1
|
Chen L, Wang X, Zou Y, Tang MC. Genome Mining of a Fungal Polyketide Synthase-Nonribosomal Peptide Synthetase Hybrid Megasynthetase Pathway to Synthesize a Phytotoxic N-Acyl Amino Acid. Org Lett 2024; 26:3597-3601. [PMID: 38661293 DOI: 10.1021/acs.orglett.4c01039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Guided by the retrobiosynthesis hypothesis, we characterized a fungal polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS) hybrid megasynthetase pathway to generate 2-trans-4-trans-2-methylsorbyl-d-leucine (1), a polyketide amino acid conjugate that inhibits Arabidopsis root growth. The biosynthesis of 1 includes a PKS-NRPS enzyme to assemble an N-acyl amino alcohol intermediate, which is further oxidized to an N-acyl amino acid (NAAA), demonstrating a new biosynthetic logic for synthesizing NAAAs and expanding the chemical space of products encoded by fungal PKS-NRPS clusters.
Collapse
Affiliation(s)
- Lin Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhang jiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 201203, China
| | - Xin Wang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Yi Zou
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Man-Cheng Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhang jiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 201203, China
| |
Collapse
|
2
|
Cordell GA. The contemporary nexus of medicines security and bioprospecting: a future perspective for prioritizing the patient. NATURAL PRODUCTS AND BIOPROSPECTING 2024; 14:11. [PMID: 38270809 PMCID: PMC10811317 DOI: 10.1007/s13659-024-00431-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 01/14/2024] [Indexed: 01/26/2024]
Abstract
Reacting to the challenges presented by the evolving nexus of environmental change, defossilization, and diversified natural product bioprospecting is vitally important for advancing global healthcare and placing patient benefit as the most important consideration. This overview emphasizes the importance of natural and synthetic medicines security and proposes areas for global research action to enhance the quality, safety, and effectiveness of sustainable natural medicines. Following a discussion of some contemporary factors influencing natural products, a rethinking of the paradigms in natural products research is presented in the interwoven contexts of the Fourth and Fifth Industrial Revolutions and based on the optimization of the valuable assets of Earth. Following COP28, bioprospecting is necessary to seek new classes of bioactive metabolites and enzymes for chemoenzymatic synthesis. Focus is placed on those performance and practice modifications which, in a sustainable manner, establish the patient, and the maintenance of their prophylactic and treatment needs, as the priority. Forty initiatives for natural products in healthcare are offered for the patient and the practitioner promoting global action to address issues of sustainability, environmental change, defossilization, quality control, product consistency, and neglected diseases to assure that quality natural medicinal agents will be accessible for future generations.
Collapse
Affiliation(s)
- Geoffrey A Cordell
- Natural Products Inc., 1320 Ashland Avenue, Evanston, IL, 60201, USA.
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA.
| |
Collapse
|
3
|
Huang N, Peng L, Yang J, Li J, Zhang S, Sun M. FAM111B Acts as an Oncogene in Bladder Cancer. Cancers (Basel) 2023; 15:5122. [PMID: 37958297 PMCID: PMC10648174 DOI: 10.3390/cancers15215122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/16/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
Bladder cancer (BLCA) is a prevalent malignancy of the urinary system, associated with a high recurrence rate and poor prognosis. FAM111B, which encodes a protein containing a trypsin-like cysteine/serine peptidase domain, has been implicated in the progression of various human cancers; however, its involvement in BLCA remains unclear. In this study, we investigated the expression of FAM111B gene in tumor tissues compared to para-tumor tissues using immunohistochemistry and observed a significantly higher FAM111B gene expression in tumor tissues. Furthermore, analysis of clinical characteristics indicated that the increased FAM111B gene expression correlated with lymphatic metastasis and reduced overall survival. To investigate its functional role, we employed FAM111B-knockdown BLCA cell models and performed cell proliferation, wound-healing, transwell, and flow cytometry assays. The results showed that decreased FAM111B gene expression inhibited proliferation and migration but induced apoptosis in BLCA cells. In vivo experiments further validated that FAM111B knockdown suppressed tumor growth. Overall, our findings suggest that FAM111B acts as an oncogene in BLCA, playing a critical role in tumorigenesis, progression, and metastasis of BLCA. In conclusion, we have demonstrated a strong correlation between the expression of FAM111B gene and the development, progression, and metastasis of bladder cancer (BLCA). Thus, FAM111B is an oncogene associated with BLCA and holds promise as a molecular target for future treatment of this cancer.
Collapse
Affiliation(s)
- Ning Huang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, China; (N.H.); (L.P.); (J.Y.); (J.L.)
| | - Lei Peng
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, China; (N.H.); (L.P.); (J.Y.); (J.L.)
| | - Jiaping Yang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, China; (N.H.); (L.P.); (J.Y.); (J.L.)
| | - Jinqian Li
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, China; (N.H.); (L.P.); (J.Y.); (J.L.)
| | - Sheng Zhang
- Medical Oncology, Shanghai Cancer Center, Fudan University, Shanghai 200032, China
| | - Mingjuan Sun
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, China; (N.H.); (L.P.); (J.Y.); (J.L.)
| |
Collapse
|
4
|
Caesar LK, Butun FA, Robey MT, Ayon NJ, Gupta R, Dainko D, Bok JW, Nickles G, Stankey RJ, Johnson D, Mead D, Cank KB, Earp CE, Raja HA, Oberlies NH, Keller NP, Kelleher NL. Correlative metabologenomics of 110 fungi reveals metabolite-gene cluster pairs. Nat Chem Biol 2023; 19:846-854. [PMID: 36879060 PMCID: PMC10313767 DOI: 10.1038/s41589-023-01276-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 01/31/2023] [Indexed: 03/08/2023]
Abstract
Natural products research increasingly applies -omics technologies to guide molecular discovery. While the combined analysis of genomic and metabolomic datasets has proved valuable for identifying natural products and their biosynthetic gene clusters (BGCs) in bacteria, this integrated approach lacks application to fungi. Because fungi are hyper-diverse and underexplored for new chemistry and bioactivities, we created a linked genomics-metabolomics dataset for 110 Ascomycetes, and optimized both gene cluster family (GCF) networking parameters and correlation-based scoring for pairing fungal natural products with their BGCs. Using a network of 3,007 GCFs (organized from 7,020 BGCs), we examined 25 known natural products originating from 16 known BGCs and observed statistically significant associations between 21 of these compounds and their validated BGCs. Furthermore, the scalable platform identified the BGC for the pestalamides, demystifying its biogenesis, and revealed more than 200 high-scoring natural product-GCF linkages to direct future discovery.
Collapse
Affiliation(s)
- Lindsay K Caesar
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Fatma A Butun
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Matthew T Robey
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Navid J Ayon
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Raveena Gupta
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - David Dainko
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Jin Woo Bok
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Grant Nickles
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | | | - Kristof B Cank
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Cody E Earp
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Huzefa A Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Nicholas H Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, IL, USA.
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA.
| |
Collapse
|
5
|
MacAlpine J, Robbins N, Cowen LE. Bacterial-fungal interactions and their impact on microbial pathogenesis. Mol Ecol 2023; 32:2565-2581. [PMID: 35231147 PMCID: PMC11032213 DOI: 10.1111/mec.16411] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/14/2022] [Accepted: 02/18/2022] [Indexed: 11/27/2022]
Abstract
Microbial communities of the human microbiota exhibit diverse effects on human health and disease. Microbial homeostasis is important for normal physiological functions and changes to the microbiota are associated with many human diseases including diabetes, cancer, and colitis. In addition, there are many microorganisms that are either commensal or acquired from environmental reservoirs that can cause diverse pathologies. Importantly, the balance between health and disease is intricately connected to how members of the microbiota interact and affect one another's growth and pathogenicity. However, the mechanisms that govern these interactions are only beginning to be understood. In this review, we outline bacterial-fungal interactions in the human body, including examining the mechanisms by which bacteria govern fungal growth and virulence, as well as how fungi regulate bacterial pathogenesis. We summarize advances in the understanding of chemical, physical, and protein-based interactions, and their role in exacerbating or impeding human disease. We focus on the three fungal species responsible for the majority of systemic fungal infections in humans: Candida albicans, Cryptococcus neoformans, and Aspergillus fumigatus. We conclude by summarizing recent studies that have mined microbes for novel antimicrobials and antivirulence factors, highlighting the potential of the human microbiota as a rich resource for small molecule discovery.
Collapse
Affiliation(s)
- Jessie MacAlpine
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
| | - Leah E. Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
| |
Collapse
|
6
|
张 梦, 程 兴, 徐 欣. [Latest Findings on Polyketides/Non-ribosomal Peptides That Are Secondary Metabolites of Streptococcus mutans]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2023; 54:685-691. [PMID: 37248606 PMCID: PMC10475436 DOI: 10.12182/20230560302] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Indexed: 05/31/2023]
Abstract
Dental caries is a chronic infectious disease that occurs in the hard tissue of teeth under the influence of multiple factors, among which bacteria being a key factor. Streptococcus mutans ( S. mutans) is considered a major pathogen that causes caries. Secondary metabolites, including bacteriocins and polyketides/non-ribosomal peptides, are a class of small-molecule compounds synthesized by S. mutans. To date, polyketides/non-ribosomal peptides identified in S. mutans include mutanobactin, mutanocyclin, and mutanofactin, which are synthesized by the mub, muc, and muf biosynthetic gene clusters, respectively. These polyketides/non-ribosomal peptides play important roles in bacterial inter-species competition, oxidative stress, and biofilm formation. In this review, we provided an overview of the synthesis, function and regulation of three polyketides/non-ribosomal peptides of S. mutans, including mutanobactin, mutanocyclin, and mutanofactin, aiming to provide new insights into the cariogenic mechanism of S. mutans and to promote the better management of dental caries.
Collapse
Affiliation(s)
- 梦碟 张
- 口腔疾病研究国家重点实验室,国家口腔疾病临床医学研究中心,四川大学华西口腔医院 牙体牙髓病科 (成都 610041)The State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Department of Cariology and Endodontics, Sichuan University, Chengdu 610041, China
| | - 兴群 程
- 口腔疾病研究国家重点实验室,国家口腔疾病临床医学研究中心,四川大学华西口腔医院 牙体牙髓病科 (成都 610041)The State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Department of Cariology and Endodontics, Sichuan University, Chengdu 610041, China
| | - 欣 徐
- 口腔疾病研究国家重点实验室,国家口腔疾病临床医学研究中心,四川大学华西口腔医院 牙体牙髓病科 (成都 610041)The State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Department of Cariology and Endodontics, Sichuan University, Chengdu 610041, China
| |
Collapse
|
7
|
Ren M, Jiang S, Wang Y, Pan X, Pan F, Wei X. Discovery and excavation of lichen bioactive natural products. Front Microbiol 2023; 14:1177123. [PMID: 37138611 PMCID: PMC10149937 DOI: 10.3389/fmicb.2023.1177123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/24/2023] [Indexed: 05/05/2023] Open
Abstract
Lichen natural products are a tremendous source of new bioactive chemical entities for drug discovery. The ability to survive in harsh conditions can be directly correlated with the production of some unique lichen metabolites. Despite the potential applications, these unique metabolites have been underutilized by pharmaceutical and agrochemical industries due to their slow growth, low biomass availability, and technical challenges involved in their artificial cultivation. At the same time, DNA sequence data have revealed that the number of encoded biosynthetic gene clusters in a lichen is much higher than in natural products, and the majority of them are silent or poorly expressed. To meet these challenges, the one strain many compounds (OSMAC) strategy, as a comprehensive and powerful tool, has been developed to stimulate the activation of silent or cryptic biosynthetic gene clusters and exploit interesting lichen compounds for industrial applications. Furthermore, the development of molecular network techniques, modern bioinformatics, and genetic tools is opening up a new opportunity for the mining, modification, and production of lichen metabolites, rather than merely using traditional separation and purification techniques to obtain small amounts of chemical compounds. Heterologous expressed lichen-derived biosynthetic gene clusters in a cultivatable host offer a promising means for a sustainable supply of specialized metabolites. In this review, we summarized the known lichen bioactive metabolites and highlighted the application of OSMAC, molecular network, and genome mining-based strategies in lichen-forming fungi for the discovery of new cryptic lichen compounds.
Collapse
Affiliation(s)
- Meirong Ren
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Shuhua Jiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yanyan Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xinhua Pan
- Jiangxi Xiankelai Biotechnology Co., Ltd., Jiujiang, China
| | - Feng Pan
- Jiangxi Xiankelai Biotechnology Co., Ltd., Jiujiang, China
| | - Xinli Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
8
|
Xu Z, Park TJ, Cao H. Advances in mining and expressing microbial biosynthetic gene clusters. Crit Rev Microbiol 2023; 49:18-37. [PMID: 35166616 DOI: 10.1080/1040841x.2022.2036099] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Natural products (NPs) especially the secondary metabolites originated from microbes exhibit great importance in biomedical, industrial and agricultural applications. However, mining biosynthetic gene clusters (BGCs) to produce novel NPs has been hindered owing that a large population of environmental microbes are unculturable. In the past decade, strategies to explore BGCs directly from (meta)genomes have been established along with the fast development of high-throughput sequencing technologies and the powerful bioinformatics data-processing tools, which greatly expedited the exploitations of novel BGCs from unculturable microbes including the extremophilic microbes. In this review, we firstly summarized the popular bioinformatics tools and databases available to mine novel BGCs from (meta)genomes based on either pure cultures or pristine environmental samples. Noticeably, approaches rooted from machine learning and deep learning with focuses on the prediction of ribosomally synthesized and post-translationally modified peptides (RiPPs) were dramatically increased in recent years. Moreover, synthetic biology techniques to express the novel BGCs in culturable native microbes or heterologous hosts were introduced. This working pipeline including the discovery and biosynthesis of novel NPs will greatly advance the exploitations of the abundant but unexplored microbial BGCs.
Collapse
Affiliation(s)
- Zeling Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China
| | - Tae-Jin Park
- HME Healthcare Co., Ltd, Suwon-si, Republic of Korea
| | - Huiluo Cao
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| |
Collapse
|
9
|
Chiang CY, Ohashi M, Tang Y. Deciphering chemical logic of fungal natural product biosynthesis through heterologous expression and genome mining. Nat Prod Rep 2023; 40:89-127. [PMID: 36125308 PMCID: PMC9906657 DOI: 10.1039/d2np00050d] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Covering: 2010 to 2022Heterologous expression of natural product biosynthetic gene clusters (BGCs) has become a widely used tool for genome mining of cryptic pathways, bottom-up investigation of biosynthetic enzymes, and engineered biosynthesis of new natural product variants. In the field of fungal natural products, heterologous expression of a complete pathway was first demonstrated in the biosynthesis of tenellin in Aspergillus oryzae in 2010. Since then, advances in genome sequencing, DNA synthesis, synthetic biology, etc. have led to mining, assignment, and characterization of many fungal BGCs using various heterologous hosts. In this review, we will highlight key examples in the last decade in integrating heterologous expression into genome mining and biosynthetic investigations. The review will cover the choice of heterologous hosts, prioritization of BGCs for structural novelty, and how shunt products from heterologous expression can reveal important insights into the chemical logic of biosynthesis. The review is not meant to be exhaustive but is rather a collection of examples from researchers in the field, including ours, that demonstrates the usefulness and pitfalls of heterologous biosynthesis in fungal natural product discovery.
Collapse
Affiliation(s)
- Chen-Yu Chiang
- Dept. of Chemical and Biomolecular Engineering, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA.
| | - Masao Ohashi
- Dept. of Chemical and Biomolecular Engineering, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA.
| | - Yi Tang
- Dept. of Chemical and Biomolecular Engineering, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA.
- Dept. of Chemistry and Biochemistry, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| |
Collapse
|
10
|
Woodcraft C, Chooi YH, Roux I. The expanding CRISPR toolbox for natural product discovery and engineering in filamentous fungi. Nat Prod Rep 2023; 40:158-173. [PMID: 36205232 DOI: 10.1039/d2np00055e] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Covering: up to May 2022Fungal genetics has transformed natural product research by enabling the elucidation of cryptic metabolites and biosynthetic steps. The enhanced capability to add, subtract, modulate, and rewrite genes via CRISPR/Cas technologies has opened up avenues for the manipulation of biosynthetic gene clusters across diverse filamentous fungi. This review discusses the innovative and diverse strategies for fungal natural product discovery and engineering made possible by CRISPR/Cas-based tools. We also provide a guide into multiple angles of CRISPR/Cas experiment design, and discuss current gaps in genetic tool development for filamentous fungi and the promising opportunities for natural product research.
Collapse
Affiliation(s)
- Clara Woodcraft
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| | - Indra Roux
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| |
Collapse
|
11
|
Singh G. Linking Lichen Metabolites to Genes: Emerging Concepts and Lessons from Molecular Biology and Metagenomics. J Fungi (Basel) 2023; 9:jof9020160. [PMID: 36836275 PMCID: PMC9964704 DOI: 10.3390/jof9020160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/19/2023] [Accepted: 01/21/2023] [Indexed: 01/26/2023] Open
Abstract
Lichen secondary metabolites have tremendous pharmaceutical and industrial potential. Although more than 1000 metabolites have been reported from lichens, less than 10 have been linked to the genes coding them. The current biosynthetic research focuses strongly on linking molecules to genes as this is fundamental to adapting the molecule for industrial application. Metagenomic-based gene discovery, which bypasses the challenges associated with culturing an organism, is a promising way forward to link secondary metabolites to genes in non-model, difficult-to-culture organisms. This approach is based on the amalgamation of the knowledge of the evolutionary relationships of the biosynthetic genes, the structure of the target molecule, and the biosynthetic machinery required for its synthesis. So far, metagenomic-based gene discovery is the predominant approach by which lichen metabolites have been linked to their genes. Although the structures of most of the lichen secondary metabolites are well-documented, a comprehensive review of the metabolites linked to their genes, strategies implemented to establish this link, and crucial takeaways from these studies is not available. In this review, I address the following knowledge gaps and, additionally, provide critical insights into the results of these studies, elaborating on the direct and serendipitous lessons that we have learned from them.
Collapse
|
12
|
Munusamy M, Tan K, Nge CE, Gakuubi MM, Crasta S, Kanagasundaram Y, Ng SB. Diversity and Biosynthetic Potential of Fungi Isolated from St. John's Island, Singapore. Int J Mol Sci 2023; 24:ijms24021033. [PMID: 36674548 PMCID: PMC9861175 DOI: 10.3390/ijms24021033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/01/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023] Open
Abstract
Adaptation to a wide variety of habitats allows fungi to develop unique abilities to produce diverse secondary metabolites with diverse bioactivities. In this study, 30 Ascomycetes fungi isolated from St. John's Island, Singapore were investigated for their general biosynthetic potential and their ability to produce antimicrobial secondary metabolites (SMs). All the 30 fungal isolates belong to the Phylum Ascomycota and are distributed into 6 orders and 18 genera with Order Hypocreales having the highest number of representative (37%). Screening for polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) genes using degenerate PCR led to the identification of 23 polyketide synthases (PKSs) and 5 nonribosomal peptide synthetases (NRPSs) grouped into nine distinct clades based on their reduction capabilities. Some of the identified PKSs genes share high similarities between species and known reference genes, suggesting the possibility of conserved biosynthesis of closely related compounds from different fungi. Fungal extracts were tested for their antimicrobial activity against S. aureus, Methicillin-resistant S. aureus (MRSA), and Candida albicans. Bioassay-guided fractionation of the active constituents from two promising isolates resulted in the isolation of seven compounds: Penilumamides A, D, and E from strain F4335 and xanthomegnin, viomellein, pretrichodermamide C and vioxanthin from strain F7180. Vioxanthin exhibited the best antibacterial activity with IC50 values of 3.0 μM and 1.6 μM against S. aureus and MRSA respectively. Viomellein revealed weak antiproliferative activity against A549 cells with an IC50 of 42 μM. The results from this study give valuable insights into the diversity and biosynthetic potential of fungi from this unique habitat and forms a background for an in-depth analysis of the biosynthetic capability of selected strains of interest with the aim of discovering novel fungal natural products.
Collapse
Affiliation(s)
- Madhaiyan Munusamy
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
| | - Kenneth Tan
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
| | - Choy Eng Nge
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
| | - Martin Muthee Gakuubi
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Sharon Crasta
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
| | - Yoganathan Kanagasundaram
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
- Correspondence:
| |
Collapse
|
13
|
Kalra R, Conlan XA, Goel M. Recent advances in research for potential utilization of unexplored lichen metabolites. Biotechnol Adv 2023; 62:108072. [PMID: 36464145 DOI: 10.1016/j.biotechadv.2022.108072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/28/2022] [Accepted: 11/26/2022] [Indexed: 12/03/2022]
Abstract
Several research studies have shown that lichens are productive organisms for the synthesis of a broad range of secondary metabolites. Lichens are a self-sustainable stable microbial ecosystem comprising an exhabitant fungal partner (mycobiont) and at least one or more photosynthetic partners (photobiont). The successful symbiosis is responsible for their persistence throughout time and allows all the partners (holobionts) to thrive in many extreme habitats, where without the synergistic relationship they would be rare or non-existent. The ability to survive in harsh conditions can be directly correlated with the production of some unique metabolites. Despite the potential applications, these unique metabolites have been underutilised by pharmaceutical and agrochemical industries due to their slow growth, low biomass availability and technical challenges involved in their artificial cultivation. However, recent development of biotechnological tools such as molecular phylogenetics, modern tissue culture techniques, metabolomics and molecular engineering are opening up a new opportunity to exploit these compounds within the lichen holobiome for industrial applications. This review also highlights the recent advances in culturing the symbionts and the computational and molecular genetics approaches of lichen gene regulation recognized for the enhanced production of target metabolites. The recent development of multi-omics novel biodiscovery strategies aided by synthetic biology in order to study the heterologous expressed lichen-derived biosynthetic gene clusters in a cultivatable host offers a promising means for a sustainable supply of specialized metabolites.
Collapse
Affiliation(s)
- Rishu Kalra
- Sustainable Agriculture Program, The Energy and Resources Institute, Gurugram, Haryana, India
| | - Xavier A Conlan
- Deakin University, School of Life and Environmental Sciences, Geelong, Victoria, Australia
| | - Mayurika Goel
- Sustainable Agriculture Program, The Energy and Resources Institute, Gurugram, Haryana, India.
| |
Collapse
|
14
|
Berger H, Bacher M, Labuda R, Eppel IM, Bayer F, Sulyok M, Gasparotto E, Zehetbauer F, Doppler M, Gratzl H, Strauss J. Polaramycin B, and not physical interaction, is the signal that rewires fungal metabolism in the Streptomyces-Aspergillus interaction. Environ Microbiol 2022; 24:4899-4914. [PMID: 35848075 PMCID: PMC9796313 DOI: 10.1111/1462-2920.16118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/26/2022] [Indexed: 01/01/2023]
Abstract
Co-culturing the bacterium Streptomyces rapamycinicus and the ascomycete Aspergillus nidulans has previously been shown to trigger the production of orsellinic acid (ORS) and its derivates in the fungal cells. Based on these studies it was assumed that direct physical contact is a prerequisite for the metabolic reaction that involves a fungal amino acid starvation response and activating chromatin modifications at the biosynthetic gene cluster (BGC). Here we show that not physical contact, but a guanidine containing macrolide, named polaramycin B, triggers the response. The substance is produced constitutively by the bacterium and above a certain concentration, provokes the production of ORS. In addition, several other secondary metabolites were induced by polaramycin B. Our genome-wide transcriptome analysis showed that polaramycin B treatment causes downregulation of fungal genes necessary for membrane stability, general metabolism and growth. A compensatory genetic response can be observed in the fungus that included upregulation of BGCs and genes necessary for ribosome biogenesis, translation and membrane stability. Our work discovered a novel chemical communication, in which the antifungal bacterial metabolite polaramycin B leads to the production of antibacterial defence chemicals and to the upregulation of genes necessary to compensate for the cellular damage caused by polaramycin B.
Collapse
Affiliation(s)
- Harald Berger
- Department of Applied Genetics and Cell Biology, Institute of Microbial GeneticsUniversity of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
| | - Markus Bacher
- Research Platform Bioactive Microbial Metabolites (BiMM)Tulln/DonauAustria,Department of Chemistry, Institute of Chemistry of Renewable ResourcesUniversity of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
| | - Roman Labuda
- Research Platform Bioactive Microbial Metabolites (BiMM)Tulln/DonauAustria,Department for Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, Milk Technology and Food ScienceUniversity of Veterinary Medicine, ViennaViennaAustria
| | - Isabel Maria Eppel
- Department of Applied Genetics and Cell Biology, Institute of Microbial GeneticsUniversity of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
| | - Florentina Bayer
- Department of Applied Genetics and Cell Biology, Institute of Microbial GeneticsUniversity of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
| | - Michael Sulyok
- Department of Agro‐BiotechnologyInstitute of Bioanalytics and Agro‐Metabolomics, University of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
| | - Erika Gasparotto
- Department of Applied Genetics and Cell Biology, Institute of Microbial GeneticsUniversity of Natural Resources and Life Sciences, ViennaTulln/DonauAustria,Research Platform Bioactive Microbial Metabolites (BiMM)Tulln/DonauAustria
| | - Franz Zehetbauer
- Department of Applied Genetics and Cell Biology, Institute of Microbial GeneticsUniversity of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
| | - Maria Doppler
- Department of Agro‐BiotechnologyInstitute of Bioanalytics and Agro‐Metabolomics, University of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
| | - Hannes Gratzl
- Research Platform Bioactive Microbial Metabolites (BiMM)Tulln/DonauAustria,Department of Agro‐BiotechnologyInstitute of Bioanalytics and Agro‐Metabolomics, University of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
| | - Joseph Strauss
- Department of Applied Genetics and Cell Biology, Institute of Microbial GeneticsUniversity of Natural Resources and Life Sciences, ViennaTulln/DonauAustria,Research Platform Bioactive Microbial Metabolites (BiMM)Tulln/DonauAustria
| |
Collapse
|
15
|
Chemometrics and genome mining reveal an unprecedented family of sugar acid-containing fungal nonribosomal cyclodepsipeptides. Proc Natl Acad Sci U S A 2022; 119:e2123379119. [PMID: 35914151 PMCID: PMC9371744 DOI: 10.1073/pnas.2123379119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Xylomyrocins, a unique group of nonribosomal peptide secondary metabolites, were discovered in Paramyrothecium and Colletotrichum spp. fungi by employing a combination of high-resolution tandem mass spectrometry (HRMS/MS)-based chemometrics, comparative genome mining, gene disruption, stable isotope feeding, and chemical complementation techniques. These polyol cyclodepsipeptides all feature an unprecedented d-xylonic acid moiety as part of their macrocyclic scaffold. This biosynthon is derived from d-xylose supplied by xylooligosaccharide catabolic enzymes encoded in the xylomyrocin biosynthetic gene cluster, revealing a novel link between carbohydrate catabolism and nonribosomal peptide biosynthesis. Xylomyrocins from different fungal isolates differ in the number and nature of their amino acid building blocks that are nevertheless incorporated by orthologous nonribosomal peptide synthetase (NRPS) enzymes. Another source of structural diversity is the variable choice of the nucleophile for intramolecular macrocyclic ester formation during xylomyrocin chain termination. This nucleophile is selected from the multiple available alcohol functionalities of the polyol moiety, revealing a surprising polyspecificity for the NRPS terminal condensation domain. Some xylomyrocin congeners also feature N-methylated amino acid residues in positions where the corresponding NRPS modules lack N-methyltransferase (M) domains, providing a rare example of promiscuous methylation in the context of an NRPS with an otherwise canonical, collinear biosynthetic program.
Collapse
|
16
|
Lee SR, Seyedsayamdost MR. Induction of Diverse Cryptic Fungal Metabolites by Steroids and Channel Blockers. Angew Chem Int Ed Engl 2022; 61:e202204519. [PMID: 35509119 PMCID: PMC9276648 DOI: 10.1002/anie.202204519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Indexed: 07/20/2023]
Abstract
Fungi offer a deep source of natural products but remain underutilized. Most biosynthetic gene clusters (BGCs) that can be detected are silent or "cryptic" in standard lab cultures and their products are thus not interrogated in routine screens. As genetic alterations are difficult and some strains can only be grown on agar, we have herein applied an agar-based high-throughput chemical genetic screen to identify inducers of fungal BGCs. Using R. solani and S. sclerotiorum as test cases, we report 13 cryptic metabolites in four compound groups, including sclerocyclane, a natural product with a novel scaffold. Steroids were the best elicitors and follow-up studies showed that plant-steroids trigger sclerocyclane synthesis, which shows antibiotic activity against B. plantarii, an ecological competitor of S. sclerotiorum. Our results open new paths to exploring the chemical ecology of fungal-plant interactions and provide a genetics-free approach for uncovering cryptic fungal metabolites.
Collapse
Affiliation(s)
- Seoung Rak Lee
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| |
Collapse
|
17
|
Dynamic description of temporal changes of gut microbiota in broilers. Poult Sci 2022; 101:102037. [PMID: 35901643 PMCID: PMC9334346 DOI: 10.1016/j.psj.2022.102037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/19/2022] [Accepted: 06/22/2022] [Indexed: 12/09/2022] Open
Abstract
The diversity of bacteria and fungi in the gut microbiota of commercial broilers that raised in cages from hatch to the end of the production cycle were examined by an analysis of 3,592 and 3,899 amplicon sequence variants (ASVs), respectively. More than 90% sequences in bacterial communities were related to Firmicutes and Proteobacteria. More than 90% sequences in fungal communities were related to Ascomycota, Basidiomycota, and Glomeromycota. A statistical analysis of the microbiota composition succession showed that age was one of the main factors affecting the intestinal microbial communities of broilers. The increasingly complex community succession of transient microbiota occurred along with an increase of age. This dynamic change was observed to be similar between bacteria and fungi. The gut microbiota had a special structure in the first 3 d after birth of broiler. The microbiota structure was quite stable in the period of rapid skeletal growth (d 14–21), and then changed significantly in the period of rapid gaining weight (d 35–42), thus indicating the composition of gut microbiota in broilers had unique structures at different developmental stages. We observed that several bacteria and fungi occupied key functions in the gut microbiota of broilers, suggesting that the gut homeostasis of broilers might be affected by losses of bacteria and fungi via altering interactions between microbiota. This study aimed to provide a data basis for manipulating the microbiota at different developmental stages, in order to improve production and the intestinal health of broilers.
Collapse
|
18
|
Lee SR, Seyedsayamdost MR. Induction of Diverse Cryptic Fungal Metabolites by Steroids and Channel Blockers. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Seoung Rak Lee
- Department of Chemistry Princeton University Princeton NJ 08544 USA
| | - Mohammad R. Seyedsayamdost
- Department of Chemistry Princeton University Princeton NJ 08544 USA
- Department of Molecular Biology Princeton University Princeton NJ 08544 USA
| |
Collapse
|
19
|
Shankar A, Sharma KK. Fungal secondary metabolites in food and pharmaceuticals in the era of multi-omics. Appl Microbiol Biotechnol 2022; 106:3465-3488. [PMID: 35546367 PMCID: PMC9095418 DOI: 10.1007/s00253-022-11945-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/12/2022] [Accepted: 04/24/2022] [Indexed: 01/16/2023]
Abstract
Fungi produce several bioactive metabolites, pigments, dyes, antioxidants, polysaccharides, and industrial enzymes. Fungal products are also the primary sources of functional food and nutrition, and their pharmacological products are used for healthy aging. Their molecular properties are validated through the use of recent high-throughput genomic, transcriptomic, and metabolomic tools and techniques. Together, these updated multi-omic tools have been used to study fungal metabolites structure and their mode of action on biological and cellular processes. Diverse groups of fungi produce different proteins and secondary metabolites, which possess tremendous biotechnological and pharmaceutical applications. Furthermore, its use and acceptability can be accelerated by adopting multi-omics, bioinformatics, and machine learning tools that generate a huge amount of molecular data. The integration of artificial intelligence and machine learning tools in the era of omics and big data has opened up a new outlook in both basic and applied researches in the area of nutraceuticals and functional food and nutrition. KEY POINTS: • Multi-omic tool helps in the identification of novel fungal metabolites • Intra-omic data from genomics to bioinformatics • Novel metabolites and application in human health.
Collapse
Affiliation(s)
- Akshay Shankar
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
| | - Krishna Kant Sharma
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, 124001, Haryana, India.
| |
Collapse
|
20
|
Watanabe K, Sato M, Osada H. Recent advances in the chemo-biological characterization of decalin natural products and unraveling of the workings of Diels-Alderases. Fungal Biol Biotechnol 2022; 9:9. [PMID: 35488322 PMCID: PMC9055775 DOI: 10.1186/s40694-022-00139-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/15/2022] [Indexed: 11/19/2022] Open
Abstract
The Diels–Alder (DA) reaction refers to a [4 + 2] cycloaddition reaction that falls under the category of pericyclic reactions. It is a reaction that allows regio- and stereo-selective construction of two carbon–carbon bonds simultaneously in a concerted manner to generate a six-membered ring structure through a six-electron cyclic transition state. The DA reaction is one of the most widely applied reactions in organic synthesis, yet its role in biological systems has been debated intensely over the last four decades. A survey of secondary metabolites produced by microorganisms suggests strongly that many of the compounds possess features that are likely formed through DA reactions, and most of them are considered to be catalyzed by enzymes that are commonly referred to as Diels–Alderases (DAases). In recent years, especially over the past 10 years or so, we have seen an accumulation of a substantial body of work that substantiates the argument that DAases indeed exist and play a critical role in the biosynthesis of complex metabolites. This review will cover the DAases involved in the biosynthesis of decalin moieties, which are found in many of the medicinally important natural products, especially those produced by fungi. In particular, we will focus on a subset of secondary metabolites referred to as pyrrolidine-2-one-bearing decalin compounds and discuss the decalin ring stereochemistry and the biological activities of those compounds. We will also look into the genes and enzymes that drive the biosynthetic construction of those complex natural products, and highlight the recent progress made on the structural and mechanistic understanding of DAases, especially regarding how those enzymes exert stereochemical control over the [4 + 2] cycloaddition reactions they catalyze.
Collapse
Affiliation(s)
- Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan.
| | - Michio Sato
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan
| | - Hiroyuki Osada
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan. .,Chemical Resource Development Research Unit, RIKEN Center for Sustainable Resource Science, Wako-shi, 351-0198, Japan.
| |
Collapse
|
21
|
Qian Z, Liu Q, Cai M. Investigating Fungal Biosynthetic Pathways Using Pichia pastoris as a Heterologous Host. Methods Mol Biol 2022; 2489:115-127. [PMID: 35524048 DOI: 10.1007/978-1-0716-2273-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Fungal natural products have extensive biological activities, and thus have been largely commercialized in the pharmaceutical, agricultural, and food industries. Recently, heterologous expression has become an irreplaceable technique to functionalize fungal biosynthetic gene clusters and synthesize fungal natural products in various chassis organisms. This chapter describes the general method of using Pichia pastoris as a chassis host to investigate fungal biosynthetic pathways.
Collapse
Affiliation(s)
- Zhilan Qian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, China
| | - Qi Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, China
| | - Menghao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, China.
| |
Collapse
|
22
|
Meng X, Fang Y, Ding M, Zhang Y, Jia K, Li Z, Collemare J, Liu W. Developing fungal heterologous expression platforms to explore and improve the production of natural products from fungal biodiversity. Biotechnol Adv 2021; 54:107866. [PMID: 34780934 DOI: 10.1016/j.biotechadv.2021.107866] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/04/2021] [Accepted: 11/05/2021] [Indexed: 12/14/2022]
Abstract
Natural products from fungi represent an important source of biologically active metabolites notably for therapeutic agent development. Genome sequencing revealed that the number of biosynthetic gene clusters (BGCs) in fungi is much larger than expected. Unfortunately, most of them are silent or barely expressed under laboratory culture conditions. Moreover, many fungi in nature are uncultivable or cannot be genetically manipulated, restricting the extraction and identification of bioactive metabolites from these species. Rapid exploration of the tremendous number of cryptic fungal BGCs necessitates the development of heterologous expression platforms, which will facilitate the efficient production of natural products in fungal cell factories. Host selection, BGC assembly methods, promoters used for heterologous gene expression, metabolic engineering strategies and compartmentalization of biosynthetic pathways are key aspects for consideration to develop such a microbial platform. In the present review, we summarize current progress on the above challenges to promote research effort in the relevant fields.
Collapse
Affiliation(s)
- Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Yu Fang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Mingyang Ding
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Yanyu Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Kaili Jia
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Zhongye Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Jérôme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China.
| |
Collapse
|
23
|
Abstract
The Pd-catalyzed carbon-carbon bond formation pioneered by Heck in 1969 has dominated medicinal chemistry development for the ensuing fifty years. As the demand for more complex three-dimensional active pharmaceuticals continues to increase, preparative enzyme-mediated assembly, by virtue of its exquisite selectivity and sustainable nature, is poised to provide a practical and affordable alternative for accessing such compounds. In this minireview, we summarize recent state-of-the-art developments in practical enzyme-mediated assembly of carbocycles. When appropriate, background information on the enzymatic transformation is provided and challenges and/or limitations are also highlighted.
Collapse
Affiliation(s)
- Weijin Wang
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Douglass F Taber
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Hans Renata
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| |
Collapse
|
24
|
Kamdem RST, Ogbole O, Wafo P, Philip FU, Ali Z, Ntie-Kang F, Khan IA, Spiteller P. Rational engineering of specialized metabolites in bacteria and fungi. PHYSICAL SCIENCES REVIEWS 2021. [DOI: 10.1515/psr-2018-0170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Abstract
Bacteria and fungi have a high potential to produce compounds that display large structural change and diversity, thus displaying an extensive range of biological activities. Secondary metabolism or specialized metabolism is a term for pathways and small molecule products of metabolism that are not mandatory for the subsistence of the organism but improve and control their phenotype. Their interesting biological activities have occasioned their application in the fields of agriculture, food, and pharmaceuticals. Metabolic engineering is a powerful approach to improve access to these treasured molecules or to rationally engineer new ones. A thorough overview of engineering methods in secondary metabolism is presented, both in heterologous and epigenetic modification. Engineering methods to modify the structure of some secondary metabolite classes in their host are also intensively assessed.
Collapse
Affiliation(s)
- Ramsay Soup Teoua Kamdem
- Institut für Organische und Analytische Chemie , Universität Bremen , Leobener Strasse 7 (NW2C) , Bremen 28359 , Germany
- Department of Organic Chemistry, Higher Teachers’ Training College , University of Yaounde I. , P. O. Box 47 , Yaoundé , Cameroon
| | - Omonike Ogbole
- Department of Pharmacognosy , University of Ibadan , Ibadan , Nigeria
| | - Pascal Wafo
- Department of Organic Chemistry, Higher Teachers’ Training College , University of Yaounde I. , P. O. Box 47 , Yaoundé , Cameroon
| | - F. Uzor Philip
- Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmaceutical Sciences , University of Nigeria , Nsukka , 410001 Nigeria
| | - Zulfiqar Ali
- National Center for Natural Products Research , School of Pharmacy , University of Mississippi , MS 38677 , USA
| | - Fidele Ntie-Kang
- Chemistry Department , University of Buea , P. O. Box 63 , Buea , Cameroon
- Department of Pharmaceutical Chemistry , Martin-Luther-Universitat Halle-Wittenberg , Wolfgang-Langenbeck Str. 4 , Halle (Saale) 06120 , Germany
- Department of Informatics and Chemistry , University of Chemistry and Technology Prague , Technická 5 166 28 , Prague 6 Dejvice , Czech Republic
| | - Ikhlas A. Khan
- National Center for Natural Products Research , School of Pharmacy , University of Mississippi , MS 38677 , USA
| | - Peter Spiteller
- Institut für Organische und Analytische Chemie , Universität Bremen , Leobener Strasse 7 (NW2C) , Bremen 28359 , Germany
| |
Collapse
|
25
|
An interpreted atlas of biosynthetic gene clusters from 1,000 fungal genomes. Proc Natl Acad Sci U S A 2021; 118:2020230118. [PMID: 33941694 DOI: 10.1073/pnas.2020230118] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Fungi are prolific producers of natural products, compounds which have had a large societal impact as pharmaceuticals, mycotoxins, and agrochemicals. Despite the availability of over 1,000 fungal genomes and several decades of compound discovery efforts from fungi, the biosynthetic gene clusters (BGCs) encoded by these genomes and the associated chemical space have yet to be analyzed systematically. Here, we provide detailed annotation and analyses of fungal biosynthetic and chemical space to enable genome mining and discovery of fungal natural products. Using 1,037 genomes from species across the fungal kingdom (e.g., Ascomycota, Basidiomycota, and non-Dikarya taxa), 36,399 predicted BGCs were organized into a network of 12,067 gene cluster families (GCFs). Anchoring these GCFs with reference BGCs enabled automated annotation of 2,026 BGCs with predicted metabolite scaffolds. We performed parallel analyses of the chemical repertoire of fungi, organizing 15,213 fungal compounds into 2,945 molecular families (MFs). The taxonomic landscape of fungal GCFs is largely species specific, though select families such as the equisetin GCF are present across vast phylogenetic distances with parallel diversifications in the GCF and MF. We compare these fungal datasets with a set of 5,453 bacterial genomes and their BGCs and 9,382 bacterial compounds, revealing dramatic differences between bacterial and fungal biosynthetic logic and chemical space. These genomics and cheminformatics analyses reveal the large extent to which fungal and bacterial sources represent distinct compound reservoirs. With a >10-fold increase in the number of interpreted strains and annotated BGCs, this work better regularizes the biosynthetic potential of fungi for rational compound discovery.
Collapse
|
26
|
Abstract
Anaerobic gut fungi are important members of the gut microbiome of herbivores, yet they exist in small numbers relative to bacteria. Here, we show that these early-branching fungi produce a wealth of secondary metabolites (natural products) that may act to regulate the gut microbiome. We use an integrated 'omics'-based approach to classify the biosynthetic genes predicted from fungal genomes, determine transcriptionally active genes, and verify the presence of their enzymatic products. Our analysis reveals that anaerobic gut fungi are an untapped reservoir of bioactive compounds that could be harnessed for biotechnology. Anaerobic fungi (class Neocallimastigomycetes) thrive as low-abundance members of the herbivore digestive tract. The genomes of anaerobic gut fungi are poorly characterized and have not been extensively mined for the biosynthetic enzymes of natural products such as antibiotics. Here, we investigate the potential of anaerobic gut fungi to synthesize natural products that could regulate membership within the gut microbiome. Complementary 'omics' approaches were combined to catalog the natural products of anaerobic gut fungi from four different representative species: Anaeromyces robustus (A. robustus), Caecomyces churrovis (C. churrovis), Neocallimastix californiae (N. californiae), and Piromyces finnis (P. finnis). In total, 146 genes were identified that encode biosynthetic enzymes for diverse types of natural products, including nonribosomal peptide synthetases and polyketide synthases. In addition, N. californiae and C. churrovis genomes encoded seven putative bacteriocins, a class of antimicrobial peptides typically produced by bacteria. During standard laboratory growth on plant biomass or soluble substrates, 26% of total core biosynthetic genes in all four strains were transcribed. Across all four fungal strains, 30% of total biosynthetic gene products were detected via proteomics when grown on cellobiose. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) characterization of fungal supernatants detected 72 likely natural products from A. robustus alone. A compound produced by all four strains of anaerobic fungi was putatively identified as the polyketide-related styrylpyrone baumin. Molecular networking quantified similarities between tandem mass spectrometry (MS/MS) spectra among these fungi, enabling three groups of natural products to be identified that are unique to anaerobic fungi. Overall, these results support the finding that anaerobic gut fungi synthesize natural products, which could be harnessed as a source of antimicrobials, therapeutics, and other bioactive compounds.
Collapse
|
27
|
Aghdam SA, Brown AMV. Deep learning approaches for natural product discovery from plant endophytic microbiomes. ENVIRONMENTAL MICROBIOME 2021; 16:6. [PMID: 33758794 PMCID: PMC7972023 DOI: 10.1186/s40793-021-00375-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/21/2021] [Indexed: 05/10/2023]
Abstract
Plant microbiomes are not only diverse, but also appear to host a vast pool of secondary metabolites holding great promise for bioactive natural products and drug discovery. Yet, most microbes within plants appear to be uncultivable, and for those that can be cultivated, their metabolic potential lies largely hidden through regulatory silencing of biosynthetic genes. The recent explosion of powerful interdisciplinary approaches, including multi-omics methods to address multi-trophic interactions and artificial intelligence-based computational approaches to infer distribution of function, together present a paradigm shift in high-throughput approaches to natural product discovery from plant-associated microbes. Arguably, the key to characterizing and harnessing this biochemical capacity depends on a novel, systematic approach to characterize the triggers that turn on secondary metabolite biosynthesis through molecular or genetic signals from the host plant, members of the rich 'in planta' community, or from the environment. This review explores breakthrough approaches for natural product discovery from plant microbiomes, emphasizing the promise of deep learning as a tool for endophyte bioprospecting, endophyte biochemical novelty prediction, and endophyte regulatory control. It concludes with a proposed pipeline to harness global databases (genomic, metabolomic, regulomic, and chemical) to uncover and unsilence desirable natural products. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1186/s40793-021-00375-0.
Collapse
Affiliation(s)
- Shiva Abdollahi Aghdam
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX 79409 USA
| | - Amanda May Vivian Brown
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX 79409 USA
| |
Collapse
|
28
|
Sulheim S, Fossheim FA, Wentzel A, Almaas E. Automatic reconstruction of metabolic pathways from identified biosynthetic gene clusters. BMC Bioinformatics 2021; 22:81. [PMID: 33622234 PMCID: PMC7901079 DOI: 10.1186/s12859-021-03985-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/18/2021] [Indexed: 12/17/2022] Open
Abstract
Background A wide range of bioactive compounds is produced by enzymes and enzymatic complexes encoded in biosynthetic gene clusters (BGCs). These BGCs can be identified and functionally annotated based on their DNA sequence. Candidates for further research and development may be prioritized based on properties such as their functional annotation, (dis)similarity to known BGCs, and bioactivity assays. Production of the target compound in the native strain is often not achievable, rendering heterologous expression in an optimized host strain as a promising alternative. Genome-scale metabolic models are frequently used to guide strain development, but large-scale incorporation and testing of heterologous production of complex natural products in this framework is hampered by the amount of manual work required to translate annotated BGCs to metabolic pathways. To this end, we have developed a pipeline for an automated reconstruction of BGC associated metabolic pathways responsible for the synthesis of non-ribosomal peptides and polyketides, two of the dominant classes of bioactive compounds. Results The developed pipeline correctly predicts 72.8% of the metabolic reactions in a detailed evaluation of 8 different BGCs comprising 228 functional domains. By introducing the reconstructed pathways into a genome-scale metabolic model we demonstrate that this level of accuracy is sufficient to make reliable in silico predictions with respect to production rate and gene knockout targets. Furthermore, we apply the pipeline to a large BGC database and reconstruct 943 metabolic pathways. We identify 17 enzymatic reactions using high-throughput assessment of potential knockout targets for increasing the production of any of the associated compounds. However, the targets only provide a relative increase of up to 6% compared to wild-type production rates. Conclusion With this pipeline we pave the way for an extended use of genome-scale metabolic models in strain design of heterologous expression hosts. In this context, we identified generic knockout targets for the increased production of heterologous compounds. However, as the predicted increase is minor for any of the single-reaction knockout targets, these results indicate that more sophisticated strain-engineering strategies are necessary for the development of efficient BGC expression hosts.
Collapse
Affiliation(s)
- Snorre Sulheim
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Sem Sælands vei 8, 7034, Trondheim, Norway. .,Department of Biotechnology and Nanomedicine, SINTEF Industry, Richard Birkelands vei 3, 7034, Trondheim, Norway.
| | - Fredrik A Fossheim
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Sem Sælands vei 8, 7034, Trondheim, Norway
| | - Alexander Wentzel
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Richard Birkelands vei 3, 7034, Trondheim, Norway
| | - Eivind Almaas
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Sem Sælands vei 8, 7034, Trondheim, Norway.,K.G. Jebsen Center for Genetic Epidemiology, NTNU - Norwegian University of Science and Technology, Håkon Jarls gate 11, 7030, Trondheim, Norway
| |
Collapse
|
29
|
Fuller AA, Dounay AB, Schirch D, Rivera DG, Hansford KA, Elliott AG, Zuegg J, Cooper MA, Blaskovich MAT, Hitchens JR, Burris-Hiday S, Tenorio K, Mendez Y, Samaritoni JG, O’Donnell MJ, Scott WL. Multi-Institution Research and Education Collaboration Identifies New Antimicrobial Compounds. ACS Chem Biol 2020; 15:3187-3196. [PMID: 33242957 PMCID: PMC7928911 DOI: 10.1021/acschembio.0c00732] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
New
antibiotics are urgently needed to address increasing rates
of multidrug resistant infections. Seventy-six diversely functionalized
compounds, comprising five structural scaffolds, were synthesized
and tested for their ability to inhibit microbial growth. Twenty-six
compounds showed activity in the primary phenotypic screen at the
Community for Open Antimicrobial Drug Discovery (CO-ADD). Follow-up
testing of active molecules confirmed that two unnatural dipeptides
inhibit the growth of Cryptococcus neoformans with
a minimum inhibitory concentration (MIC) ≤ 8 μg/mL. Syntheses
were carried out by undergraduate students at five schools implementing
Distributed Drug Discovery (D3) programs. This report showcases that
a collaborative research and educational process is a powerful approach
to discover new molecules inhibiting microbial growth. Educational
gains for students engaged in this project are highlighted in parallel
to the research advances. Aspects of D3 that contribute to its success,
including an emphasis on reproducibility of procedures, are discussed
to underscore the power of this approach to solve important research
problems and to inform other coupled chemical biology research and
teaching endeavors.
Collapse
Affiliation(s)
- Amelia A. Fuller
- Santa Clara University, Department of Chemistry & Biochemistry, Santa Clara, California 95053, United States
| | - Amy B. Dounay
- Department of Chemistry and Biochemistry, Colorado College, 14 E. Cache La Poudre Street, Colorado Springs, Colorado 80903, United States
| | - Douglas Schirch
- Department of Chemistry, Goshen College, 1700 South Main Street, Goshen, Indiana 46526, United States
| | - Daniel G. Rivera
- Center for Natural Products Research, Faculty of Chemistry, University of Havana, Zapata y G, 10400, La Habana, Cuba
| | - Karl A. Hansford
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Alysha G. Elliott
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Johannes Zuegg
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Matthew A Cooper
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Mark A. T. Blaskovich
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Jacob R. Hitchens
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
| | - Sarah Burris-Hiday
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
| | - Kristiana Tenorio
- Santa Clara University, Department of Chemistry & Biochemistry, Santa Clara, California 95053, United States
| | - Yanira Mendez
- Center for Natural Products Research, Faculty of Chemistry, University of Havana, Zapata y G, 10400, La Habana, Cuba
| | - J. Geno Samaritoni
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
| | - Martin J. O’Donnell
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
| | - William L. Scott
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
| |
Collapse
|
30
|
Newman DJ, Cragg GM. Plant Endophytes and Epiphytes: Burgeoning Sources of Known and "Unknown" Cytotoxic and Antibiotic Agents? PLANTA MEDICA 2020; 86:891-905. [PMID: 32023633 DOI: 10.1055/a-1095-1111] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
In the last 20 or so years, the influence of endophytes and, quite recently, epiphytes of plants upon the compounds found in those plants, which were usually assumed to be phytochemicals produced by the plant for a variety of reasons, often as a defense against predators, is becoming more evident, in particular in the case of antitumor agents originally isolated from plant sources, though antibiotic agents might also be found, particularly from epiphytes. In this review, we started with the first report in 1993 of a taxol-producing endophyte and then expanded the compounds discussed to include camptothecin, the vinca alkaloids, podophyllotoxin, and homoharringtonine from endophytic microbes and then the realization that maytansine is not a plant secondary metabolite at all, and that even such a well-studied plant such as Arabidopsis thaliana has a vast repertoire of potential bioactive agents in its leaf epiphytic bacteria. We have taken data from a variety of sources, including a reasonable history of these discoveries that were not given in recent papers by us, nor in other papers covering this topic. The sources included the Scopus database, but we also performed other searches using bibliographic tools, thus, the majority of the papers referenced are the originals, though we note some very recent papers that have built on previous results. We concluded with a discussion of the more modern techniques that can be utilized to "persuade" endophytes and epiphytes to switch on silent biosynthetic pathways and how current analytical techniques may aid in evaluating such programs. We also comment at times on some findings, particularly in the case of homoharringtonine, where there are repetitious data reports differing by a few years claiming the same endophyte as the producer.
Collapse
Affiliation(s)
- David J Newman
- NIH Special Volunteer, NCI Natural Products Branch, Wayne, PA, USA
| | - Gordon M Cragg
- NIH Special Volunteer, NCI Natural Products Branch, Gaithersburg, MD, USA
| |
Collapse
|
31
|
Heterologous Expression of the Unusual Terreazepine Biosynthetic Gene Cluster Reveals a Promising Approach for Identifying New Chemical Scaffolds. mBio 2020; 11:mBio.01691-20. [PMID: 32843555 PMCID: PMC7448278 DOI: 10.1128/mbio.01691-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Advances in genome sequencing have revitalized natural product discovery efforts, revealing the untapped biosynthetic potential of fungi. While the volume of genomic data continues to expand, discovery efforts are slowed due to the time-consuming nature of experiments required to characterize new molecules. To direct efforts toward uncharacterized biosynthetic gene clusters most likely to encode novel chemical scaffolds, we took advantage of comparative metabolomics and heterologous gene expression using fungal artificial chromosomes (FACs). By linking mass spectral profiles with structural clues provided by FAC-encoded gene clusters, we targeted a compound originating from an unusual gene cluster containing an indoleamine 2,3-dioxygenase (IDO). With this approach, we isolate and characterize R and S forms of the new molecule terreazepine, which contains a novel chemical scaffold resulting from cyclization of the IDO-supplied kynurenine. The discovery of terreazepine illustrates that FAC-based approaches targeting unusual biosynthetic machinery provide a promising avenue forward for targeted discovery of novel scaffolds and their biosynthetic enzymes, and it also represents another example of a biosynthetic gene cluster "repurposing" a primary metabolic enzyme to diversify its secondary metabolite arsenal.IMPORTANCE Here, we provide evidence that Aspergillus terreus encodes a biosynthetic gene cluster containing a repurposed indoleamine 2,3-dioxygenase (IDO) dedicated to secondary metabolite synthesis. The discovery of this neofunctionalized IDO not only enabled discovery of a new compound with an unusual chemical scaffold but also provided insight into the numerous strategies fungi employ for diversifying and protecting themselves against secondary metabolites. The observations in this study set the stage for further in-depth studies into the function of duplicated IDOs present in fungal biosynthetic gene clusters and presents a strategy for accessing the biosynthetic potential of gene clusters containing duplicated primary metabolic genes.
Collapse
|
32
|
The Literature of Chemoinformatics: 1978-2018. Int J Mol Sci 2020; 21:ijms21155576. [PMID: 32759729 PMCID: PMC7432360 DOI: 10.3390/ijms21155576] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 11/16/2022] Open
Abstract
This article presents a study of the literature of chemoinformatics, updating and building upon an analogous bibliometric investigation that was published in 2008. Data on outputs in the field, and citations to those outputs, were obtained by means of topic searches of the Web of Science Core Collection. The searches demonstrate that chemoinformatics is by now a well-defined sub-discipline of chemistry, and one that forms an essential part of the chemical educational curriculum. There are three core journals for the subject: The Journal of Chemical Information and Modeling, the Journal of Cheminformatics, and Molecular Informatics, and, having established itself, chemoinformatics is now starting to export knowledge to disciplines outside of chemistry.
Collapse
|
33
|
Gilchrist CLM, Lacey HJ, Vuong D, Pitt JI, Lange L, Lacey E, Pilgaard B, Chooi YH, Piggott AM. Comprehensive chemotaxonomic and genomic profiling of a biosynthetically talented Australian fungus, Aspergillus burnettii sp. nov. Fungal Genet Biol 2020; 143:103435. [PMID: 32702474 DOI: 10.1016/j.fgb.2020.103435] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 01/09/2023]
Abstract
Aspergillus burnettii is a new species belonging to the A. alliaceus clade in Aspergillus subgenus Circumdati section Flavi isolated from peanut-growing properties in southern Queensland, Australia. A. burnettii is a fast-growing, floccose fungus with distinctive brown conidia and is a talented producer of biomass-degrading enzymes and secondary metabolites. Chemical profiling of A. burnettii revealed the metabolites ochratoxin A, kotanins, isokotanins, asperlicin E, anominine and paspalinine, which are common to subgenus Circumdati, together with burnettiene A, burnettramic acids, burnettides, and high levels of 14α-hydroxypaspalinine and hirsutide. The genome of A. burnettii was sequenced and an annotated draft genome is presented. A. burnettii is rich in secondary metabolite biosynthetic gene clusters, containing 51 polyketide synthases, 28 non-ribosomal peptide synthetases and 19 genes related to terpene biosynthesis. Functional annotation of digestive enzymes of A. burnettii and A. alliaceus revealed overlapping carbon utilisation profiles, consistent with a close phylogenetic relationship.
Collapse
Affiliation(s)
- Cameron L M Gilchrist
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Heather J Lacey
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - Daniel Vuong
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - John I Pitt
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - Lene Lange
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; BioEconomy, Research & Advisory, Karensgade 5, 2500 Valby, Copenhagen, Denmark
| | - Ernest Lacey
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia; Department of Molecular Sciences, Macquarie University, NSW 2109, Australia
| | - Bo Pilgaard
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Yit-Heng Chooi
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia.
| | - Andrew M Piggott
- Department of Molecular Sciences, Macquarie University, NSW 2109, Australia.
| |
Collapse
|
34
|
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: 69] [Impact Index Per Article: 17.3] [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.
Collapse
Affiliation(s)
- Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
| | | | | | | | | |
Collapse
|
35
|
Kautsar SA, Blin K, Shaw S, Navarro-Muñoz JC, Terlouw BR, van der Hooft JJJ, van Santen JA, Tracanna V, Suarez Duran HG, Pascal Andreu V, Selem-Mojica N, Alanjary M, Robinson SL, Lund G, Epstein SC, Sisto AC, Charkoudian LK, Collemare J, Linington RG, Weber T, Medema MH. MIBiG 2.0: a repository for biosynthetic gene clusters of known function. Nucleic Acids Res 2020; 48:D454-D458. [PMID: 31612915 PMCID: PMC7145714 DOI: 10.1093/nar/gkz882] [Citation(s) in RCA: 263] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/25/2019] [Accepted: 10/01/2019] [Indexed: 11/18/2022] Open
Abstract
Fueled by the explosion of (meta)genomic data, genome mining of specialized metabolites has become a major technology for drug discovery and studying microbiome ecology. In these efforts, computational tools like antiSMASH have played a central role through the analysis of Biosynthetic Gene Clusters (BGCs). Thousands of candidate BGCs from microbial genomes have been identified and stored in public databases. Interpreting the function and novelty of these predicted BGCs requires comparison with a well-documented set of BGCs of known function. The MIBiG (Minimum Information about a Biosynthetic Gene Cluster) Data Standard and Repository was established in 2015 to enable curation and storage of known BGCs. Here, we present MIBiG 2.0, which encompasses major updates to the schema, the data, and the online repository itself. Over the past five years, 851 new BGCs have been added. Additionally, we performed extensive manual data curation of all entries to improve the annotation quality of our repository. We also redesigned the data schema to ensure the compliance of future annotations. Finally, we improved the user experience by adding new features such as query searches and a statistics page, and enabled direct link-outs to chemical structure databases. The repository is accessible online at https://mibig.secondarymetabolites.org/.
Collapse
Affiliation(s)
- Satria A Kautsar
- Bioinformatics Group, Wageningen University, Wageningen, NL, The Netherlands
| | - Kai Blin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DK, The Netherlands
| | - Simon Shaw
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DK, The Netherlands
| | - Jorge C Navarro-Muñoz
- Fungal Natural Products Group, Westerdijk Fungal Biodiversity Institute, Utrecht, NL, The Netherlands
| | - Barbara R Terlouw
- Bioinformatics Group, Wageningen University, Wageningen, NL, The Netherlands
| | | | | | - Vittorio Tracanna
- Bioinformatics Group, Wageningen University, Wageningen, NL, The Netherlands
| | | | | | - Nelly Selem-Mojica
- Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Irapuato, MX, Mexico
| | - Mohammad Alanjary
- Bioinformatics Group, Wageningen University, Wageningen, NL, The Netherlands
| | - Serina L Robinson
- BioTechnology Institute, University of Minnesota-Twin Cities, MN, USA
| | - George Lund
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | | | - Ashley C Sisto
- Department of Chemistry, Haverford College, Haverford, PA, USA
| | | | - Jérôme Collemare
- Fungal Natural Products Group, Westerdijk Fungal Biodiversity Institute, Utrecht, NL, The Netherlands
| | | | - Tilmann Weber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DK, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, NL, The Netherlands
| |
Collapse
|
36
|
A Penicillium rubens platform strain for secondary metabolite production. Sci Rep 2020; 10:7630. [PMID: 32376967 PMCID: PMC7203126 DOI: 10.1038/s41598-020-64893-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 04/08/2020] [Indexed: 12/18/2022] Open
Abstract
We present a Penicillium rubens strain with an industrial background in which the four highly expressed biosynthetic gene clusters (BGC) required to produce penicillin, roquefortine, chrysogine and fungisporin were removed. This resulted in a minimal secondary metabolite background. Amino acid pools under steady-state growth conditions showed reduced levels of methionine and increased intracellular aromatic amino acids. Expression profiling of remaining BGC core genes and untargeted mass spectrometry did not identify products from uncharacterized BGCs. This platform strain was repurposed for expression of the recently identified polyketide calbistrin gene cluster and achieved high yields of decumbenone A, B and C. The penicillin BGC could be restored through in vivo assembly with eight DNA segments with short overlaps. Our study paves the way for fast combinatorial assembly and expression of biosynthetic pathways in a fungal strain with low endogenous secondary metabolite burden.
Collapse
|
37
|
Deng H, Bai Y, Fan TP, Zheng X, Cai Y. Advanced strategy for metabolite exploration in filamentous fungi. Crit Rev Biotechnol 2020; 40:180-198. [PMID: 31906740 DOI: 10.1080/07388551.2019.1709798] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Filamentous fungi comprise an abundance of gene clusters that encode high-value metabolites, whereas affluent gene clusters remain silent during laboratory conditions. Complex cellular metabolism further limits these metabolite yields. Therefore, diverse strategies such as genetic engineering and chemical mutagenesis have been developed to activate these cryptic pathways and improve metabolite productivity. However, lower efficiencies of gene modifications and screen tools delayed the above processes. To address the above issues, this review describes an alternative design-construction evaluation optimization (DCEO) approach. The DCEO tool provides theoretical and practical principles to identify potential pathways, modify endogenous pathways, integrate exogenous pathways, and exploit novel pathways for their diverse metabolites and desirable productivities. This DCEO method also offers different tactics to balance the cellular metabolisms, facilitate the genetic engineering, and exploit the scalable metabolites in filamentous fungi.
Collapse
Affiliation(s)
- Huaxiang Deng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Center for Synthetic Biochemistry, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen, China
| | - Yajun Bai
- College of Life Sciences, Northwest University, Xi'an, Shanxi, China
| | - Tai-Ping Fan
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Xiaohui Zheng
- College of Life Sciences, Northwest University, Xi'an, Shanxi, China
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| |
Collapse
|
38
|
Salwan R, Sharma A, Sharma V. Recent Advances in Molecular Approaches for Mining Potential Candidate Genes of Trichoderma for Biofuel. Fungal Biol 2020. [DOI: 10.1007/978-3-030-41870-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
39
|
Helfrich EJN, Ueoka R, Dolev A, Rust M, Meoded RA, Bhushan A, Califano G, Costa R, Gugger M, Steinbeck C, Moreno P, Piel J. Automated structure prediction of trans-acyltransferase polyketide synthase products. Nat Chem Biol 2019; 15:813-821. [PMID: 31308532 PMCID: PMC6642696 DOI: 10.1038/s41589-019-0313-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 05/23/2019] [Indexed: 12/01/2022]
Abstract
Bacterial trans-acyltransferase polyketide synthases (trans-AT PKSs) are among the most complex known enzymes from secondary metabolism and are responsible for the biosynthesis of highly diverse bioactive polyketides. However, most of these metabolites remain uncharacterized, since trans-AT PKSs frequently occur in poorly studied microbes and feature a remarkable array of non-canonical biosynthetic components with poorly understood functions. As a consequence, genome-guided natural product identification has been challenging. To enable de novo structural predictions for trans-AT PKS-derived polyketides, we developed the trans-AT PKS polyketide predictor (TransATor). TransATor is a versatile bio- and chemoinformatics web application that suggests informative chemical structures for even highly aberrant trans-AT PKS biosynthetic gene clusters, thus permitting hypothesis-based, targeted biotechnological discovery and biosynthetic studies. We demonstrate the applicative scope in several examples, including the characterization of new variants of bioactive natural products as well as structurally new polyketides from unusual bacterial sources.
Collapse
Affiliation(s)
- Eric J N Helfrich
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Reiko Ueoka
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Alon Dolev
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Michael Rust
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Roy A Meoded
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Agneya Bhushan
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Gianmaria Califano
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Rodrigo Costa
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Muriel Gugger
- Institut Pasteur, Collection des Cyanobactéries, Paris, France
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-Universität Jena, Jena, Germany
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge, UK
| | - Pablo Moreno
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge, UK.
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland.
| |
Collapse
|
40
|
Khater S, Gupta M, Agrawal P, Sain N, Prava J, Gupta P, Grover M, Kumar N, Mohanty D. SBSPKSv2: structure-based sequence analysis of polyketide synthases and non-ribosomal peptide synthetases. Nucleic Acids Res 2019; 45:W72-W79. [PMID: 28460065 PMCID: PMC5570206 DOI: 10.1093/nar/gkx344] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/25/2017] [Indexed: 01/05/2023] Open
Abstract
Genome guided discovery of novel natural products has been a promising approach for identification of new bioactive compounds. SBSPKS web-server has been a valuable resource for analysis of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) gene clusters. We have developed an updated version - SBSPKSv2 which is based on comprehensive analysis of sequence, structure and secondary metabolite chemical structure data from 311 experimentally characterized PKS/NRPS gene clusters with known biosynthetic products. A completely new feature of SBSPKSv2 is the inclusion of features for search in chemical space. It allows the user to compare the chemical structure of a given secondary metabolite to the chemical structures of biosynthetic intermediates and final products. For identification of catalytic domains, SBSPKS now uses profile based searches, which are computationally faster and have high sensitivity. HMM profiles have also been added for a number of new domains and motif information has been used for distinguishing condensation (C), epimerization (E) and cyclization (Cy) domains of NRPS. In summary, the new and updated SBSPKSv2 is a versatile tool for genome mining and analysis of polyketide and non-ribosomal peptide biosynthetic pathways in chemical space. The server is available at: http://www.nii.ac.in/sbspks2.html.
Collapse
Affiliation(s)
- Shradha Khater
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Money Gupta
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Priyesh Agrawal
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Neetu Sain
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Jyoti Prava
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Priya Gupta
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Mansi Grover
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Narendra Kumar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Debasisa Mohanty
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| |
Collapse
|
41
|
Jia Q, Chen X, Köllner TG, Rinkel J, Fu J, Labbé J, Xiong W, Dickschat JS, Gershenzon J, Chen F. Terpene Synthase Genes Originated from Bacteria through Horizontal Gene Transfer Contribute to Terpenoid Diversity in Fungi. Sci Rep 2019; 9:9223. [PMID: 31239482 PMCID: PMC6592883 DOI: 10.1038/s41598-019-45532-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/07/2019] [Indexed: 12/18/2022] Open
Abstract
Fungi are successful eukaryotes of wide distribution. They are known as rich producers of secondary metabolites, especially terpenoids, which are important for fungi-environment interactions. Horizontal gene transfer (HGT) is an important mechanism contributing to genetic innovation of fungi. However, it remains unclear whether HGT has played a role in creating the enormous chemical diversity of fungal terpenoids. Here we report that fungi have acquired terpene synthase genes (TPSs), which encode pivotal enzymes for terpenoid biosynthesis, from bacteria through HGT. Phylogenetic analysis placed the majority of fungal and bacterial TPS genes from diverse taxa into two clades, indicating ancient divergence. Nested in the bacterial TPS clade is a number of fungal TPS genes that are inferred as the outcome of HGT. These include a monophyletic clade of nine fungal TPS genes, designated as BTPSL for bacterial TPS-like genes, from eight species of related entomopathogenic fungi, including seven TPSs from six species in the genus Metarhizium. In vitro enzyme assays demonstrate that all seven BTPSL genes from the genus Metarhizium encode active enzymes with sesquiterpene synthase activities of two general product profiles. By analyzing the catalytic activity of two resurrected ancestral BTPSLs and one closely related bacterial TPS, the trajectory of functional evolution of BTPSLs after HGT from bacteria to fungi and functional divergence within Metarhizium could be traced. Using M. brunneum as a model species, both BTPSLs and typical fungal TPSs were demonstrated to be involved in the in vivo production of terpenoids, illustrating the general importance of HGT of TPS genes from bacteria as a mechanism contributing to terpenoid diversity in fungi.
Collapse
Affiliation(s)
- Qidong Jia
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA. .,Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
| | - Xinlu Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Tobias G Köllner
- Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, D-07745, Jena, Germany
| | - Jan Rinkel
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Jianyu Fu
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Jessy Labbé
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Wangdan Xiong
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Jonathan Gershenzon
- Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, D-07745, Jena, Germany
| | - Feng Chen
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA. .,Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA.
| |
Collapse
|
42
|
Quijano MR, Zach C, Miller FS, Lee AR, Imani AS, Künzler M, Freeman MF. Distinct Autocatalytic α-N-Methylating Precursors Expand the Borosin RiPP Family of Peptide Natural Products. J Am Chem Soc 2019; 141:9637-9644. [DOI: 10.1021/jacs.9b03690] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marissa R. Quijano
- Department of Biochemistry, Molecular Biology, and Biophysics and BioTechnology Institute, University of Minnesota−Twin Cities, St. Paul, Minnesota 55108, United States
| | - Christina Zach
- Department of Biology, Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Fredarla S. Miller
- Department of Biochemistry, Molecular Biology, and Biophysics and BioTechnology Institute, University of Minnesota−Twin Cities, St. Paul, Minnesota 55108, United States
| | - Aileen R. Lee
- Department of Biochemistry, Molecular Biology, and Biophysics and BioTechnology Institute, University of Minnesota−Twin Cities, St. Paul, Minnesota 55108, United States
| | - Aman S. Imani
- Department of Biochemistry, Molecular Biology, and Biophysics and BioTechnology Institute, University of Minnesota−Twin Cities, St. Paul, Minnesota 55108, United States
| | - Markus Künzler
- Department of Biology, Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Michael F. Freeman
- Department of Biochemistry, Molecular Biology, and Biophysics and BioTechnology Institute, University of Minnesota−Twin Cities, St. Paul, Minnesota 55108, United States
| |
Collapse
|
43
|
Natural product drug discovery in the genomic era: realities, conjectures, misconceptions, and opportunities. ACTA ACUST UNITED AC 2019; 46:281-299. [DOI: 10.1007/s10295-018-2115-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/20/2018] [Indexed: 12/21/2022]
Abstract
Abstract
Natural product discovery from microorganisms provided important sources for antibiotics, anti-cancer agents, immune-modulators, anthelminthic agents, and insecticides during a span of 50 years starting in the 1940s, then became less productive because of rediscovery issues, low throughput, and lack of relevant new technologies to unveil less abundant or not easily detected drug-like natural products. In the early 2000s, it was observed from genome sequencing that Streptomyces species encode about ten times as many secondary metabolites as predicted from known secondary metabolomes. This gave rise to a new discovery approach—microbial genome mining. As the cost of genome sequencing dropped, the numbers of sequenced bacteria, fungi and archaea expanded dramatically, and bioinformatic methods were developed to rapidly scan whole genomes for the numbers, types, and novelty of secondary metabolite biosynthetic gene clusters. This methodology enabled the identification of microbial taxa gifted for the biosynthesis of drug-like secondary metabolites. As genome sequencing technology progressed, the realities relevant to drug discovery have emerged, the conjectures and misconceptions have been clarified, and opportunities to reinvigorate microbial drug discovery have crystallized. This perspective addresses these critical issues for drug discovery.
Collapse
|
44
|
Biosynthetic Gene Content of the 'Perfume Lichens' Evernia prunastri and Pseudevernia furfuracea. Molecules 2019; 24:molecules24010203. [PMID: 30626017 PMCID: PMC6337363 DOI: 10.3390/molecules24010203] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 12/29/2018] [Accepted: 01/04/2019] [Indexed: 12/26/2022] Open
Abstract
Lichen-forming fungi produce a vast number of unique natural products with a wide variety of biological activities and human uses. Although lichens have remarkable potential in natural product research and industry, the molecular mechanisms underlying the biosynthesis of lichen metabolites are poorly understood. Here we use genome mining and comparative genomics to assess biosynthetic gene clusters and their putative regulators in the genomes of two lichen-forming fungi, which have substantial commercial value in the perfume industry, Evernia prunastri and Pseudevernia furfuracea. We report a total of 80 biosynthetic gene clusters (polyketide synthases (PKS), non-ribosomal peptide synthetases and terpene synthases) in E. prunastri and 51 in P. furfuracea. We present an in-depth comparison of 11 clusters, which show high homology between the two species. A ketosynthase (KS) phylogeny shows that biosynthetic gene clusters from E. prunastri and P. furfuracea are widespread across the Fungi. The phylogeny includes 15 genomes of lichenized fungi and all fungal PKSs with known functions from the MIBiG database. Phylogenetically closely related KS domains predict not only similar PKS architecture but also similar cluster architecture. Our study highlights the untapped biosynthetic richness of lichen-forming fungi, provides new insights into lichen biosynthetic pathways and facilitates heterologous expression of lichen biosynthetic gene clusters.
Collapse
|
45
|
Tang M, Zou Y, Yee D, Tang Y. Identification of the Pyranonigrin A Biosynthetic Gene Cluster by Genome Mining in Penicillium thymicola IBT 5891. AIChE J 2018; 64:4182-4186. [PMID: 31588145 DOI: 10.1002/aic.16324] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Man‐Cheng Tang
- Dept. of Chemical and Biomolecular EngineeringUniversity of CaliforniaLos AngelesCA 90095
| | - Yi Zou
- Dept. of Chemical and Biomolecular EngineeringUniversity of CaliforniaLos AngelesCA 90095
| | - Danielle Yee
- Dept. of Chemical and Biomolecular EngineeringUniversity of CaliforniaLos AngelesCA 90095
| | - Yi Tang
- Dept. of Chemical and Biomolecular EngineeringUniversity of CaliforniaLos AngelesCA 90095
- Dept. of Chemistry and BiochemistryUniversity of CaliforniaLos AngelesCA 90095
| |
Collapse
|
46
|
Zhou ZZ, Zhu HJ, Lin LP, Zhang X, Ge HM, Jiao RH, Tan RX. Dalmanol biosyntheses require coupling of two separate polyketide gene clusters. Chem Sci 2018; 10:73-82. [PMID: 30746075 PMCID: PMC6335865 DOI: 10.1039/c8sc03697g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 11/21/2018] [Indexed: 11/29/2022] Open
Abstract
Polyketide–polyketide hybrids are unique natural products with promising bioactivity, but the hybridization processes remain poorly understood.
Polyketide–polyketide hybrids are unique natural products with promising bioactivity, but the hybridization processes remain poorly understood. Herein, we present that the biosynthetic pathways of two immunosuppressants, dalmanol A and acetodalmanol A, result from an unspecific monooxygenase triggered hybridization of two distinct polyketide (naphthalene and chromane) biosynthetic gene clusters. The orchestration of the functional dimorphism of the polyketide synthase (ChrA) ketoreductase (KR) domain (shortened as ChrA KR) with that of the KR partner (ChrB) in the bioassembly line increases the polyketide diversity and allows the fungal generation of plant chromanes (e.g., noreugenin) and phloroglucinols (e.g., 2,4,6-trihydroxyacetophenone). The simultaneous fungal biosynthesis of 1,3,6,8- and 2-acetyl-1,3,6,8-tetrahydroxynaphthalenes was addressed as well. Collectively, the work may symbolize a movement in understanding the multiple-gene-cluster involved natural product biosynthesis, and highlights the possible fungal generations of some chromane- and phloroglucinol-based phytochemicals.
Collapse
Affiliation(s)
- Zhen Zhen Zhou
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , Nanjing University , Nanjing 210023 , China .
| | - Hong Jie Zhu
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , Nanjing University , Nanjing 210023 , China .
| | - Li Ping Lin
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy , Nanjing University of Chinese Medicine , Nanjing 210023 , China.,State Key Laboratory Elemento-Organic Chemistry , Nankai University , Tianjin 300071 , China
| | - Xuan Zhang
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , Nanjing University , Nanjing 210023 , China .
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , Nanjing University , Nanjing 210023 , China .
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , Nanjing University , Nanjing 210023 , China .
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , Nanjing University , Nanjing 210023 , China . .,State Key Laboratory Cultivation Base for TCM Quality and Efficacy , Nanjing University of Chinese Medicine , Nanjing 210023 , China
| |
Collapse
|
47
|
Exploitation of Mangrove Endophytic Fungi for Infectious Disease Drug Discovery. Mar Drugs 2018; 16:md16100376. [PMID: 30308948 PMCID: PMC6212984 DOI: 10.3390/md16100376] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 01/14/2023] Open
Abstract
There is an acute need for new and effective agents to treat infectious diseases. We conducted a screening program to assess the potential of mangrove-derived endophytic fungi as a source of new antibiotics. Fungi cultured in the presence and absence of small molecule epigenetic modulators were screened against Mycobacterium tuberculosis and the ESKAPE panel of bacterial pathogens, as well as two eukaryotic infective agents, Leishmania donovani and Naegleria fowleri. By comparison of bioactivity data among treatments and targets, trends became evident, such as the result that more than 60% of active extracts were revealed to be selective to a single target. Validating the technique of using small molecules to dysregulate secondary metabolite production pathways, nearly half (44%) of those fungi producing active extracts only did so following histone deacetylase inhibitory (HDACi) or DNA methyltransferase inhibitory (DNMTi) treatment.
Collapse
|
48
|
Walsh CT. Nature Builds Macrocycles and Heterocycles into Its Antimicrobial Frameworks: Deciphering Biosynthetic Strategy. ACS Infect Dis 2018; 4:1283-1299. [PMID: 29993235 DOI: 10.1021/acsinfecdis.8b00101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Natural products with anti-infective activity are largely of polyketide or peptide origin. The nascent scaffolds typically undergo further enzymatic morphing to produce mature active structures. Two kinds of common constraints during maturation of immature scaffolds to active end point metabolites are macrocyclizations and hetrocyclizations. Each builds compact architectures characteristic of many high affinity, specific ligands for therapeutic targets. The chemical logic and enzymatic machinery for macrolactone and macrolactam formations are analyzed for antibiotics such as erythromycins, daptomycin, polymyxins, and vancomycin. In parallel, biosynthetic enzymes build small ring heterocycles, including epoxides, β-lactams, and β-lactones, cyclic ethers such as tetrahydrofurans and tetrahydropyrans, thiazoles, and oxazoles, as well as some seven- and eight-member heterocyclic rings. Combinations of fused heterocyclic scaffolds and heterocycles embedded in macrocycles reveal nature's chemical logic for building active molecular frameworks in short efficient pathways.
Collapse
Affiliation(s)
- Christopher T. Walsh
- ChEM-H Institute, Stanford University, Shriram 279, 443 Via Ortega, Stanford, California 94305, United States
| |
Collapse
|
49
|
Epstein SC, Charkoudian LK, Medema MH. A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences. Stand Genomic Sci 2018; 13:16. [PMID: 30008988 PMCID: PMC6042397 DOI: 10.1186/s40793-018-0318-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 06/04/2018] [Indexed: 11/18/2022] Open
Abstract
Microorganisms utilize complex enzymatic pathways to biosynthesize structurally complex and pharmacologically relevant molecules. These pathways are encoded by gene clusters and are found in a diverse set of organisms. The Minimum Information about a Biosynthetic Gene cluster repository facilitates standardized and centralized storage of experimental data on these gene clusters and their molecular products, by utilizing user-submitted data to translate scientific discoveries into a format that can be analyzed computationally. This accelerates the processes of connecting genes to chemical structures, understanding biosynthetic gene clusters in the context of environmental diversity, and performing computer-assisted design of synthetic gene clusters. Here, we present a Standard Operating Procedure, Excel templates, a tutorial video, and a collection of relevant review literature to support scientists in their efforts to submit data into MiBIG. Further, we provide tools to integrate gene cluster annotation projects into the classroom environment, including workflows and assessment materials.
Collapse
Affiliation(s)
- Samuel C. Epstein
- Department of Chemistry, Haverford College, Haverford, PA 19041-1391 USA
| | | | - Marnix H. Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| |
Collapse
|
50
|
Raistrickiones A-E from a Highly Productive Strain of Penicillium raistrickii Generated through Thermo Change. Mar Drugs 2018; 16:md16060213. [PMID: 29912165 PMCID: PMC6025261 DOI: 10.3390/md16060213] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/13/2018] [Accepted: 06/15/2018] [Indexed: 02/06/2023] Open
Abstract
Three new diastereomers of polyketides (PKs), raistrickiones A−C (1⁻3), together with two new analogues, raistrickiones D and E (4 and 5), were isolated from a highly productive strain of Penicillium raistrickii, which was subjected to an experimental thermo-change strategy to tap its potential of producing new secondary metabolites. Metabolites 1 and 2 existed in a diastereomeric mixture in the crystal packing according to the X-ray data, and were laboriously separated by semi-preparative HPLC on a chiral column. The structures of 1⁻5 were determined on the basis of the detailed analyses of the spectroscopic data (UV, IR, HRESIMS, 1D, and 2D NMR), single-crystal X-ray diffractions, and comparison of the experimental and calculated electronic circular dichroism spectra. Compounds 1⁻5 represented the first case of 3,5-dihydroxy-4-methylbenzoyl derivatives of natural products. Compounds 1⁻5 exhibited moderate radical scavenging activities against 1,1-diphenyl-2-picrylhydrazyl radical 2,2-diphenyl-1-(2,4,6-trinitrophenyl) hydrazyl (DPPH).
Collapse
|