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Lu Y, Liu D. Optimization of polysaccharide conditions and analysis of antioxidant capacity in the co-culture of Sanghuangporus vaninii and Pleurotus sapidus. PeerJ 2024; 12:e17571. [PMID: 38938607 PMCID: PMC11210461 DOI: 10.7717/peerj.17571] [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: 01/23/2024] [Accepted: 05/23/2024] [Indexed: 06/29/2024] Open
Abstract
Fungal polysaccharides are commonly utilized in the food industry and biomedical fields as a natural and safe immune modulator. Co-culturing is a valuable method for enhancing the production of secondary metabolites. This study used intracellular polysaccharide (IPS) content as a screening index, co-culturing seven different fungi with Sanghuangporus vaninii. The seed pre-culture liquid culture time was selected through screening, and conditions were assessed using single factor experimentation, a Plackett-Burman (PB) design, and response surface methodology (RSM) optimization. RSM optimization was conducted, leading to the measurement of antioxidant capacity. Results indicated that the co-culture of S. vaninii and Pleurotus sapidus exhibited the most effective outcome. Specifically, pre-culturing S. vaninii and P. sapidus seed cultures for 2 days and 0 days, respectively, followed by co-culturing, significantly increased IPS content compared to single-strain culturing. Further optimization of co-culture conditions revealed that yeast extract concentration, liquid volume, and S. vaninii inoculum ratio notably influenced IPS content in the order of yeast extract concentration > liquid volume > S. vaninii inoculum ratio. Under the optimal conditions, IPS content reached 69.9626 mg/g, a 17.04% increase from pre-optimization co-culture conditions. Antioxidant capacity testing demonstrated that co-cultured IPS exhibited greater scavenging abilities for DPPH and ABTS free radicals compared to single strain cultures. These findings highlight the potential of co-culturing S. vaninii and P. sapidus to enhance IPS content and improve antioxidant capacity, presenting an effective strategy for increasing fungal polysaccharide production.
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Affiliation(s)
- Yuantian Lu
- Agricultural College, Yanbian University, Yanji, Jilin, China
| | - Di Liu
- Agricultural College, Yanbian University, Yanji, Jilin, China
- Institute of Edible and Medicinal Fungi, Agricultural College, Yanbian University, Yanji, Jilin, China
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2
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Qi J, Kang SJ, Zhao L, Gao JM, Liu C. Natural and engineered xylosyl products from microbial source. NATURAL PRODUCTS AND BIOPROSPECTING 2024; 14:13. [PMID: 38296905 PMCID: PMC10830979 DOI: 10.1007/s13659-024-00435-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 01/18/2024] [Indexed: 02/02/2024]
Abstract
Glycosylation is a prevalent post-modification found in natural products and has a significant impact on the structural diversity and activity variation of natural products. Glucosylation is the most common type of glycosylation, whereas xylosylation is relatively rare. Despite their unique chemical structures and beneficial activities, xylosylated natural products from microorganisms have received little attention. This review provides, for the first time, a comprehensive summary of 126 microbial-derived xylosylated natural products, including xylosyl-cyathane diterpenes, xylosylated triterpenes, xylosyl aromatic compounds, and others. Among these compounds, xylosyl-cyathane diterpenes represent the highest number of derivatives, followed by xylosylated triterpenes. Xylosyl compounds from bacterial sources have less defined structural profiles compared to those from fungi. The characterization of xylosyltransferase EriJ from Basidiomycota extended the structural diversity of xylosyl cyathane diterpenes. This work provides a valuable reference for the research and use of xylosyltransferase for drug discovery and synthetic chemistry. Further work is needed to explore the potential applications of microbial derived xylosyl compounds and to develop novel xylosyl transferases. With the deepening of genomic sequencing of medicinal fungi, more biosynthesis of bioactive xylosyl compounds is expected to be elucidated in the future.
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Affiliation(s)
- Jianzhao Qi
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, China.
- Department of Pharmacy, School of Medicine, Xi'an International University, Xi'an, 710077, China.
- Key Laboratory for Enzyme and Enzyme‑Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin, 150040, China.
| | - Shi-Jie Kang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, China
| | - Ling Zhao
- Department of Pharmacy, School of Medicine, Xi'an International University, Xi'an, 710077, China
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, China
| | - Chengwei Liu
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, China.
- Key Laboratory for Enzyme and Enzyme‑Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin, 150040, China.
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3
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Jeong E, Kim W, Son S, Yang S, Gwon D, Hong J, Cho Y, Jang CY, Steinegger M, Lim YW, Kang KB. Qualitative metabolomics-based characterization of a phenolic UDP-xylosyltransferase with a broad substrate spectrum from Lentinus brumalis. Proc Natl Acad Sci U S A 2023; 120:e2301007120. [PMID: 37399371 PMCID: PMC10334773 DOI: 10.1073/pnas.2301007120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/06/2023] [Indexed: 07/05/2023] Open
Abstract
Wood-decaying fungi are the major decomposers of plant litter. Heavy sequencing efforts on genomes of wood-decaying fungi have recently been made due to the interest in their lignocellulolytic enzymes; however, most parts of their proteomes remain uncharted. We hypothesized that wood-decaying fungi would possess promiscuous enzymes for detoxifying antifungal phytochemicals remaining in the dead plant bodies, which can be useful biocatalysts. We designed a computational mass spectrometry-based untargeted metabolomics pipeline for the phenotyping of biotransformation and applied it to 264 fungal cultures supplemented with antifungal plant phenolics. The analysis identified the occurrence of diverse reactivities by the tested fungal species. Among those, we focused on O-xylosylation of multiple phenolics by one of the species tested, Lentinus brumalis. By integrating the metabolic phenotyping results with publicly available genome sequences and transcriptome analysis, a UDP-glycosyltransferase designated UGT66A1 was identified and validated as an enzyme catalyzing O-xylosylation with broad substrate specificity. We anticipate that our analytical workflow will accelerate the further characterization of fungal enzymes as promising biocatalysts.
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Affiliation(s)
- Eunah Jeong
- College of Pharmacy, Sookmyung Women’s University, Seoul04310, Korea
- Research Institute of Pharmaceutical Sciences and Muscle Physiome Research Center, Sookmyung Women’s University, Seoul04310, Korea
| | - Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon57922, Korea
| | - Seungju Son
- College of Pharmacy, Sookmyung Women’s University, Seoul04310, Korea
| | - Sungyeon Yang
- College of Pharmacy, Sookmyung Women’s University, Seoul04310, Korea
| | - Dasom Gwon
- College of Pharmacy, Sookmyung Women’s University, Seoul04310, Korea
- Research Institute of Pharmaceutical Sciences and Muscle Physiome Research Center, Sookmyung Women’s University, Seoul04310, Korea
| | - Jihee Hong
- College of Pharmacy, Sookmyung Women’s University, Seoul04310, Korea
- Research Institute of Pharmaceutical Sciences and Muscle Physiome Research Center, Sookmyung Women’s University, Seoul04310, Korea
| | - Yoonhee Cho
- School of Biological Sciences, Seoul National University, Seoul08826, Korea
| | - Chang-Young Jang
- College of Pharmacy, Sookmyung Women’s University, Seoul04310, Korea
- Research Institute of Pharmaceutical Sciences and Muscle Physiome Research Center, Sookmyung Women’s University, Seoul04310, Korea
| | - Martin Steinegger
- School of Biological Sciences, Seoul National University, Seoul08826, Korea
- Artificial Intelligence Institute, Seoul National University, Seoul08826, Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul08826, Korea
| | - Young Woon Lim
- School of Biological Sciences, Seoul National University, Seoul08826, Korea
- Institute of Microbiology, Seoul National University, Seoul08826, Korea
| | - Kyo Bin Kang
- College of Pharmacy, Sookmyung Women’s University, Seoul04310, Korea
- Research Institute of Pharmaceutical Sciences and Muscle Physiome Research Center, Sookmyung Women’s University, Seoul04310, Korea
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The Potential Use of Fungal Co-Culture Strategy for Discovery of New Secondary Metabolites. Microorganisms 2023; 11:microorganisms11020464. [PMID: 36838429 PMCID: PMC9965835 DOI: 10.3390/microorganisms11020464] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
Fungi are an important and prolific source of secondary metabolites (SMs) with diverse chemical structures and a wide array of biological properties. In the past two decades, however, the number of new fungal SMs by traditional monoculture method had been greatly decreasing. Fortunately, a growing number of studies have shown that co-culture strategy is an effective approach to awakening silent SM biosynthetic gene clusters (BGCs) in fungal strains to produce cryptic SMs. To enrich our knowledge of this approach and better exploit fungal biosynthetic potential for new drug discovery, this review comprehensively summarizes all fungal co-culture methods and their derived new SMs as well as bioactivities on the basis of an extensive literature search and data analysis. Future perspective on fungal co-culture study, as well as its interaction mechanism, is supplied.
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Selegato DM, Castro-Gamboa I. Enhancing chemical and biological diversity by co-cultivation. Front Microbiol 2023; 14:1117559. [PMID: 36819067 PMCID: PMC9928954 DOI: 10.3389/fmicb.2023.1117559] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/06/2023] [Indexed: 02/04/2023] Open
Abstract
In natural product research, microbial metabolites have tremendous potential to provide new therapeutic agents since extremely diverse chemical structures can be found in the nearly infinite microbial population. Conventionally, these specialized metabolites are screened by single-strain cultures. However, owing to the lack of biotic and abiotic interactions in monocultures, the growth conditions are significantly different from those encountered in a natural environment and result in less diversity and the frequent re-isolation of known compounds. In the last decade, several methods have been developed to eventually understand the physiological conditions under which cryptic microbial genes are activated in an attempt to stimulate their biosynthesis and elicit the production of hitherto unexpressed chemical diversity. Among those, co-cultivation is one of the most efficient ways to induce silenced pathways, mimicking the competitive microbial environment for the production and holistic regulation of metabolites, and has become a golden methodology for metabolome expansion. It does not require previous knowledge of the signaling mechanism and genome nor any special equipment for cultivation and data interpretation. Several reviews have shown the potential of co-cultivation to produce new biologically active leads. However, only a few studies have detailed experimental, analytical, and microbiological strategies for efficiently inducing bioactive molecules by co-culture. Therefore, we reviewed studies applying co-culture to induce secondary metabolite pathways to provide insights into experimental variables compatible with high-throughput analytical procedures. Mixed-fermentation publications from 1978 to 2022 were assessed regarding types of co-culture set-ups, metabolic induction, and interaction effects.
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Increasing the production of the bioactive compounds in medicinal mushrooms: an omics perspective. Microb Cell Fact 2023; 22:11. [PMID: 36647087 PMCID: PMC9841694 DOI: 10.1186/s12934-022-02013-x] [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: 06/09/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
Macroscopic fungi, mainly higher basidiomycetes and some ascomycetes, are considered medicinal mushrooms and have long been used in different areas due to their pharmaceutically/nutritionally valuable bioactive compounds. However, the low production of these bioactive metabolites considerably limits the utilization of medicinal mushrooms both in commerce and clinical trials. As a result, many attempts, ranging from conventional methods to novel approaches, have been made to improve their production. The novel strategies include conducting omics investigations, constructing genome-scale metabolic models, and metabolic engineering. So far, genomics and the combined use of different omics studies are the most utilized omics analyses in medicinal mushroom research (both with 31% contribution), while metabolomics (with 4% contribution) is the least. This article is the first attempt for reviewing omics investigations in medicinal mushrooms with the ultimate aim of bioactive compound overproduction. In this regard, the role of these studies and systems biology in elucidating biosynthetic pathways of bioactive compounds and their contribution to metabolic engineering will be highlighted. Also, limitations of omics investigations and strategies for overcoming them will be provided in order to facilitate the overproduction of valuable bioactive metabolites in these valuable organisms.
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7
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DNA Authentication and Chemical Analysis of Psilocybe Mushrooms Reveal Widespread Misdeterminations in Fungaria and Inconsistencies in Metabolites. Appl Environ Microbiol 2022; 88:e0149822. [PMID: 36445079 PMCID: PMC9764976 DOI: 10.1128/aem.01498-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The mushroom genus Psilocybe is best known as the core group of psychoactive mushrooms, yet basic information on their diversity, taxonomy, chemistry, and general biology is still largely lacking. In this study, we reexamined 94 Psilocybe fungarium specimens, representing 18 species, by DNA barcoding, evaluated the stability of psilocybin, psilocin, and their related tryptamine alkaloids in 25 specimens across the most commonly vouchered species (Psilocybe cubensis, Psilocybe cyanescens, and Psilocybe semilanceata), and explored the metabolome of cultivated P. cubensis. Our data show that, apart from a few well-known species, the taxonomic accuracy of specimen determinations is largely unreliable, even at the genus level. A substantial quantity of poor-quality and mislabeled sequence data in public repositories, as well as a paucity of sequences derived from types, further exacerbates the problem. Our data also support taxon- and time-dependent decay of psilocybin and psilocin, with some specimens having no detectable quantities of them. We also show that the P. cubensis metabolome possibly contains thousands of uncharacterized compounds, at least some of which may be bioactive. Taken together, our study undermines commonly held assumptions about the accuracy of names and presence of controlled substances in fungarium specimens identified as Psilocybe spp. and reveals that our understanding of the chemical diversity of these mushrooms is largely incomplete. These results have broader implications for regulatory policies pertaining to the storage and sharing of fungarium specimens as well as the use of psychoactive mushrooms for recreation and therapy. IMPORTANCE The therapeutic use of psilocybin, the active ingredient in "magic mushrooms," is revolutionizing mental health care for a number of conditions, including depression, posttraumatic stress disorder (PTSD), and end-of-life care. This has spotlighted the current state of knowledge of psilocybin, including the organisms that endogenously produce it. However, because of international regulation of psilocybin as a controlled substance (often included on the same list as cocaine and heroin), basic research has lagged far behind. Our study highlights how the poor state of knowledge of even the most fundamental scientific information can impact the use of psilocybin-containing mushrooms for recreational or therapeutic applications and undermines critical assumptions that underpin their regulation by legal authorities. Our study shows that currently available chemical studies are mainly inaccurate, irreproducible, and inconsistent, that there exists a high rate of misidentification in museum collections and public databases rendering even names unreliable, and that the concentration of psilocybin and its tryptamine derivatives in three of the most commonly collected Psilocybe species (P. cubensis, P. cyanescens, and P. semilanceata) is highly variable and unstable in museum specimens spanning multiple decades, and our study generates the first-ever insight into the highly complex and largely uncharacterized metabolomic profile for the most commonly cultivated magic mushroom, P. cubensis.
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8
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Li G, Jian T, Liu X, Lv Q, Zhang G, Ling J. Application of Metabolomics in Fungal Research. Molecules 2022; 27:7365. [PMID: 36364192 PMCID: PMC9654507 DOI: 10.3390/molecules27217365] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 08/27/2023] Open
Abstract
Metabolomics is an essential method to study the dynamic changes of metabolic networks and products using modern analytical techniques, as well as reveal the life phenomena and their inherent laws. Currently, more and more attention has been paid to the development of metabolic histochemistry in the fungus field. This paper reviews the application of metabolomics in fungal research from five aspects: identification, response to stress, metabolite discovery, metabolism engineering, and fungal interactions with plants.
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Affiliation(s)
- Guangyao Li
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Tongtong Jian
- Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Xiaojin Liu
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Qingtao Lv
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Guoying Zhang
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Jianya Ling
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
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Liu Z, Fu B, Duan X, Lv W, Kang S, Zhou M, Wang C, Li D, Xu N. Effects of cell-cell interactions between A. oryzae and Z. rouxii on morphology and secondary metabolites. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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10
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Yao L, Zhang H, Liu Y, Ji Q, Xie J, Zhang R, Huang L, Mei K, Wang J, Gao W. Engineering of triterpene metabolism and overexpression of the lignin biosynthesis gene PAL promotes ginsenoside Rg 3 accumulation in ginseng plant chassis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1739-1754. [PMID: 35731022 DOI: 10.1111/jipb.13315] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/20/2022] [Indexed: 05/28/2023]
Abstract
The ginsenoside Rg3 found in Panax species has extensive pharmacological properties, in particular anti-cancer effects. However, its natural yield in Panax plants is limited. Here, we report a multi-modular strategy to improve yields of Rg3 in a Panax ginseng chassis, combining engineering of triterpene metabolism and overexpression of a lignin biosynthesis gene, phenylalanine ammonia lyase (PAL). We first performed semi-rational design and site mutagenesis to improve the enzymatic efficiency of Pq3-O-UGT2, a glycosyltransferase that directly catalyzes the biosynthesis of Rg3 from Rh2 . Next, we used clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing to knock down the branch pathway of protopanaxatriol-type ginsenoside biosynthesis to enhance the metabolic flux of the protopanaxadiol-type ginsenoside Rg3 . Overexpression of PAL accelerated the formation of the xylem structure, significantly improving ginsenoside Rg3 accumulation (to 6.19-fold higher than in the control). We combined overexpression of the ginsenoside aglycon synthetic genes squalene epoxidase, Pq3-O-UGT2, and PAL with CRISPR/Cas9-based knockdown of CYP716A53v2 to improve ginsenoside Rg3 accumulation. Finally, we produced ginsenoside Rg3 at a yield of 83.6 mg/L in a shake flask (7.0 mg/g dry weight, 21.12-fold higher than with wild-type cultures). The high-production system established in this study could be a potential platform to produce the ginsenoside Rg3 commercially for pharmaceutical use.
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Affiliation(s)
- Lu Yao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Wenzhou Safety (Emergency) Institute of Tianjin University, Wenzhou, 325000, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, China
| | - Huanyu Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Wenzhou Safety (Emergency) Institute of Tianjin University, Wenzhou, 325000, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, China
| | - Yirong Liu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Qiushuang Ji
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Jing Xie
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Ru Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Luqi Huang
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Kunrong Mei
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Juan Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Wenzhou Safety (Emergency) Institute of Tianjin University, Wenzhou, 325000, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, China
| | - Wenyuan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Wenzhou Safety (Emergency) Institute of Tianjin University, Wenzhou, 325000, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, China
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11
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Schüller A, Studt-Reinhold L, Strauss J. How to Completely Squeeze a Fungus-Advanced Genome Mining Tools for Novel Bioactive Substances. Pharmaceutics 2022; 14:1837. [PMID: 36145585 PMCID: PMC9505985 DOI: 10.3390/pharmaceutics14091837] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/23/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
Fungal species have the capability of producing an overwhelming diversity of bioactive substances that can have beneficial but also detrimental effects on human health. These so-called secondary metabolites naturally serve as antimicrobial "weapon systems", signaling molecules or developmental effectors for fungi and hence are produced only under very specific environmental conditions or stages in their life cycle. However, as these complex conditions are difficult or even impossible to mimic in laboratory settings, only a small fraction of the true chemical diversity of fungi is known so far. This also implies that a large space for potentially new pharmaceuticals remains unexplored. We here present an overview on current developments in advanced methods that can be used to explore this chemical space. We focus on genetic and genomic methods, how to detect genes that harbor the blueprints for the production of these compounds (i.e., biosynthetic gene clusters, BGCs), and ways to activate these silent chromosomal regions. We provide an in-depth view of the chromatin-level regulation of BGCs and of the potential to use the CRISPR/Cas technology as an activation tool.
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Affiliation(s)
| | | | - Joseph Strauss
- Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, A-3430 Tulln/Donau, Austria
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12
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Troiano D, Orsat V, Dumont MJ. Solid-state co-culture fermentation of simulated food waste with filamentous fungi for production of bio-pigments. Appl Microbiol Biotechnol 2022; 106:4029-4039. [PMID: 35608668 DOI: 10.1007/s00253-022-11984-1] [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: 03/28/2022] [Revised: 05/09/2022] [Accepted: 05/13/2022] [Indexed: 11/29/2022]
Abstract
The use of waste stream residues as feedstock for material production simultaneously helps reduce dependence on fossil-based resources and to shift toward a circular economy. This study explores the conversion of food waste into valuable chemicals, namely, bio-pigments. Here, a simulated food waste feedstock was converted into pigments via solid-state fermentation with the filamentous fungus Talaromyces albobiverticillius (NRRL 2120). Pigments including monascorubrin, rubropunctatin, and 7-(2-hydroxyethyl)-monascorubramine were identified as products of the fermentation via ultra-performance liquid chromatography coupled with quadrupole-time-of-flight electrospray ionization mass spectrometry. Pigments were obtained at concentrations of 32.5, 20.9, and 22.4 AU/gram dry substrate for pigments absorbing at 400, 475, and 500 nm, respectively. Pigment production was further enhanced by co-culturing T. albobiverticillius with Trichoderma reesei (NRRL 3652), and ultimately yielded 63.8, 35.6, and 43.6 AU/gds at the same respective wavelengths. This represents the highest reported production of pigments via solid-state fermentation of a non-supplemented waste stream feedstock. KEY POINTS: • Simulated food waste underwent solid-state fermentation via filamentous fungi. • Bio-pigments were obtained from fermentation of the simulated food waste. • Co-culturing multiple fungal species substantially improved pigment production.
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Affiliation(s)
- Derek Troiano
- Department of Bioresource Engineering, McGill University, Ste-Anne-de-Bellevue, QC, H9X 3V9, Canada.
| | - Valérie Orsat
- Department of Bioresource Engineering, McGill University, Ste-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Marie-Josée Dumont
- Department of Bioresource Engineering, McGill University, Ste-Anne-de-Bellevue, QC, H9X 3V9, Canada.,Deptartment of Chemical Engineering, Université Laval, Québec, QC, G1V 0A6, Canada
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13
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Liu Z, Kang B, Duan X, Hu Y, Li W, Wang C, Li D, Xu N. Metabolomic profiles of the liquid state fermentation in co-culture of A. oryzae and Z. rouxii. Food Microbiol 2022; 103:103966. [DOI: 10.1016/j.fm.2021.103966] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/31/2021] [Accepted: 12/07/2021] [Indexed: 12/15/2022]
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14
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Wang J, Li L, Xu H, Zhang Y, Liu Y, Zhang F, Shen G, Yan L, Wang W, Tang H, Qiu H, Gu JD, Wang W. Construction of a fungal consortium for effective degradation of rice straw lignin and potential application in bio-pulping. BIORESOURCE TECHNOLOGY 2022; 344:126168. [PMID: 34737050 DOI: 10.1016/j.biortech.2021.126168] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/14/2021] [Accepted: 10/16/2021] [Indexed: 06/13/2023]
Abstract
To improve the lignin degradation efficiency, we established a co-culture consortium (LDFC) consisting of Trametes hirsuta BYL-3, Trametes versicolor BYL-7 and Trametes hirsuta BYL-8. The testing results showed that the constructed consortium showed improved the lignin degradation rate by fungi. The optimal cultivation conditions were mixture at 1:1:1 vol ratio of each fungus, 7% (w/v) of inoculum amount, culture temperature at 26 °C, pH was 6.9 and 10 days of culturing time. Under these conditions, the degradation rate of lignin was 39.7%, which was 9.3% higher than those before optimization (30.4%). Using rice straw for treatment by LDFC to papermaking, the paper tensile strength was 8 N, and the ring pressure index was 2.46 N·m/g, which meets the standards for the production of corrugated paper for packaging. These results indicate that LDFC has potential application value to convert rice straw resources for bio-pulping to make papers.
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Affiliation(s)
- Jinghong Wang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, People's Republic of China; Engineering Research Center of Processing and Utilization of Grain By-products, Ministry of Education, Daqing 163319, People's Republic of China
| | - Lingling Li
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, People's Republic of China; Engineering Research Center of Processing and Utilization of Grain By-products, Ministry of Education, Daqing 163319, People's Republic of China
| | - Hongmin Xu
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, People's Republic of China; Engineering Research Center of Processing and Utilization of Grain By-products, Ministry of Education, Daqing 163319, People's Republic of China
| | - Yali Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, People's Republic of China; Engineering Research Center of Processing and Utilization of Grain By-products, Ministry of Education, Daqing 163319, People's Republic of China
| | - Yuxin Liu
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, People's Republic of China; Engineering Research Center of Processing and Utilization of Grain By-products, Ministry of Education, Daqing 163319, People's Republic of China
| | - Fangzheng Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, People's Republic of China; Engineering Research Center of Processing and Utilization of Grain By-products, Ministry of Education, Daqing 163319, People's Republic of China
| | - Guinan Shen
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, People's Republic of China; Engineering Research Center of Processing and Utilization of Grain By-products, Ministry of Education, Daqing 163319, People's Republic of China
| | - Lei Yan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, People's Republic of China; Engineering Research Center of Processing and Utilization of Grain By-products, Ministry of Education, Daqing 163319, People's Republic of China
| | - Weiwei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Huajiao Qiu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, People's Republic of China
| | - Ji-Dong Gu
- Environmental Science and Technology Research Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People's Republic of China
| | - Weidong Wang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, People's Republic of China; Engineering Research Center of Processing and Utilization of Grain By-products, Ministry of Education, Daqing 163319, People's Republic of China; Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, People's Republic of China.
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15
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Dullah S, Hazarika DJ, Parveen A, Kakoti M, Borgohain T, Gautom T, Bhattacharyya A, Barooah M, Boro RC. Fungal interactions induce changes in hyphal morphology and enzyme production. Mycology 2021; 12:279-295. [PMID: 34900382 PMCID: PMC8654418 DOI: 10.1080/21501203.2021.1932627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
In nature, species interacts/competes with one other within their surrounding for food and space and the type of interactions are unique to each species. The interacting partners secrete different metabolites, which may have high importance in human welfare. Fungal-fungal interactions are complex mechanisms that need better understanding. Here, 14 fungal isolates were facilitated in 105 possible combinations to interact on potato dextrose agar. Morphologically, no changes were observed when the same fungal isolates were allowed to interact within them. However, 10 interactions between different fungal isolates showed mutual replacement with each fungus; capturing territory from the other. Contrastingly, 35 interactions resulted into complete replacement as one of the fungi was inhibited by rapid growth of the other fungus. In 46 interactions, formation of barrage was observed leading to deadlock type of interaction wherein both fungi have restricted growth. To study in details about the barrage formation, two fungal interactions were taken (i) T. coccinea vs. L. lactinea and (ii) T. coccinea vs. T. versicolor. Microscopic changes in the hyphal growth during interaction were observed. There was significant increase in the enzymatic activities including cellulase, xylanase and chitinase during in-vitro fungal-fungal interaction, suggesting the importance of such interactions for commercial enzyme production.
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Affiliation(s)
- Samim Dullah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Dibya Jyoti Hazarika
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Assma Parveen
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Merilin Kakoti
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Tanushree Borgohain
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Trishnamoni Gautom
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India.,Royal School of Bio-Sciences, Royal Global University, Guwahati, India
| | - Ashok Bhattacharyya
- Department of Plant Pathology, Assam Agricultural University, Jorhat, Assam, India
| | - Madhumita Barooah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Robin Chandra Boro
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
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16
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Charria-Girón E, Espinosa MC, Zapata-Montoya A, Méndez MJ, Caicedo JP, Dávalos AF, Ferro BE, Vasco-Palacios AM, Caicedo NH. Evaluation of the Antibacterial Activity of Crude Extracts Obtained From Cultivation of Native Endophytic Fungi Belonging to a Tropical Montane Rainforest in Colombia. Front Microbiol 2021; 12:716523. [PMID: 34603244 PMCID: PMC8485978 DOI: 10.3389/fmicb.2021.716523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/09/2021] [Indexed: 01/08/2023] Open
Abstract
Bioactive secondary metabolite production from endophytic fungi has gained a recurring research focus in recent decades as these microorganisms represent an unexplored biological niche for their diverse biotechnological potential. Despite this focus, studies involving tropical endophytes remain scarce, particularly those isolated from medicinal plants of these ecosystems. In addition, the state of the art of the pharmaceutical industry has experienced stagnation in the past 30years, which has pushed pathogenic infections to get one step ahead, resulting in the development of resistance to existing treatments. Here, five fungal endophytes were isolated from the medicinal plant Otoba gracilipes (Myristicaceae), which corresponded to the genera Xylaria and Diaporthe, and screened to demonstrate the promissory potential of these microorganisms for producing bioactive secondary metabolites with broad-spectrum antibacterial activities. Thus, the evaluation of crude organic extracts obtained from the mycelia and exhaust medium allowed the elucidation of Xylaria sp. and Diaporthe endophytica potential toward providing crude extracellular extracts with promising bioactivities against reference strains of Escherichia coli (ATCC 25922) and Staphylococcus aureus (ATCC 25923), according to the determined half-maximum inhibitory concentration (IC50) with values down to 3.91 and 10.50mg/ml against each pathogen, respectively. Follow-up studies provided insights into the polarity nature of bioactive compounds in the crude extracts through bioactivity guided fractionation using a polymeric resin absorbent alternative extraction procedure. In addition, evaluation of the co-culturing methods demonstrated how this strategy can enhance endophytes biosynthetic capacity and improve their antibacterial potential with a 10-fold decrease in the IC50 values against both pathogens compared to the obtained values in the preliminary evaluations of Xylaria sp. and D. endophytica crude extracts. These results support the potential of Colombian native biodiversity to provide new approaches concerning the global emergence of antibiotics resistance and future production of undiscovered compounds different from the currently used antibiotics classes and simultaneously call for the value of preserving native habitats due to their promising ecosystemic applications in the biotechnological and pharmaceutical industries.
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Affiliation(s)
- Esteban Charria-Girón
- Departamento de Ingeniería Bioquímica, Facultad de Ingeniería, Universidad Icesi, Cali, Colombia
| | - María C Espinosa
- Departamento de Ingeniería Bioquímica, Facultad de Ingeniería, Universidad Icesi, Cali, Colombia
| | - Andrea Zapata-Montoya
- Departamento de Ingeniería Bioquímica, Facultad de Ingeniería, Universidad Icesi, Cali, Colombia
| | - María J Méndez
- Departamento de Ingeniería Bioquímica, Facultad de Ingeniería, Universidad Icesi, Cali, Colombia
| | - Juan P Caicedo
- Departamento de Ingeniería Bioquímica, Facultad de Ingeniería, Universidad Icesi, Cali, Colombia
| | - Andrés F Dávalos
- Departamento de Ciencias Biológicas, Facultad de Ciencias Naturales, Universidad Icesi, Cali, Colombia
| | - Beatriz E Ferro
- Departamento de Salud Pública y Medicina Comunitaria, Facultad de Ciencias de la Salud, Universidad Icesi, Cali, Colombia
| | - Aida M Vasco-Palacios
- Grupo de Microbiología Ambiental - BioMicro, Escuela de Microbiología, Universidad de Antioquia (UdeA), Medellín, Colombia.,Asociación Colombiana de Micología (ASCOLMIC), Medellin, Colombia
| | - Nelson H Caicedo
- Departamento de Ingeniería Bioquímica, Facultad de Ingeniería, Universidad Icesi, Cali, Colombia.,Centro BioInc, Universidad Icesi, Cali, Colombia
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17
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Liu R, Bao ZX, Zhao PJ, Li GH. Advances in the Study of Metabolomics and Metabolites in Some Species Interactions. Molecules 2021; 26:3311. [PMID: 34072976 PMCID: PMC8197931 DOI: 10.3390/molecules26113311] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/24/2021] [Accepted: 05/28/2021] [Indexed: 12/15/2022] Open
Abstract
In the natural environment, interactions between species are a common natural phenomena. The mechanisms of interaction between different species are mainly studied using genomic, transcriptomic, proteomic, and metabolomic techniques. Metabolomics is a crucial part of system biology and is based on precision instrument analysis. In the last decade, the emerging field of metabolomics has received extensive attention. Metabolomics not only provides a qualitative and quantitative method for studying the mechanisms of interactions between different species, but also helps clarify the mechanisms of defense between the host and pathogen, and to explore new metabolites with various biological activities. This review focuses on the methods and progress of interspecies metabolomics. Additionally, the prospects and challenges of interspecies metabolomics are discussed.
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Affiliation(s)
| | | | | | - Guo-Hong Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China; (R.L.); (Z.-X.B.); (P.-J.Z.)
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18
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Yu G, Sun Y, Han H, Yan X, Wang Y, Ge X, Qiao B, Tan L. Coculture, An Efficient Biotechnology for Mining the Biosynthesis Potential of Macrofungi via Interspecies Interactions. Front Microbiol 2021; 12:663924. [PMID: 33815350 PMCID: PMC8010659 DOI: 10.3389/fmicb.2021.663924] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Macrofungi, which are also known as mushrooms, can produce various bioactive constituents and have become promising resources as lead drugs and foods rich in nutritional value. However, the production of these bioactive constituents under standard laboratory conditions is inefficiency due to the silent expression of their relevant genes. Coculture, as an important activation strategy that simulates the natural living conditions of macrofungi, can activate silent genes or clusters through interspecific interactions. Coculturing not only can trigger the biosynthesis of diverse secondary metabolites and enzymes of macrofungi, but is also useful for uncovering the mechanisms of fungal interspecific interactions and novel gene functions. In this paper, coculturing among macrofungi or between macrofungi and other microorganisms, the triggering and upregulation of secondary metabolites and enzymes, the potential medicinal applications, and the fungal-fungal interaction mechanisms are reviewed. Finally, future challenges and perspectives in further advancing coculture systems are discussed.
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Affiliation(s)
- Guihong Yu
- Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Yuman Sun
- Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Heyang Han
- College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Xiu Yan
- Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Yu Wang
- Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Xiaoxuan Ge
- Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Bin Qiao
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Lingling Tan
- Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
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19
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Utilizing cross-species co-cultures for discovery of novel natural products. Curr Opin Biotechnol 2021; 69:252-262. [PMID: 33647849 DOI: 10.1016/j.copbio.2021.01.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 01/12/2021] [Accepted: 01/24/2021] [Indexed: 12/11/2022]
Abstract
Discovery of new natural products, especially those with high biological activities and application values, is of great research significance. However, conventional methods based on the cultivation of microbial mono-cultures can hardly satisfy the increasing need of novel natural product generation. Recently, the development of co-cultures composed of different species has emerged as an effective approach for mining novel natural products. Inspired by microbial communities in nature, these co-culture systems create favorable environmental conditions to promote interactions between co-culture members for activating the natural product biosynthesis that is hard to induce otherwise. A large variety of novel natural products have been identified using this robust approach. This review summarizes the recent achievements of using cross-species co-cultures for natural products discovery and discusses the existing challenges and future directions.
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20
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Triastuti A, Haddad M, Barakat F, Mejia K, Rabouille G, Fabre N, Amasifuen C, Jargeat P, Vansteelandt M. Dynamics of Chemical Diversity during Co-Cultures: An Integrative Time-Scale Metabolomics Study of Fungal Endophytes Cophinforma mamane and Fusarium solani. Chem Biodivers 2021; 18:e2000672. [PMID: 33289281 DOI: 10.1002/cbdv.202000672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/07/2020] [Indexed: 11/07/2022]
Abstract
A rapid and efficient metabolomic study of Cophinforma mamane and Fusarium solani co-cultivation in time-series based analysis was developed to study metabolome variations during their fungal interactions. The fungal metabolomes were studied through the integration of four metabolomic tools: MS-DIAL, a chromatographic deconvolution of liquid-chromatography-mass spectrometry (LC/MS); MS-FINDER, a structure-elucidation program with a wide range metabolome database; GNPS, an effective method to organize MS/MS fragmentation spectra, and MetaboAnalyst, a comprehensive web application for metabolomic data analysis and interpretation. Co-cultures of C. mamane and F. solani induced different patterns of metabolite production over 10 days of incubation and induced production of five de novo compounds not occurring in monocultures. These results emphasize that co-culture in time-frame analysis is an interesting method to unravel hidden metabolome in the investigation of fungal chemodiversity.
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Affiliation(s)
- Asih Triastuti
- UMR 152 Pharma Dev, Université de Toulouse, IRD, UPS, 31400, Toulouse, France.,Department of Pharmacy, Universitas Islam Indonesia, Yogyakarta, 55584, Indonesia
| | - Mohamed Haddad
- UMR 152 Pharma Dev, Université de Toulouse, IRD, UPS, 31400, Toulouse, France
| | - Fatima Barakat
- UMR 152 Pharma Dev, Université de Toulouse, IRD, UPS, 31400, Toulouse, France
| | - Kember Mejia
- Instituto de Investigaciones de la Amazonía Peruana, Avenida Abelardo Quiñonez Km. 4.5, Iquitos, 1600, Peru
| | - Gabriel Rabouille
- UMR 152 Pharma Dev, Université de Toulouse, IRD, UPS, 31400, Toulouse, France
| | - Nicolas Fabre
- UMR 152 Pharma Dev, Université de Toulouse, IRD, UPS, 31400, Toulouse, France
| | - Carlos Amasifuen
- Facultad de Ingeniería Civil y Ambiental [FICIAM], Escuela de Ingeniería Ambiental, Universidad Nacional Toribio Rodríguez de Mendoza [UNTRM, Chachapoyas, 01001, Peru
| | - Patricia Jargeat
- Laboratoire Evolution et Diversité Biologique UMR 5174, Université de Toulouse, CNRS, IRD, UPS, 31062, Toulouse, France
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21
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Alberti F, Kaleem S, Weaver JA. Recent developments of tools for genome and metabolome studies in basidiomycete fungi and their application to natural product research. Biol Open 2020; 9:bio056010. [PMID: 33268478 PMCID: PMC7725599 DOI: 10.1242/bio.056010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Basidiomycota are a large and diverse phylum of fungi. They can make bioactive metabolites that are used or have inspired the synthesis of antibiotics and agrochemicals. Terpenoids are the most abundant class of natural products encountered in this taxon. Other natural product classes have been described, including polyketides, peptides, and indole alkaloids. The discovery and study of natural products made by basidiomycete fungi has so far been hampered by several factors, which include their slow growth and complex genome architecture. Recent developments of tools for genome and metabolome studies are allowing researchers to more easily tackle the secondary metabolome of basidiomycete fungi. Inexpensive long-read whole-genome sequencing enables the assembly of high-quality genomes, improving the scaffold upon which natural product gene clusters can be predicted. CRISPR/Cas9-based engineering of basidiomycete fungi has been described and will have an important role in linking natural products to their genetic determinants. Platforms for the heterologous expression of basidiomycete genes and gene clusters have been developed, enabling natural product biosynthesis studies. Molecular network analyses and publicly available natural product databases facilitate data dereplication and natural product characterisation. These technological advances combined are prompting a revived interest in natural product discovery from basidiomycete fungi.This article has an associated Future Leader to Watch interview with the first author of the paper.
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Affiliation(s)
- Fabrizio Alberti
- School of Life Sciences and Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Saraa Kaleem
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Jack A Weaver
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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22
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Biocatalytic Potential of Native Basidiomycetes from Colombia for Flavour/Aroma Production. Molecules 2020; 25:molecules25184344. [PMID: 32971920 PMCID: PMC7570902 DOI: 10.3390/molecules25184344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 11/17/2022] Open
Abstract
Aromas and flavours can be produced from fungi by either de novo synthesis or biotransformation processes. Herein, the biocatalytic potential of seven basidiomycete species from Colombia fungal strains isolated as endophytes or basidioma was evaluated. Ganoderma webenarium, Ganoderma chocoense, and Ganoderma stipitatum were the most potent strains capable of decolourizing β,β-carotene as evidence of their potential as biocatalysts for de novo aroma synthesis. Since a species’ biocatalytic potential cannot solely be determined via qualitative screening using β,β-carotene biotransformation processes, we focused on using α-pinene biotransformation with mycelium as a measure of catalytic potential. Here, two strains of Trametes elegans—namely, the endophytic (ET-06) and basidioma (EBB-046) strains—were screened. Herein, T. elegans is reported for the first time as a novel biocatalyst for the oxidation of α-pinene, with a product yield of 2.9 mg of cis-Verbenol per gram of dry weight mycelia used. The EBB-046 strain generated flavour compounds via the biotransformation of a Cape gooseberry medium and de novo synthesis in submerged cultures. Three aroma-producing compounds were identified via GC–MS—namely, methyl-3-methoxy-4H-pyran-4-one, hexahydro-3-(methylpropyl)-pyrrolo[1,2-a]pyrazine-1,4-dione, and hexahydro-3-(methylphenyl)-pyrrolo[1,2-a]pyrazine-1,4-dione.
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23
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Presley GN, Zhang J, Purvine SO, Schilling JS. Functional Genomics, Transcriptomics, and Proteomics Reveal Distinct Combat Strategies Between Lineages of Wood-Degrading Fungi With Redundant Wood Decay Mechanisms. Front Microbiol 2020; 11:1646. [PMID: 32849338 PMCID: PMC7399148 DOI: 10.3389/fmicb.2020.01646] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/24/2020] [Indexed: 01/06/2023] Open
Abstract
Wood-degrading fungi vary in their strategies for deconstructing wood, and their competitive successes shape the rate and fate of carbon released from wood, Earth’s largest pool of aboveground terrestrial carbon. In this study, one-on-one interspecific interactions between two model brown rot (carbohydrate-selective) fungi, Gloeophyllum trabeum and Rhodonia (Postia) placenta, were studied on wood wafers where a clearly resolved interaction zone (IZ) could be generated, reproducibly. Comparative RNAseq and proteomics between the IZ and non-interacting hyphae of each species identified combative strategies for each fungus. Glycoside hydrolases were a relatively smaller portion of the interaction secretome compared to non-interacting hyphae. The interaction zone showed higher pectinase specific activity than all other sampling locations, and higher laminarinase specific activity (branched β-glucan proxy) was seen in the IZ secretome relative to equivalent hyphae in single-species cultures. Our efforts also identified two distinct competitive strategies in these two fungi with a shared nutritional mode (brown rot) but polyphyletic ancestral lineages. Gloeophyllum trabeum (Gloeophyllum clade) upregulated more secondary metabolite (SM) synthesis genes in response to a competitor than did R. placenta. R. placenta (Antrodia clade) upregulated a larger variety of uncharacterized oxidoreductases in interacting hyphae, suggesting that these may play a role in mediating competitor response in this fungus. Both species produced several hypothetical proteins exclusively in the interaction zone, leaving questions as to the function of these proteins. This work supports the existence of multiple interaction strategies among brown rot fungi and highlights the functional diversity among wood decay fungi.
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Affiliation(s)
- Gerald N Presley
- Department of Wood Science and Engineering, Oregon State University, Corvallis, OR, United States
| | - Jiwei Zhang
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN, United States
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jonathan S Schilling
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, United States
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24
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Aron AT, Gentry EC, McPhail KL, Nothias LF, Nothias-Esposito M, Bouslimani A, Petras D, Gauglitz JM, Sikora N, Vargas F, van der Hooft JJJ, Ernst M, Kang KB, Aceves CM, Caraballo-Rodríguez AM, Koester I, Weldon KC, Bertrand S, Roullier C, Sun K, Tehan RM, Boya P CA, Christian MH, Gutiérrez M, Ulloa AM, Tejeda Mora JA, Mojica-Flores R, Lakey-Beitia J, Vásquez-Chaves V, Zhang Y, Calderón AI, Tayler N, Keyzers RA, Tugizimana F, Ndlovu N, Aksenov AA, Jarmusch AK, Schmid R, Truman AW, Bandeira N, Wang M, Dorrestein PC. Reproducible molecular networking of untargeted mass spectrometry data using GNPS. Nat Protoc 2020; 15:1954-1991. [PMID: 32405051 DOI: 10.1038/s41596-020-0317-5] [Citation(s) in RCA: 286] [Impact Index Per Article: 71.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 03/03/2020] [Indexed: 02/06/2023]
Abstract
Global Natural Product Social Molecular Networking (GNPS) is an interactive online small molecule-focused tandem mass spectrometry (MS2) data curation and analysis infrastructure. It is intended to provide as much chemical insight as possible into an untargeted MS2 dataset and to connect this chemical insight to the user's underlying biological questions. This can be performed within one liquid chromatography (LC)-MS2 experiment or at the repository scale. GNPS-MassIVE is a public data repository for untargeted MS2 data with sample information (metadata) and annotated MS2 spectra. These publicly accessible data can be annotated and updated with the GNPS infrastructure keeping a continuous record of all changes. This knowledge is disseminated across all public data; it is a living dataset. Molecular networking-one of the main analysis tools used within the GNPS platform-creates a structured data table that reflects the molecular diversity captured in tandem mass spectrometry experiments by computing the relationships of the MS2 spectra as spectral similarity. This protocol provides step-by-step instructions for creating reproducible, high-quality molecular networks. For training purposes, the reader is led through a 90- to 120-min procedure that starts by recalling an example public dataset and its sample information and proceeds to creating and interpreting a molecular network. Each data analysis job can be shared or cloned to disseminate the knowledge gained, thus propagating information that can lead to the discovery of molecules, metabolic pathways, and ecosystem/community interactions.
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Affiliation(s)
- Allegra T Aron
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Emily C Gentry
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Louis-Félix Nothias
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Mélissa Nothias-Esposito
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Amina Bouslimani
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Daniel Petras
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Julia M Gauglitz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Nicole Sikora
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Fernando Vargas
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Madeleine Ernst
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kyo Bin Kang
- College of Pharmacy, Sookmyung Women's University, Seoul, Korea
| | - Christine M Aceves
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Irina Koester
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kelly C Weldon
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center of Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Samuel Bertrand
- Groupe Mer, Molécules, Santé-EA 2160, UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes, Nantes, France
- ThalassOMICS Metabolomics Facility, Plateforme Corsaire, Biogenouest, Nantes, France
| | - Catherine Roullier
- College of Pharmacy, Sookmyung Women's University, Seoul, Korea
- ThalassOMICS Metabolomics Facility, Plateforme Corsaire, Biogenouest, Nantes, France
| | - Kunyang Sun
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Richard M Tehan
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Cristopher A Boya P
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, Nagarjuna Nagar, India
| | - Martin H Christian
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
| | - Marcelino Gutiérrez
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
| | | | | | - Randy Mojica-Flores
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
- Departamento de Química, Universidad Autónoma de Chiriquí (UNACHI), David, Chiriquí, Panama
| | - Johant Lakey-Beitia
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
| | - Victor Vásquez-Chaves
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
| | - Yilue Zhang
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
| | - Angela I Calderón
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
| | - Nicole Tayler
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, Nagarjuna Nagar, India
| | - Robert A Keyzers
- School of Chemical & Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Fidele Tugizimana
- Centre for Plant Metabolomics Research, Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
- International R&D Division, Omnia Group (Pty) Ltd., Johannesburg, South Africa
| | - Nombuso Ndlovu
- Centre for Plant Metabolomics Research, Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
| | - Alexander A Aksenov
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Alan K Jarmusch
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Robin Schmid
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
| | - Mingxun Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA, USA.
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
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25
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Integrated Proteomics and Metabolomics Analysis Provides Insights into Ganoderic Acid Biosynthesis in Response to Methyl Jasmonate in Ganoderma Lucidum. Int J Mol Sci 2019; 20:ijms20246116. [PMID: 31817230 PMCID: PMC6941157 DOI: 10.3390/ijms20246116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/01/2019] [Accepted: 12/02/2019] [Indexed: 02/06/2023] Open
Abstract
Ganoderma lucidum is widely recognized as a medicinal basidiomycete. It was previously reported that the plant hormone methyl jasmonate (MeJA) could induce the biosynthesis of ganoderic acids (GAs), which are the main active ingredients of G. lucidum. However, the regulatory mechanism is still unclear. In this study, integrated proteomics and metabolomics were employed on G. lucidum to globally identify differences in proteins and metabolites under MeJA treatment for 15 min (M15) and 24 h (M24). Our study successfully identified 209 differential abundance proteins (DAPs) in M15 and 202 DAPs in M24. We also identified 154 metabolites by GC-MS and 70 metabolites by LC-MS in M24 that are involved in several metabolic pathways. With an in-depth analysis, we found some DAPs and metabolites that are involved in the oxidoreduction process, secondary metabolism, energy metabolism, transcriptional and translational regulation, and protein synthesis. In particular, our results reveal that MeJA treatment leads to metabolic rearrangement that inhibited the normal glucose metabolism, energy supply, and protein synthesis of cells but promoted secondary metabolites, including GAs. In conclusion, our proteomics and metabolomics data further confirm the promoting effect of MeJA on the biosynthesis of GAs in G. lucidum and will provide a valuable resource for further investigation of the molecular mechanisms of MeJA signal response and GA biosynthesis in G. lucidum and other related species.
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Unusual and Highly Bioactive Sesterterpenes Synthesized by Pleurotus ostreatus during Coculture with Trametes robiniophila Murr. Appl Environ Microbiol 2019; 85:AEM.00293-19. [PMID: 31053589 DOI: 10.1128/aem.00293-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/30/2019] [Indexed: 12/15/2022] Open
Abstract
Candida albicans and Cryptococcus neoformans, human-pathogenic fungi found worldwide, are receiving increasing attention due to high morbidity and mortality in immunocompromised patients. In the present work, 110 fungus pairs were constructed by coculturing 16 wood-decaying basidiomycetes, among which coculture of Trametes robiniophila Murr and Pleurotus ostreatus was found to strongly inhibit pathogenic fungi through bioactivity-guided assays. A combination of metabolomics and molecular network analysis revealed that 44 features were either newly synthesized or produced at high levels in this coculture system and that 6 of the features that belonged to a family of novel and unusual linear sesterterpenes contributed to high activity with MICs of 1 to 32 μg/ml against pathogenic fungi. Furthermore, dynamic 13C-labeling analysis revealed an association between induced features and the corresponding fungi. Unusual sesterterpenes were 13C labeled only in P. ostreatus in a time course after stimulation by the coculture, suggesting that these sesterterpenes were synthesized by P. ostreatus instead of T. robiniophila Murr. Sesterterpene compounds 1 to 3 were renamed postrediene A to C. Real-time reverse transcription-quantitative PCR (RT-qPCR) analysis revealed that transcriptional levels of three genes encoding terpene synthase, farnesyl-diphosphate farnesyltransferase, and oxidase were found to be 8.2-fold, 88.7-fold, and 21.6-fold higher, respectively, in the coculture than in the monoculture, indicating that biosynthetic gene cluster 10 was most likely responsible for the synthesis of these sesterterpenes. A putative biosynthetic pathway of postrediene A to postrediene C was then proposed based on structures of sesterterpenes and molecular network analysis.IMPORTANCE A number of gene clusters involved in biosynthesis of secondary metabolites are presumably silent or expressed at low levels under conditions of standard laboratory cultivation, resulting in a large gap between the pool of discovered metabolites and genome capability. This work mimicked naturally occurring competition by construction of an artificial coculture of basidiomycete fungi for the identification of secondary metabolites with novel scaffolds and excellent bioactivity. Unusual linear sesterterpenes of postrediene A to C synthesized by P. ostreatus not only were promising lead drugs against human-pathogenic fungi but also highlighted a distinct pathway for sesterterpene biosynthesis in basidiomycetes. The current work provides an important basis for uncovering novel gene functions involved in sesterterpene synthesis and for gaining insights into the mechanism of silent gene activation in fungal defense.
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Lu J, Yao L, Li JX, Liu SJ, Hu YY, Wang SH, Liang WX, Huang LQ, Dai YJ, Wang J, Gao WY. Characterization of UDP-Glycosyltransferase Involved in Biosynthesis of Ginsenosides Rg 1 and Rb 1 and Identification of Critical Conserved Amino Acid Residues for Its Function. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:9446-9455. [PMID: 30095259 DOI: 10.1021/acs.jafc.8b02544] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Ginsenosides attract great attention for their bioactivities. However, their contents are low, and many UDP-glycosyltransferases (UGTs) that play crucial roles in the ginsenoside biosynthesis pathways have not been identified, which hinders the biosynthesis of ginsenosides. In this study, we reported that one UDP-glycosyltransferase, UGTPg71A29, from Panax ginseng could glycosylate C20-OH of Rh1 and transfer a glucose moiety to Rd, producing ginsenosides Rg1 and Rb1, respectively. Ectopic expression of UGTPg71A29 in Saccharomyces cerevisiae stably generated Rg1 and Rb1 under its corresponding substrate. Overexpression of UGTPg71A29 in transgenic cells of P. ginseng could significantly enhance the accumulation of Rg1 and Rb1, with their contents of 3.2- and 3.5-fold higher than those in the control, respectively. Homology modeling, molecular dynamics, and mutational analysis revealed the key catalytic site, Gln283, which provided insights into the catalytic mechanism of UGTPg71A29. These results not only provide an efficient enzymatic tool for the synthesis of glycosides but also help achieve large-scale industrial production of glycosides.
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Affiliation(s)
| | | | | | - Shu-Jie Liu
- Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Ministry of Education , Tianjin University of Science and Technology , Tianjin 300457 , People's Republic of China
| | - Yan-Ying Hu
- Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Ministry of Education , Tianjin University of Science and Technology , Tianjin 300457 , People's Republic of China
| | - Shi-Hui Wang
- Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Ministry of Education , Tianjin University of Science and Technology , Tianjin 300457 , People's Republic of China
| | - Wen-Xia Liang
- Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Ministry of Education , Tianjin University of Science and Technology , Tianjin 300457 , People's Republic of China
| | - Lu-Qi Huang
- National Resource Center for Chinese Meteria Medica , China Academy of Chinese Medical Sciences , Beijing 100700 , People's Republic of China
| | - Yu-Jie Dai
- Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Ministry of Education , Tianjin University of Science and Technology , Tianjin 300457 , People's Republic of China
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28
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Xu XY, Shen XT, Yuan XJ, Zhou YM, Fan H, Zhu LP, Du FY, Sadilek M, Yang J, Qiao B, Yang S. Metabolomics Investigation of an Association of Induced Features and Corresponding Fungus during the Co-culture of Trametes versicolor and Ganoderma applanatum. Front Microbiol 2018; 8:2647. [PMID: 29375514 PMCID: PMC5767234 DOI: 10.3389/fmicb.2017.02647] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 12/19/2017] [Indexed: 11/26/2022] Open
Abstract
The co-culture of Trametes versicolor and Ganoderma applanatum is a model of intense basidiomycete interaction, which induces many newly synthesized or highly produced features. Currently, one of the major challenges is an identification of the origin of induced features during the co-culture. Herein, we report a 13C-dynamic labeling analysis used to determine an association of induced features and corresponding fungus even if the identities of metabolites were not available or almost nothing was known of biochemical aspects. After the co-culture of T. versicolor and G. applanatum for 10 days, the mycelium pellets of T. versicolor and G. applanatum were sterilely harvested and then mono-cultured in the liquid medium containing half fresh medium with 13C-labeled glucose as carbon source and half co-cultured supernatants collected on day 10. 13C-labeled metabolome analyzed by LC-MS revealed that 31 induced features including 3-phenyllactic acid and orsellinic acid were isotopically labeled in the mono-culture after the co-culture stimulation. Twenty features were derived from T. versicolor, 6 from G. applanatum, and 5 features were synthesized by both T. versicolor and G. applanatum. 13C-labeling further suggested that 12 features such as previously identified novel xyloside [N-(4-methoxyphenyl)formamide 2-O-beta-D-xyloside] were likely induced through the direct physical interaction of mycelia. Use of molecular network analysis combined with 13C-labeling provided an insight into the link between the generation of structural analogs and producing fungus. Compound 1 with m/z 309.0757, increased 15.4-fold in the co-culture and observed 13C incorporation in the mono-culture of both T. versicolor and G. applanatum, was purified and identified as a phenyl polyketide, 2,5,6-trihydroxy-4, 6-diphenylcyclohex-4-ene-1,3-dione. The biological activity study indicated that this compound has a potential to inhibit cell viability of leukemic cell line U937. The current work sets an important basis for further investigations including novel metabolites discovery and biosynthetic capacity improvement.
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Affiliation(s)
- Xiao-Yan Xu
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, School of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Xiao-Ting Shen
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, School of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Xiao-Jie Yuan
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, School of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Yuan-Ming Zhou
- Central Laboratory, Qingdao Agricultural University, Qingdao, China
| | - Huan Fan
- Tianjin Animal Science and Veterinary Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Li-Ping Zhu
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, School of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Feng-Yu Du
- School of Chemistry and Pharmacy, Qingdao Agricultural University, Qingdao, China
| | - Martin Sadilek
- Department of Chemistry, University of Washington, Seattle, WA, United States
| | - Jie Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Bin Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Song Yang
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, School of Life Science, Qingdao Agricultural University, Qingdao, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
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29
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Gilchrist CLM, Li H, Chooi YH. Panning for gold in mould: can we increase the odds for fungal genome mining? Org Biomol Chem 2018; 16:1620-1626. [DOI: 10.1039/c7ob03127k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A perspective on existing and emerging strategies for the prioritisation of secondary metabolite biosynthetic gene clusters (BGCs) to increase the odds of fruitful mining of fungal genomes.
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Affiliation(s)
| | - Hang Li
- School of Molecular Sciences
- The University of Western Australia
- Perth
- Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences
- The University of Western Australia
- Perth
- Australia
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Making Use of Genomic Information to Explore the Biotechnological Potential of Medicinal Mushrooms. MEDICINAL AND AROMATIC PLANTS OF THE WORLD 2017. [DOI: 10.1007/978-981-10-5978-0_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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