 12338, S. chartreusis NRRL 3882, and S. lysosuperificus ATCC 31396. J Bacteriol 193(24):7021–7022
Dorrestein PC, Blackhall J, Straight PD, Fischbach MA, Garneau-Tsodikova S, Edwards DJ, McLaughlin S, Lin M, Gerwick WH, Kolter R, Walsh CT, Kelleher NL (2006) Activity screening of carrier domains within nonribosomal peptide synthetases using complex substrate mixtures and large molecule mass spectrometry. Biochem US 45(6):1537–1546
Evans BS, Ntai I, Chen YQ, Robinson SJ, Kelleher NL (2011) Proteomics-based discovery of koranimine, a cyclic imine natural product. J Am Chem Soc 133(19):7316–7319
Fischbach MA, Walsh CT (2006) Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: logic, machinery, and mechanisms. Chem Rev 106(8):3468–3496
Igarashi M, Shida T, Sasaki Y, Kinoshita N, Naganawa H, Hamada M, Takeuchi T (1999) Vinylamycin, a new depsipeptide antibiotic, from Streptomyces sp. Jpn J Antibiot 52(10):873–879
Igarishi Y, Shimasaki R, Miyanaga S, Oku N, Onaka H, Sakurai H, Saiki I, Kitani S, Nihara T, Wimonsiravude W, Panbangred W (2010) Rakicidin D: an inhibitor of tumor cell invasion from marine-derived Streptomyces sp. Nature 63:563–5654
Meier JL, Niessen S, Hoover HS, Foley TL, Cravatt BF, Burkart MD (2009) An orthogonal active site identification system (OASIS) for proteomic profiling of natural product biosynthesis. ACS Chem Biol 4(11):948–957
Meier JL, Patel AD, Niessen S, Meehan M, Kersten R, Yang JY, Rothmann M, Cravatt BF, Dorrestein PC, Burkart MD, Bafna V (2011) Practical 4’-phosphopantetheine active site discovery from proteomic samples. J Proteome Res 10(1):320–329
Meluzzi D, Zheng WH, Hensler M, Nizet V, Dorrestein PC (2008) Top-down mass spectrometry on low-resolution instruments: characterization of phosphopantetheinylated carrier domains in polyketide and non-ribosomal biosynthetic pathways. Bioorg Med Chem Lett 18(10):3107–3111
Newman DJ, Cragg GM (2007) Natural products as sources of new drugs over the last 25 years. J Nat Prod 70(3):461–477
Patzer SI, Braun V (2010) Gene cluster involved in the biosynthesis of griseobactin, a catechol-peptide siderophore of Streptomyces sp. ATCC 700974. J Bacteriol 192(2):426–435
Rottig M, Medema MH, Blin K, Weber T, Rausch C, Kohlbacher O (2011) NRPSpredictor2-a web server for predicting NRPS adenylation domain specificity. Nucleic Acids Res 39:W362–W367
Scherlach K, Hertweck C (2009) Triggering cryptic natural product biosynthesis in microorganisms. Org Biomol Chem 7(9):1753–1760
Udwary DW, Gontang EA, Jones AC, Jones CS, Schultz AW, Winter JM, Yang JY, Beauchemin N, Capson TL, Clark BR, Esquenazi E, Eustaquio AS, Freel K, Gerwick L, Gerwick WH, Gonzalez D, Liu WT, Malloy KL, Maloney KN, Nett M, Nunnery JK, Penn K, Prieto-Davo A, Simmons TL, Weitz S, Wilson MC, Tisa LS, Dorrestein PC, Moore BS (2011) Significant natural product biosynthetic potential of actinorhizal symbionts of the genus Frankia, as revealed by comparative genomic and proteomic analyses. Appl Environ Microb 77(11):3617–3625
van Wezel GP, McDowall KJ (2011) The regulation of the secondary metabolism of Streptomyces: new links and experimental advances. Nat Prod Rep 28(7):1311–1333
Walsh CT (2004) Polyketide and nonribosomal peptide antibiotics. Science 303:1805–1810
Walsh CT, Fischbach MA (2010) Natural products version 2.0: connecting genes to molecules. J Am Chem Soc 132(8):2469–2493
Yamazaki Y, Kunimoto S, Ikeda D (2007) Rakicidin A: a hypoxia-selective cytotoxin. Biol Pharm Bull 30(2):261–265
Acknowledgments
The Department of Chemistry at Northwestern University and the following grants from the National Institutes of Health supported this work: GM 067725 from NIGMS (NLK) and GM 077596 from NIGMS (WWM). We also acknowledge support from the Institute for Genomic Biology IGB Fellows Program at UIUC (JRD). The authors would also like to thank Claudia K. Jones for her scholarly work.
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J. C. Albright and A. W. Goering contributed equally to this work.
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Albright, J.C., Goering, A.W., Doroghazi, J.R. et al. Strain-specific proteogenomics accelerates the discovery of natural products via their biosynthetic pathways. J Ind Microbiol Biotechnol 41, 451–459 (2014). https://doi.org/10.1007/s10295-013-1373-4
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DOI: https://doi.org/10.1007/s10295-013-1373-4