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Garello M, Piombo E, Buonsenso F, Prencipe S, Valente S, Meloni GR, Marcet-Houben M, Gabaldón T, Spadaro D. Several secondary metabolite gene clusters in the genomes of ten Penicillium spp. raise the risk of multiple mycotoxin occurrence in chestnuts. Food Microbiol 2024; 122:104532. [PMID: 38839238 DOI: 10.1016/j.fm.2024.104532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 03/14/2024] [Accepted: 04/02/2024] [Indexed: 06/07/2024]
Abstract
Penicillium spp. produce a great variety of secondary metabolites, including several mycotoxins, on food substrates. Chestnuts represent a favorable substrate for Penicillium spp. development. In this study, the genomes of ten Penicillium species, virulent on chestnuts, were sequenced and annotated: P. bialowiezense. P. pancosmium, P. manginii, P. discolor, P. crustosum, P. palitans, P. viridicatum, P. glandicola, P. taurinense and P. terrarumae. Assembly size ranges from 27.5 to 36.8 Mb and the number of encoded genes ranges from 9,867 to 12,520. The total number of predicted biosynthetic gene clusters (BGCs) in the ten species is 551. The most represented families of BGCs are non ribosomal peptide synthase (191) and polyketide synthase (175), followed by terpene synthases (87). Genome-wide collections of gene phylogenies (phylomes) were reconstructed for each of the newly sequenced Penicillium species allowing for the prediction of orthologous relationships among our species, as well as other 20 annotated Penicillium species available in the public domain. We investigated in silico the presence of BGCs for 10 secondary metabolites, including 5 mycotoxins, whose production was validated in vivo through chemical analyses. Among the clusters present in this set of species we found andrastin A and its related cluster atlantinone A, mycophenolic acid, patulin, penitrem A and the cluster responsible for the synthesis of roquefortine C/glandicoline A/glandicoline B/meleagrin. We confirmed the presence of these clusters in several of the Penicillium species conforming our dataset and verified their capacity to synthesize them in a chestnut-based medium with chemical analysis. Interestingly, we identified mycotoxin clusters in some species for the first time, such as the andrastin A cluster in P. flavigenum and P. taurinense, and the roquefortine C cluster in P. nalgiovense and P. taurinense. Chestnuts proved to be an optimal substrate for species of Penicillium with different mycotoxigenic potential, opening the door to risks related to the occurrence of multiple mycotoxins in the same food matrix.
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Affiliation(s)
- Marco Garello
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy; AGROINNOVA - Interdepartmental Centre for the Innovation in the Agro-Environmental Sector, University of Torino, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Edoardo Piombo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Almas Allé 5, 75651, Uppsala, Sweden
| | - Fabio Buonsenso
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy; AGROINNOVA - Interdepartmental Centre for the Innovation in the Agro-Environmental Sector, University of Torino, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Simona Prencipe
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Silvia Valente
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy; AGROINNOVA - Interdepartmental Centre for the Innovation in the Agro-Environmental Sector, University of Torino, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Giovanna Roberta Meloni
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy; AGROINNOVA - Interdepartmental Centre for the Innovation in the Agro-Environmental Sector, University of Torino, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Marina Marcet-Houben
- Barcelona Supercomputing Centre (BSC-CNS), Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS), Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain; CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain.
| | - Davide Spadaro
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy; AGROINNOVA - Interdepartmental Centre for the Innovation in the Agro-Environmental Sector, University of Torino, Largo Braccini 2, 10095, Grugliasco, TO, Italy.
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Wang X, Jarmusch SA, Frisvad JC, Larsen TO. Current status of secondary metabolite pathways linked to their related biosynthetic gene clusters in Aspergillus section Nigri. Nat Prod Rep 2023; 40:237-274. [PMID: 35587705 DOI: 10.1039/d1np00074h] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Covering: up to the end of 2021Aspergilli are biosynthetically 'talented' micro-organisms and therefore the natural products community has continually been interested in the wealth of biosynthetic gene clusters (BGCs) encoding numerous secondary metabolites related to these fungi. With the rapid increase in sequenced fungal genomes combined with the continuous development of bioinformatics tools such as antiSMASH, linking new structures to unknown BGCs has become much easier when taking retro-biosynthetic considerations into account. On the other hand, in most cases it is not as straightforward to prove proposed biosynthetic pathways due to the lack of implemented genetic tools in a given fungal species. As a result, very few secondary metabolite biosynthetic pathways have been characterized even amongst some of the most well studied Aspergillus spp., section Nigri (black aspergilli). This review will cover all known biosynthetic compound families and their structural diversity known from black aspergilli. We have logically divided this into sub-sections describing major biosynthetic classes (polyketides, non-ribosomal peptides, terpenoids, meroterpenoids and hybrid biosynthesis). Importantly, we will focus the review on metabolites which have been firmly linked to their corresponding BGCs.
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Affiliation(s)
- Xinhui Wang
- DTU Bioengineering, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark.
| | - Scott A Jarmusch
- DTU Bioengineering, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark.
| | - Jens C Frisvad
- DTU Bioengineering, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark.
| | - Thomas O Larsen
- DTU Bioengineering, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark.
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Jarczynska ZD, Rendsvig JKH, Pagels N, Viana VR, Nødvig CS, Kirchner FH, Strucko T, Nielsen ML, Mortensen UH. DIVERSIFY: A Fungal Multispecies Gene Expression Platform. ACS Synth Biol 2021; 10:579-588. [PMID: 33651591 DOI: 10.1021/acssynbio.0c00587] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent sequencing of numerous fungal species revealed large repertoires of putative biotechnologically relevant genes and secondary metabolite gene clusters. However, often the commercial potential of these species is impeded by difficulties to predict host physiological and metabolic compatibility with a given product, and lack of adequate genetic tools. Consequently, most heterologous production is performed in standard hosts where genetic tools and experience are in place. However, these species may not be suitable for all products. To increase chances of successful heterologous production, we have created a flexible platform, DIVERSIFY, for multispecies heterologous gene expression. This reduces the workload to construction of a single gene expression cassette, used to transform all DIVERSIFY strains in order to identify the optimal cell factory host. As proof of principle of the DIVERSIFY concept, we present the first version of our platform, DIVERSIFY 1.0, which we have successfully used for the production of three proteins and a metabolite in four different Aspergilli species, and for the identification of the best producer for each of the products. Moreover, we show that DIVERSIFY 1.0 is compatible with marker-free gene targeting induced by the CRISPR nucleases Cas9 and MAD7.
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Affiliation(s)
- Zofia D Jarczynska
- Eukaryotic Molecular Cell Biology, Section for Synthetic Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kongens Lyngby, Denmark
| | - Jakob K H Rendsvig
- Eukaryotic Molecular Cell Biology, Section for Synthetic Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kongens Lyngby, Denmark
| | | | - Veronica R Viana
- Eukaryotic Molecular Cell Biology, Section for Synthetic Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kongens Lyngby, Denmark
| | | | - Ferdinand H Kirchner
- Eukaryotic Molecular Cell Biology, Section for Synthetic Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kongens Lyngby, Denmark
| | - Tomas Strucko
- Eukaryotic Molecular Cell Biology, Section for Synthetic Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kongens Lyngby, Denmark
| | | | - Uffe H Mortensen
- Eukaryotic Molecular Cell Biology, Section for Synthetic Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kongens Lyngby, Denmark
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Twists and Turns in the Salicylate Catabolism of Aspergillus terreus, Revealing New Roles of the 3-Hydroxyanthranilate Pathway. mSystems 2021; 6:6/1/e00230-20. [PMID: 33500329 PMCID: PMC7842363 DOI: 10.1128/msystems.00230-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Aspergilli are versatile cell factories used in industry for the production of organic acids, enzymes, and pharmaceutical drugs. To date, bio-based production of organic acids relies on food substrates. In fungi, salicylate catabolism was believed to proceed only through the catechol branch of the 3-oxoadipate pathway, as shown, e.g., in Aspergillus nidulans. However, the observation of a transient accumulation of gentisate upon the cultivation of Aspergillus terreus in salicylate medium questions this concept. To address this, we have run a comparative analysis of the transcriptome of these two species after growth in salicylate using acetate as a control condition. The results revealed the high complexity of the salicylate metabolism in A. terreus with the concomitant positive regulation of several pathways for the catabolism of aromatic compounds. This included the unexpected joint action of two pathways—3-hydroxyanthranilate and nicotinate—possibly crucial for the catabolism of aromatics in this fungus. Importantly, the 3-hydroxyanthranilate catabolic pathway in fungi is described here for the first time, whereas new genes participating in the nicotinate metabolism are also proposed. The transcriptome analysis showed also for the two species an intimate relationship between salicylate catabolism and secondary metabolism. This study emphasizes that the central pathways for the catabolism of aromatic hydrocarbons in fungi hold many mysteries yet to be discovered. IMPORTANCE Aspergilli are versatile cell factories used in industry for the production of organic acids, enzymes, and pharmaceutical drugs. To date, bio-based production of organic acids relies on food substrates. These processes are currently being challenged to switch to renewable nonfood raw materials—a reality that should inspire the use of lignin-derived aromatic monomers. In this context, aspergilli emerge at the forefront of future bio-based approaches due to their industrial relevance and recognized prolific catabolism of aromatic compounds. Notwithstanding considerable advances in the field, there are still important knowledge gaps in the central catabolism of aromatic hydrocarbons in fungi. Here, we disclose a novel central pathway, 3-hydroxyanthranilate, defying previously established ideas on the central metabolism of the aromatic amino acid tryptophan in Ascomycota. We also observe that the catabolism of the aromatic salicylate greatly activated the secondary metabolism, furthering the significance of using lignin-derived aromatic hydrocarbons as a distinctive biomass source.
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Rokas A, Mead ME, Steenwyk JL, Raja HA, Oberlies NH. Biosynthetic gene clusters and the evolution of fungal chemodiversity. Nat Prod Rep 2020; 37:868-878. [PMID: 31898704 PMCID: PMC7332410 DOI: 10.1039/c9np00045c] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering: up to 2019Fungi produce a remarkable diversity of secondary metabolites: small, bioactive molecules not required for growth but which are essential to their ecological interactions with other organisms. Genes that participate in the same secondary metabolic pathway typically reside next to each other in fungal genomes and form biosynthetic gene clusters (BGCs). By synthesizing state-of-the-art knowledge on the evolution of BGCs in fungi, we propose that fungal chemodiversity stems from three molecular evolutionary processes involving BGCs: functional divergence, horizontal transfer, and de novo assembly. We provide examples of how these processes have contributed to the generation of fungal chemodiversity, discuss their relative importance, and outline major, outstanding questions in the field.
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Affiliation(s)
- Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
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Acurin A, a novel hybrid compound, biosynthesized by individually translated PKS- and NRPS-encoding genes in Aspergillus aculeatus. Fungal Genet Biol 2020; 139:103378. [PMID: 32234543 DOI: 10.1016/j.fgb.2020.103378] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/10/2020] [Accepted: 03/12/2020] [Indexed: 11/21/2022]
Abstract
This work presents the identification and proposed biosynthetic pathway for a compound of mixed polyketide-nonribosomal peptide origin that we named acurin A. The compound was isolated from an extract of the filamentous fungus Aspergillus aculeatus, and its core structure resemble that of the mycotoxin fusarin C produced by several Fusarium species. Based on bioinformatics in combination with RT-qPCR experiments and gene-deletion analysis, we identified a biosynthetic gene cluster (BGC) in A. aculeatus responsible for the biosynthesis of acurin A. Moreover, we were able to show that a polyketide synthase (PKS) and a nonribosomal peptide synthetase (NRPS) enzyme separately encoded by this BGC are responsible for the synthesis of the PK-NRP compound, acurin A, core structure. In comparison, the production of fusarin C is reported to be facilitated by a linked PKS-NRPS hybrid enzyme. Phylogenetic analyses suggest the PKS and NRPS in A. aculeatus resulted from a recent fission of an ancestral hybrid enzyme followed by gene duplication. In addition to the PKS- and NRPS-encoding genes of acurin A, we show that six other genes are influencing the biosynthesis including a regulatory transcription factor. Altogether, we have demonstrated the involvement of eight genes in the biosynthesis of acurin A, including an in-cluster transcription factor. This study highlights the biosynthetic capacity of A. aculeatus and serves as an example of how the CRISPR/Cas9 system can be exploited for the construction of fungal strains that can be readily engineered.
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Hautbergue T, Jamin EL, Debrauwer L, Puel O, Oswald IP. From genomics to metabolomics, moving toward an integrated strategy for the discovery of fungal secondary metabolites. Nat Prod Rep 2019; 35:147-173. [PMID: 29384544 DOI: 10.1039/c7np00032d] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fungal secondary metabolites are defined by bioactive properties that ensure adaptation of the fungus to its environment. Although some of these natural products are promising sources of new lead compounds especially for the pharmaceutical industry, others pose risks to human and animal health. The identification of secondary metabolites is critical to assessing both the utility and risks of these compounds. Since fungi present biological specificities different from other microorganisms, this review covers the different strategies specifically used in fungal studies to perform this critical identification. Strategies focused on the direct detection of the secondary metabolites are firstly reported. Particularly, advances in high-throughput untargeted metabolomics have led to the generation of large datasets whose exploitation and interpretation generally require bioinformatics tools. Then, the genome-based methods used to study the entire fungal metabolic potential are reported. Transcriptomic and proteomic tools used in the discovery of fungal secondary metabolites are presented as links between genomic methods and metabolomic experiments. Finally, the influence of the culture environment on the synthesis of secondary metabolites by fungi is highlighted as a major factor to consider in research on fungal secondary metabolites. Through this review, we seek to emphasize that the discovery of natural products should integrate all of these valuable tools. Attention is also drawn to emerging technologies that will certainly revolutionize fungal research and to the use of computational tools that are necessary but whose results should be interpreted carefully.
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Affiliation(s)
- T Hautbergue
- Toxalim (Research Centre in Food Toxicology) Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, F-31027 Toulouse, France.
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8
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Theobald S, Vesth TC, Rendsvig JK, Nielsen KF, Riley R, de Abreu LM, Salamov A, Frisvad JC, Larsen TO, Andersen MR, Hoof JB. Uncovering secondary metabolite evolution and biosynthesis using gene cluster networks and genetic dereplication. Sci Rep 2018; 8:17957. [PMID: 30560908 PMCID: PMC6298953 DOI: 10.1038/s41598-018-36561-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/19/2018] [Indexed: 01/01/2023] Open
Abstract
The increased interest in secondary metabolites (SMs) has driven a number of genome sequencing projects to elucidate their biosynthetic pathways. As a result, studies revealed that the number of secondary metabolite gene clusters (SMGCs) greatly outnumbers detected compounds, challenging current methods to dereplicate and categorize this amount of gene clusters on a larger scale. Here, we present an automated workflow for the genetic dereplication and analysis of secondary metabolism genes in fungi. Focusing on the secondary metabolite rich genus Aspergillus, we categorize SMGCs across genomes into SMGC families using network analysis. Our method elucidates the diversity and dynamics of secondary metabolism in section Nigri, showing that SMGC diversity within the section has the same magnitude as within the genus. Using our genome analysis we were able to predict the gene cluster responsible for biosynthesis of malformin, a potentiator of anti-cancer drugs, in 18 strains. To proof the general validity of our predictions, we developed genetic engineering tools in Aspergillus brasiliensis and subsequently verified the genes for biosynthesis of malformin.
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Affiliation(s)
- Sebastian Theobald
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark.,The Novo Nordisk Foundation for Biosustainability, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Tammi C Vesth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Jakob Kræmmer Rendsvig
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Kristian Fog Nielsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark.,Chr. Hansen Holding A/S, DK-2970, Hoersholm, Denmark
| | - Robert Riley
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.,Amyris, Inc., Emeryville, CA, USA
| | | | - Asaf Salamov
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jens Christian Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Thomas Ostenfeld Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Mikael Rørdam Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark.
| | - Jakob Blæsbjerg Hoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark.
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Does Osmotic Stress Affect Natural Product Expression in Fungi? Mar Drugs 2017; 15:md15080254. [PMID: 28805714 PMCID: PMC5577608 DOI: 10.3390/md15080254] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/27/2017] [Accepted: 08/08/2017] [Indexed: 11/16/2022] Open
Abstract
The discovery of new natural products from fungi isolated from the marine environment has increased dramatically over the last few decades, leading to the identification of over 1000 new metabolites. However, most of the reported marine-derived species appear to be terrestrial in origin yet at the same time, facultatively halo- or osmotolerant. An unanswered question regarding the apparent chemical productivity of marine-derived fungi is whether the common practice of fermenting strains in seawater contributes to enhanced secondary metabolism? To answer this question, a terrestrial isolate of Aspergillus aculeatus was fermented in osmotic and saline stress conditions in parallel across multiple sites. The ex-type strain of A. aculeatus was obtained from three different culture collections. Site-to-site variations in metabolite expression were observed, suggesting that subculturing of the same strain and subtle variations in experimental protocols can have pronounced effects upon metabolite expression. Replicated experiments at individual sites indicated that secondary metabolite production was divergent between osmotic and saline treatments. Titers of some metabolites increased or decreased in response to increasing osmolite (salt or glycerol) concentrations. Furthermore, in some cases, the expression of some secondary metabolites in relation to osmotic and saline stress was attributed to specific sources of the ex-type strains.
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Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species. Nat Microbiol 2017; 2:17044. [DOI: 10.1038/nmicrobiol.2017.44] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 03/02/2017] [Indexed: 12/22/2022]
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Henke MT, Kelleher NL. Modern mass spectrometry for synthetic biology and structure-based discovery of natural products. Nat Prod Rep 2016; 33:942-50. [PMID: 27376415 PMCID: PMC4981503 DOI: 10.1039/c6np00024j] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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.
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Affiliation(s)
- Matthew T Henke
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
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12
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Yang Y, Zhou H, Du G, Feng K, Feng T, Fu X, Liu J, Zeng Y. A Monooxygenase from
Boreostereum vibrans
Catalyzes Oxidative Decarboxylation in a Divergent Vibralactone Biosynthesis Pathway. Angew Chem Int Ed Engl 2016; 55:5463-6. [PMID: 27007916 DOI: 10.1002/anie.201510928] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/09/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Yan‐Long Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Hui Zhou
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Gang Du
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Ke‐Na Feng
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Tao Feng
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
- School of Pharmaceutical Sciences South-Central University for Nationalities Wuhan 430074 China
| | - Xiao‐Li Fu
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
| | - Ji‐Kai Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
- School of Pharmaceutical Sciences South-Central University for Nationalities Wuhan 430074 China
| | - Ying Zeng
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
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13
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Yang Y, Zhou H, Du G, Feng K, Feng T, Fu X, Liu J, Zeng Y. A Monooxygenase from
Boreostereum vibrans
Catalyzes Oxidative Decarboxylation in a Divergent Vibralactone Biosynthesis Pathway. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201510928] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yan‐Long Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Hui Zhou
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Gang Du
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Ke‐Na Feng
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Tao Feng
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
- School of Pharmaceutical Sciences South-Central University for Nationalities Wuhan 430074 China
| | - Xiao‐Li Fu
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
| | - Ji‐Kai Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
- School of Pharmaceutical Sciences South-Central University for Nationalities Wuhan 430074 China
| | - Ying Zeng
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China
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14
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Hill RA, Sutherland A. Hot off the press. Nat Prod Rep 2015. [DOI: 10.1039/c5np90047f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as salviaprione from Salvia prionitis.
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