Modern Mass Spectrometry for Synthetic Biology and Structure-based Discovery of Natural Products

Overview

Journal Nat Prod Rep

Publisher Royal Society of Chemistry

Date 2016 Jul 5

PMID 27376415

Citations 21

Authors

Matthew T Henke

Neil L Kelleher

Affiliations

Soon will be listed here.

Abstract

Covering: up to 2016In this highlight, we describe the current landscape for dereplication and discovery of natural products based on the measurement of the intact mass by LC-MS. Often it is assumed that because better mass accuracy (provided by higher resolution mass spectrometers) is necessary for absolute chemical formula determination (≤1 part-per-million), that it is also necessary for dereplication of natural products. However, the average ability to dereplicate tapers off at ∼10 ppm, with modest improvement gained from better mass accuracy when querying focused databases of natural products. We also highlight some recent examples of how these platforms are applied to synthetic biology, and recent methods for dereplication and correlation of substructures using tandem MS data. We also offer this highlight to serve as a brief primer for those entering the field of mass spectrometry-based natural products discovery.

Citing Articles

Fighting Antimicrobial Resistance: Innovative Drugs in Antibacterial Research.

Sussmuth R, Sussmuth R, Kulike-Koczula M, Kulike-Koczula M, Gao P, Kosol S Angew Chem Int Ed Engl. 2024; 64(10):e202414325.

PMID: 39611429 PMC: 11878372. DOI: 10.1002/anie.202414325.

Photoprotection-related properties of a raw extract from EUFUS-Z928: A culturable rare actinomycete associated with the Caribbean octocoral .

Sanchez-Suarez J, Villamil L, Coy-Barrera E, Diaz L Sci Prog. 2024; 107(3):368504241272454.

PMID: 39119690 PMC: 11311175. DOI: 10.1177/00368504241272454.

Discovery of Streptomyces species CS-62, a novel producer of the Acinetobacter baumannii selective antibiotic factumycin.

Alwali A, Santos D, Aguilar C, Birch A, Rodriguez-Orduna L, Roberts C J Ind Microbiol Biotechnol. 2024; 51.

PMID: 38632045 PMC: 11066910. DOI: 10.1093/jimb/kuae014.

Discovering New Natural Products Using Metabolomics-Based Approaches.

de Medeiros L, de Araujo Junior M, Peres E, Carlos Ipuchima da Silva J, Bassicheto M, Di Gioia G Adv Exp Med Biol. 2023; 1439:185-224.

PMID: 37843810 DOI: 10.1007/978-3-031-41741-2_8.

: A computational tool to discover structural novelty in natural extracts libraries.

Quiros-Guerrero L, Nothias L, Gaudry A, Marcourt L, Allard P, Rutz A Front Mol Biosci. 2022; 9:1028334.

PMID: 36438653 PMC: 9692083. DOI: 10.3389/fmolb.2022.1028334.

References

Nielsen K, Mansson M, Rank C, Frisvad J, Larsen T . Dereplication of microbial natural products by LC-DAD-TOFMS. J Nat Prod. 2011; 74(11):2338-48. DOI: 10.1021/np200254t. View

Nielsen K, Larsen T . The importance of mass spectrometric dereplication in fungal secondary metabolite analysis. Front Microbiol. 2015; 6:71. PMC: 4330896. DOI: 10.3389/fmicb.2015.00071. View

Nguyen D, Wu C, Moree W, Lamsa A, Medema M, Zhao X . MS/MS networking guided analysis of molecule and gene cluster families. Proc Natl Acad Sci U S A. 2013; 110(28):E2611-20. PMC: 3710860. DOI: 10.1073/pnas.1303471110. View

El-Elimat T, Figueroa M, Ehrmann B, Cech N, Pearce C, Oberlies N . High-resolution MS, MS/MS, and UV database of fungal secondary metabolites as a dereplication protocol for bioactive natural products. J Nat Prod. 2013; 76(9):1709-16. PMC: 3856222. DOI: 10.1021/np4004307. View

Watve M, Tickoo R, Jog M, Bhole B . How many antibiotics are produced by the genus Streptomyces?. Arch Microbiol. 2001; 176(5):386-90. DOI: 10.1007/s002030100345. View

Heiling S, Khanal S, Barsch A, Zurek G, Baldwin I, Gaquerel E . Using the knowns to discover the unknowns: MS-based dereplication uncovers structural diversity in 17-hydroxygeranyllinalool diterpene glycoside production in the Solanaceae. Plant J. 2016; 85(4):561-77. DOI: 10.1111/tpj.13119. View

Mohimani H, Liu W, Kersten R, Moore B, Dorrestein P, Pevzner P . NRPquest: Coupling Mass Spectrometry and Genome Mining for Nonribosomal Peptide Discovery. J Nat Prod. 2014; 77(8):1902-9. PMC: 4143176. DOI: 10.1021/np500370c. View

Potterat O, Wagner K, Haag H . Liquid chromatography-electrospray time-of-flight mass spectrometry for on-line accurate mass determination and identification of cyclodepsipeptides in a crude extract of the fungus Metarrhizium anisopliae. J Chromatogr A. 2000; 872(1-2):85-90. DOI: 10.1016/s0021-9673(99)01268-6. View

Mao X, Xu W, Li D, Yin W, Chooi Y, Li Y . Epigenetic genome mining of an endophytic fungus leads to the pleiotropic biosynthesis of natural products. Angew Chem Int Ed Engl. 2015; 54(26):7592-6. PMC: 4487767. DOI: 10.1002/anie.201502452. View

10.

Gao P, Xu G . Mass-spectrometry-based microbial metabolomics: recent developments and applications. Anal Bioanal Chem. 2014; 407(3):669-80. DOI: 10.1007/s00216-014-8127-7. View

11.

Newman D, Cragg G . Natural Products as Sources of New Drugs from 1981 to 2014. J Nat Prod. 2016; 79(3):629-61. DOI: 10.1021/acs.jnatprod.5b01055. View

12.

Duhrkop K, Shen H, Meusel M, Rousu J, Bocker S . Searching molecular structure databases with tandem mass spectra using CSI:FingerID. Proc Natl Acad Sci U S A. 2015; 112(41):12580-5. PMC: 4611636. DOI: 10.1073/pnas.1509788112. View

13.

Vizcaino M, Crawford J . The colibactin warhead crosslinks DNA. Nat Chem. 2015; 7(5):411-7. PMC: 4499846. DOI: 10.1038/nchem.2221. View

14.

Baltz R . Marcel Faber Roundtable: is our antibiotic pipeline unproductive because of starvation, constipation or lack of inspiration?. J Ind Microbiol Biotechnol. 2006; 33(7):507-13. DOI: 10.1007/s10295-005-0077-9. View

15.

Asai T, Tsukada K, Ise S, Shirata N, Hashimoto M, Fujii I . Use of a biosynthetic intermediate to explore the chemical diversity of pseudo-natural fungal polyketides. Nat Chem. 2015; 7(9):737-43. DOI: 10.1038/nchem.2308. View

16.

Newman A, Vagstad A, Storm P, Townsend C . Systematic domain swaps of iterative, nonreducing polyketide synthases provide a mechanistic understanding and rationale for catalytic reprogramming. J Am Chem Soc. 2014; 136(20):7348-62. PMC: 4046768. DOI: 10.1021/ja5007299. View

17.

Doroghazi J, Albright J, Goering A, Ju K, Haines R, Tchalukov K . A roadmap for natural product discovery based on large-scale genomics and metabolomics. Nat Chem Biol. 2014; 10(11):963-8. PMC: 4201863. DOI: 10.1038/nchembio.1659. View

18.

Hagen A, Poust S, de Rond T, Fortman J, Katz L, Petzold C . Engineering a Polyketide Synthase for In Vitro Production of Adipic Acid. ACS Synth Biol. 2015; 5(1):21-7. DOI: 10.1021/acssynbio.5b00153. View

19.

Sica V, Raja H, El-Elimat T, Kertesz V, Van Berkel G, Pearce C . Dereplicating and Spatial Mapping of Secondary Metabolites from Fungal Cultures in Situ. J Nat Prod. 2015; 78(8):1926-36. PMC: 4570219. DOI: 10.1021/acs.jnatprod.5b00268. View

20.

Benton H, Wong D, Trauger S, Siuzdak G . XCMS2: processing tandem mass spectrometry data for metabolite identification and structural characterization. Anal Chem. 2008; 80(16):6382-9. PMC: 2728033. DOI: 10.1021/ac800795f. View