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Ayon NJ, Earp CE, Gupta R, Butun FA, Clements AE, Lee AG, Dainko D, Robey MT, Khin M, Mardiana L, Longcake A, Rangel-Grimaldo M, Hall MJ, Probert MR, Burdette JE, Keller NP, Raja HA, Oberlies NH, Kelleher NL, Caesar LK. Bioactivity-driven fungal metabologenomics identifies antiproliferative stemphone analogs and their biosynthetic gene cluster. Metabolomics 2024; 20:90. [PMID: 39095664 PMCID: PMC11296971 DOI: 10.1007/s11306-024-02153-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 07/16/2024] [Indexed: 08/04/2024]
Abstract
INTRODUCTION Fungi biosynthesize chemically diverse secondary metabolites with a wide range of biological activities. Natural product scientists have increasingly turned towards bioinformatics approaches, combining metabolomics and genomics to target secondary metabolites and their biosynthetic machinery. We recently applied an integrated metabologenomics workflow to 110 fungi and identified more than 230 high-confidence linkages between metabolites and their biosynthetic pathways. OBJECTIVES To prioritize the discovery of bioactive natural products and their biosynthetic pathways from these hundreds of high-confidence linkages, we developed a bioactivity-driven metabologenomics workflow combining quantitative chemical information, antiproliferative bioactivity data, and genome sequences. METHODS The 110 fungi from our metabologenomics study were tested against multiple cancer cell lines to identify which strains produced antiproliferative natural products. Three strains were selected for further study, fractionated using flash chromatography, and subjected to an additional round of bioactivity testing and mass spectral analysis. Data were overlaid using biochemometrics analysis to predict active constituents early in the fractionation process following which their biosynthetic pathways were identified using metabologenomics. RESULTS We isolated three new-to-nature stemphone analogs, 19-acetylstemphones G (1), B (2) and E (3), that demonstrated antiproliferative activity ranging from 3 to 5 µM against human melanoma (MDA-MB-435) and ovarian cancer (OVACR3) cells. We proposed a rational biosynthetic pathway for these compounds, highlighting the potential of using bioactivity as a filter for the analysis of integrated-Omics datasets. CONCLUSIONS This work demonstrates how the incorporation of biochemometrics as a third dimension into the metabologenomics workflow can identify bioactive metabolites and link them to their biosynthetic machinery.
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Affiliation(s)
- Navid J Ayon
- Department of Chemistry, Northwestern University, Evanston, IL, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Cody E Earp
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Raveena Gupta
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Fatma A Butun
- Department of Chemistry, Northwestern University, Evanston, IL, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Ashley E Clements
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA, USA
| | - Alexa G Lee
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA, USA
| | - David Dainko
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Matthew T Robey
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Manead Khin
- College of Pharmacy-Pharmaceutical Science, University of Illinois Chicago, Chicago, IL, USA
| | - Lina Mardiana
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
- Department of Chemistry, Universitas Indonesia, Depok, Jawa Barat, Indonesia
- Indicatrix Crystallography, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Alexandra Longcake
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Manuel Rangel-Grimaldo
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Michael J Hall
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Michael R Probert
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Joanna E Burdette
- College of Pharmacy-Pharmaceutical Science, University of Illinois Chicago, Chicago, IL, 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
| | - 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
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, IL, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Lindsay K Caesar
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA, USA.
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Khalkho JP, Beck A, Priyanka, Panda B, Chandra R. Microbial allies: exploring fungal endophytes for biosynthesis of terpenoid indole alkaloids. Arch Microbiol 2024; 206:340. [PMID: 38960981 DOI: 10.1007/s00203-024-04067-4] [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: 01/30/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/05/2024]
Abstract
Terpenoid indole alkaloids (TIAs) are natural compounds found in medicinal plants that exhibit various therapeutic activities, such as antimicrobial, anti-inflammatory, antioxidant, anti-diabetic, anti-helminthic, and anti-tumor properties. However, the production of these alkaloids in plants is limited, and there is a high demand for them due to the increasing incidence of cancer cases. To address this research gap, researchers have focused on optimizing culture media, eliciting metabolic pathways, overexpressing genes, and searching for potential sources of TIAs in organisms other than plants. The insufficient number of essential genes and enzymes in the biosynthesis pathway is the reason behind the limited production of TIAs. As the field of natural product discovery from biological species continues to grow, endophytes are being investigated more and more as potential sources of bioactive metabolites with a variety of chemical structures. Endophytes are microorganisms (fungi, bacteria, archaea, and actinomycetes), that exert a significant influence on the metabolic pathways of both the host plants and the endophytic cells. Bio-prospection of fungal endophytes has shown the discovery of novel, high-value bioactive compounds of commercial significance. The discovery of therapeutically significant secondary metabolites has been made easier by endophytic entities' abundant but understudied diversity. It has been observed that fungal endophytes have better intermediate processing ability due to cellular compartmentation. This paper focuses on fungal endophytes and their metabolic ability to produce complex TIAs, recent advancements in this area, and addressing the limitations and future perspectives related to TIA production.
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Affiliation(s)
- Jaya Prabha Khalkho
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Abhishek Beck
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Priyanka
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Banishree Panda
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Ramesh Chandra
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India.
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Steinert K, Atanasoff-Kardjalieff AK, Messner E, Gorfer M, Niehaus EM, Humpf HU, Studt-Reinhold L, Kalinina SA. Tools to make Stachybotrys chartarum genetically amendable: Key to unlocking cryptic biosynthetic gene clusters. Fungal Genet Biol 2024; 172:103892. [PMID: 38636782 DOI: 10.1016/j.fgb.2024.103892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 04/12/2024] [Accepted: 04/13/2024] [Indexed: 04/20/2024]
Abstract
The soil and indoor fungus Stachybotrys chartarum can induce respiratory disorders, collectively referred to as stachybotryotoxicosis, owing to its prolific production of diverse bioactive secondary metabolites (SMs) or mycotoxins. Although many of these toxins responsible for the harmful effects on animals and humans have been identified in the genus Stachybotrys, however a number of SMs remain elusive. Through in silico analyses, we have identified 37 polyketide synthase (PKS) genes, highlighting that the chemical profile potential of Stachybotrys is far from being fully explored. Additionally, by leveraging phylogenetic analysis of known SMs produced by non-reducing polyketide synthases (NR-PKS) in other filamentous fungi, we showed that Stachybotrys possesses a rich reservoir of untapped SMs. To unravel natural product biosynthesis in S. chartarum, genetic engineering methods are crucial. For this purpose, we have developed a reliable protocol for the genetic transformation of S. chartarum and applied it to the ScPKS14 biosynthetic gene cluster. This cluster is homologous to the already known Claviceps purpurea CpPKS8 BGC, responsible for the production of ergochromes. While no novel SMs were detected, we successfully applied genetic tools, such as the generation of deletionand overexpression strains of single cluster genes. This toolbox can now be readily employed to unravel not only this particular BGC but also other candidate BGCs present in S. chartarum, making this fungus accessible for genetic engineering.
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Affiliation(s)
| | - Anna K Atanasoff-Kardjalieff
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau, Austria
| | - Elias Messner
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau, Austria
| | - Markus Gorfer
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Eva-Maria Niehaus
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | - Lena Studt-Reinhold
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau, Austria.
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Guo Y, Liu JZ, Limwachiranon J, Xu F, Han Y, Xu L, Xiong Z, Zhang N, Ding G, Scharf DH. Reconstitution of the Early Stage of Chetomin Biosynthesis in Aspergillus fumigatus Leads to the Production of Epipolythiodioxopiperazines. Org Lett 2024; 26:4469-4474. [PMID: 38767929 DOI: 10.1021/acs.orglett.4c01274] [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: 05/22/2024]
Abstract
Using CRISPR-Cas9 technology and a microhomology-mediated end-joining repair system, we substituted genes of the gliotoxin pathway in Aspergillus fumigatus with genes responsible for chetomin biosynthesis from Chaetomium cochliodes, leading to the production of three new epipolythiodioxopiperazines (ETPs). This work represents the first successful endeavor to produce ETPs in a non-native host. Additionally, the simultaneous disruption of five genes in a single transformation marks the most extensive gene knockout event in filamentous fungi to date.
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Affiliation(s)
- Yaojie Guo
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, People's Republic of China
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310052, People's Republic of China
| | - Jian-Zi Liu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, People's Republic of China
| | - Jarukitt Limwachiranon
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Fan Xu
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Yi Han
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Liru Xu
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Zhenzhen Xiong
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Nan Zhang
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Gang Ding
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, People's Republic of China
| | - Daniel H Scharf
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, People's Republic of China
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang 322000, People's Republic of China
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Ning Y, Gu Q, Zheng T, Xu Y, Li S, Zhu Y, Hu B, Yu H, Liu X, Zhang Y, Jiao B, Lu X. Genome Mining Leads to Diverse Sesquiterpenes with Anti-inflammatory Activity from an Arctic-Derived Fungus. JOURNAL OF NATURAL PRODUCTS 2024; 87:1426-1440. [PMID: 38690764 DOI: 10.1021/acs.jnatprod.4c00237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
With the advancement of bioinformatics, the integration of genome mining with efficient separation technology enables the discovery of a greater number of novel bioactive compounds. The deletion of the key gene responsible for triterpene cyclase biosynthesis in the polar strain Eutypella sp. D-1 instigated metabolic shunting, resulting in the activation of dormant genes and the subsequent production of detectable, new compounds. Fifteen sesquiterpenes were isolated from the mutant strain, with eight being new compounds. The structural elucidation of these compounds was obtained through a combination of HRESIMS, NMR spectroscopy, and ECD calculations, revealing six distinct skeleton types. Compound 7 possessed a unique skeleton of 5/10 macrocyclic ether structure. Based on the gene functions and newly acquired secondary metabolites, the metabolic shunting pathway in the mutant strain was inferred. Compounds 6, 8, 11, 14, and 15 exhibited anti-inflammatory effects without cytotoxicity through the release of nitric oxide from lipopolysaccharide-stimulated RAW264.7 cells. Notably, acorane-type sesquiterpene 8 inhibited nitric oxide production and modulated the MAPK and NLRP3/caspase-1 signaling pathways. Compound 8 also alleviated the CuSO4-induced systemic neurological inflammation symptoms in a transgenic fluorescent zebrafish model.
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Affiliation(s)
- Yaodong Ning
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, People's Republic of China
| | - Qinwufeng Gu
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of Naval Medical University, Shanghai 200433, People's Republic of China
| | - Te Zheng
- Biology Institute, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250000, People's Republic of China
| | - Yao Xu
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, People's Republic of China
| | - Song Li
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, People's Republic of China
| | - Yuping Zhu
- College of Basic Medical Sciences, Experimental Teacher Center, Naval Medical University, Shanghai 200433, People's Republic of China
| | - Bo Hu
- Department of Marine Biomedicine and Polar Medicine, Naval Medical Center of PLA, Naval Medical University, Shanghai 200433, People's Republic of China
| | - Haobing Yu
- Department of Marine Biomedicine and Polar Medicine, Naval Medical Center of PLA, Naval Medical University, Shanghai 200433, People's Republic of China
| | - Xiaoyu Liu
- Department of Marine Biomedicine and Polar Medicine, Naval Medical Center of PLA, Naval Medical University, Shanghai 200433, People's Republic of China
| | - Yun Zhang
- Biology Institute, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250000, People's Republic of China
| | - Binghua Jiao
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, People's Republic of China
| | - Xiaoling Lu
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, People's Republic of China
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Bejenari M, Spedtsberg EML, Mathiesen J, Jeppesen AC, Cernat L, Toussaint A, Apostol C, Stoianov V, Pedersen TB, Nielsen MR, Sørensen JL. First-class - biosynthesis of 6-MSA and bostrycoidin type I polyketides in Yarrowia lipolytica. FRONTIERS IN FUNGAL BIOLOGY 2024; 5:1327777. [PMID: 38586602 PMCID: PMC10995274 DOI: 10.3389/ffunb.2024.1327777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/09/2024] [Indexed: 04/09/2024]
Abstract
Fungal polyketides are a large group of secondary metabolites, valuable due to their diverse spectrum of pharmacological activities. Polyketide biosynthesis in filamentous fungi presents some challenges: small yield and low-purity titers. To tackle these issues, we switched to the yeast Yarrowia lipolytica, an easily cultivable heterologous host. As an oleaginous yeast, Y. lipolytica displays a high flux of acetyl- and malonyl-CoA precursors used in lipid synthesis. Likewise, acetyl- and malonyl-CoA are the building blocks of many natural polyketides, and we explored the possibility of redirecting this flux toward polyketide production. Despite its promising prospect, Y. lipolytica has so far only been used for heterologous expression of simple type III polyketide synthases (PKSs) from plants. Therefore, we decided to evaluate the potential of Y. lipolytica by targeting the more complex fungal polyketides synthesized by type I PKSs. We employed a CRISPR-Cas9-mediated genome editing method to achieve markerless gene integration of the genes responsible for bostrycoidin biosynthesis in Fusarium solani (fsr1, fsr2, and fsr3) and 6-methylsalicylic acid (6-MSA) biosynthesis in Aspergillus hancockii (6MSAS). Moreover, we attempted titer optimization through metabolic engineering by overexpressing two enzymes, TGL4 and AOX2, involved in lipid β-oxidation, but we did not observe an effect on polyketide production. With maximum titers of 403 mg/L 6-MSA and 35 mg/L bostrycoidin, the latter being substantially higher than our previous results in Saccharomyces cerevisiae (2.2 mg/L), this work demonstrates the potential of Y. lipolytica as a platform for heterologous production of complex fungal polyketides.
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Affiliation(s)
- Mihaela Bejenari
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | - Eva Mie Lang Spedtsberg
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
- Department of Energy, Aalborg University, Esbjerg, Denmark
| | - Julie Mathiesen
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | | | - Lucia Cernat
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | - Aouregane Toussaint
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire Végétale, CEA, CNRS, INRA, IRIG-LPCV, Grenoble, France
| | - Cristina Apostol
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | - Victor Stoianov
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | | | - Mikkel Rank Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
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Li SS, Qu SL, Xie J, Li D, Zhao PJ. Secondary metabolites and their bioactivities from Paecilomyces gunnii YMF1.00003. Front Microbiol 2024; 15:1347601. [PMID: 38444802 PMCID: PMC10913189 DOI: 10.3389/fmicb.2024.1347601] [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: 12/01/2023] [Accepted: 02/01/2024] [Indexed: 03/07/2024] Open
Abstract
Four new polyketides (1-4) and seven known compounds (5-11) including three polyketides and four sterols were isolated from the fermented extracts of Paecilomyces gunnii YMF1.00003. The new chemical structures were determined through the analysis of the nuclear magnetic resonance and high-resolution electrospray ionization mass spectrometry, and their configurations were subsequently confirmed by nuclear overhauser effect spectroscopy, the calculated electronic circular dichroism (ECD) spectra, and quantum chemical calculations of the NMR data (qcc NMR). Based on the results of pre-activity screening and compound structure target prediction, certain metabolites were assayed to evaluate their cytotoxic and protein kinase Cα inhibitory activities. Results indicated that 3β-hydroxy-7α-methoxy-5α,6α-epoxy-8(14),22E-dien-ergosta (8) exhibited potent cytotoxic activity, with half-maximal inhibitory concentration values of 3.00 ± 0.27 to 15.69 ± 0.61 μM against five tumor cells, respectively. The new compound gunniiol A (1) showed weak cytotoxic activity at a concentration of 40 μM. At a concentration of 20 μg/mL, compounds 1, 6, and 7 exhibited protein kinase Cα inhibition by 43.63, 40.93, and 57.66%, respectively. This study is the first to report steroids demonstrating good cytotoxicity and polyketides exhibiting inhibitory activity against protein kinase Cα from the extracts of P. gunnii.
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Affiliation(s)
- Su-Su Li
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
- The Maternal and Child Health Hospital of Qianxinan, Xingyi, Guizhou, China
| | - Shuai-Ling Qu
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Juan Xie
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Dong Li
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Pei-Ji Zhao
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
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Zhang X, Guo R, Bi F, Chen Y, Xue X, Wang D. Overexpression of kojR and the entire koj gene cluster affect the kojic acid synthesis in Aspergillus oryzae 3.042. Gene 2024; 892:147852. [PMID: 37776988 DOI: 10.1016/j.gene.2023.147852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/07/2023] [Accepted: 09/27/2023] [Indexed: 10/02/2023]
Abstract
Kojic acid (KA), a fungal secondary metabolite, has various applications in the cosmetics, pharmaceutical, and food industries. Aspergillus oryzae, the primary strain, has been identified as a koj gene cluster positively responsible for KA biosynthesis. In this study, we obtained transformants T58 and T31, which overexpressed either solo kojR or the entire koj gene cluster, respectively. These transformants exhibited peak KA production on the 5th day of shake flask fermentation, with 32.5 g/L and 26.57 g/L that 324.28 % and 246.87 % higher than the control strain with 7.64 g/L, respectively. Morphological analysis revealed that the highly productive KA strains had reduced conidial production but increased antioxidant capacity. The qRT-PCR analysis revealed that relative expression levels of kojR in the transformants were remarkably higher that the primary cause for the increased KA yield. Moreover, the high expression of kojR could also influence the expression of the key enzymes involved in the KA biosynthesis process, such as glucose dehydrogenase and gluconate dehydrogenase. These findings can assist in discovering more about how the koj gene cluster in A. oryzae influences its growth and KA production. And provides valuable insights into facilitating strain improvement and benefits for the future.
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Affiliation(s)
- Xuemei Zhang
- Key Laboratory of Industrial Microbiology & Engineering Research Center of Food Biotechnology of Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Rui Guo
- Key Laboratory of Industrial Microbiology & Engineering Research Center of Food Biotechnology of Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Futi Bi
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China.
| | - Yue Chen
- Key Laboratory of Industrial Microbiology & Engineering Research Center of Food Biotechnology of Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Xianli Xue
- Key Laboratory of Industrial Microbiology & Engineering Research Center of Food Biotechnology of Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; Tianjin Key Laboratory of Industrial Fermentation Microbiology, Tianjin 300457, China.
| | - Depei Wang
- Key Laboratory of Industrial Microbiology & Engineering Research Center of Food Biotechnology of Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; Tianjin Key Laboratory of Industrial Fermentation Microbiology, Tianjin 300457, China.
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Wang J, Liu M, Mao C, Li S, Zhou J, Fan Y, Guo L, Yu H, Yang X. Comparative proteomics reveals the mechanism of cyclosporine production and mycelial growth in Tolypocladium inflatum affected by different carbon sources. Front Microbiol 2023; 14:1259101. [PMID: 38163081 PMCID: PMC10757567 DOI: 10.3389/fmicb.2023.1259101] [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: 07/15/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024] Open
Abstract
Cyclosporine A (CsA) is a secondary cyclopeptide metabolite produced by Tolypocladium inflatum that is widely used clinically as an immunosuppressant. CsA production and mycelial growth differed when T. inflatum was cultured in different carbon source media. During early fermentation, CsA was preferred to be produced in fructose medium, while the mycelium preferred to accumulate in sucrose medium. On the sixth day, the difference was most pronounced. In this study, high-throughput comparative proteomics methods were applied to analyze differences in protein expression of mycelial samples on day 6, revealing the proteins and mechanisms that positively regulate CsA production related to carbon metabolism. The differences included small molecule acid metabolism, lipid metabolism, organic catabolism, exocrine secretion, CsA substrate Bmt synthesis, and transcriptional regulation processes. The proteins involved in the regulation of mycelial growth related to carbon metabolism were also revealed and were associated with waste reoxidation processes or coenzyme metabolism, small molecule synthesis or metabolism, the stress response, genetic information or epigenetic changes, cell component assembly, cell wall integrity, membrane metabolism, vesicle transport, intramembrane localization, and the regulation of filamentous growth. This study provides a reliable reference for CsA production from high-efficiency fermentation. This study provides key information for obtaining more CsA high-yielding strains through metabolic engineering strategies.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xiuqing Yang
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong Province, China
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Kirk A, Stavrinides J. A replica plating method for efficient, high-throughput screening of antibiotic gene clusters in bacteria uncovers a holomycin-like cluster in the clinical isolate, Pantoea agglomerans 20KB447973. J Microbiol Methods 2023; 213:106822. [PMID: 37708943 DOI: 10.1016/j.mimet.2023.106822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
Bacterial natural products remain a major untapped source for novel antimicrobial scaffolds. Many of these products are encoded by biosynthetic gene clusters (BGCs), which can be identified using functional genomics. We developed a replica-plating approach to quickly screen for antibiotic production mutants from transposon mutant libraries and identify candidate antibiotic BGCs. In this technique, filter paper is used to transfer up to 200 mutants simultaneously onto a soft agar overlay or spread plate containing a target microbe to identify antibiotic-production mutants. These mutants can then be analyzed to identify disrupted genes and antibiotic BGCs. We first tested and optimized this technique by screening for previously characterized BGCs in Pantoea. We then applied the technique to uncover the gene cluster responsible for the production of an unknown broad-spectrum antibiotic from P. agglomerans 20KB447973, which we call Pantoea Natural Product 5 (PNP-5). Analysis of the predicted gene cluster for PNP-5 showed similarity to previously identified gene clusters for the broad-spectrum dithiolopyrrolone antibiotic, holomycin. Analysis of the spectrum of activity of PNP-5 showed activity against members of the Enterobacteriaceae, Erwiniaceae, and Streptococcaceae, including clinically relevant pathogens such as Klebsiella sp. and Escherichia coli. We also identified the production of a second antibiotic, pantocin A. Our findings demonstrate the utility of our replica-plating mutant transfer method in exploring unknown antibiotic BGCs. Adoption of this technique may accelerate the identification of potentially novel antimicrobial BGCs within strain collections, advancing the search for novel antimicrobials that can be used to treat multi-drug resistant infections.
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Affiliation(s)
- Ashlyn Kirk
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, Saskatchewan S4S 0A2, Canada
| | - John Stavrinides
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, Saskatchewan S4S 0A2, Canada.
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Kiss A, Hariri Akbari F, Marchev A, Papp V, Mirmazloum I. The Cytotoxic Properties of Extreme Fungi's Bioactive Components-An Updated Metabolic and Omics Overview. Life (Basel) 2023; 13:1623. [PMID: 37629481 PMCID: PMC10455657 DOI: 10.3390/life13081623] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 08/27/2023] Open
Abstract
Fungi are the most diverse living organisms on planet Earth, where their ubiquitous presence in various ecosystems offers vast potential for the research and discovery of new, naturally occurring medicinal products. Concerning human health, cancer remains one of the leading causes of mortality. While extensive research is being conducted on treatments and their efficacy in various stages of cancer, finding cytotoxic drugs that target tumor cells with no/less toxicity toward normal tissue is a significant challenge. In addition, traditional cancer treatments continue to suffer from chemical resistance. Fortunately, the cytotoxic properties of several natural products derived from various microorganisms, including fungi, are now well-established. The current review aims to extract and consolidate the findings of various scientific studies that identified fungi-derived bioactive metabolites with antitumor (anticancer) properties. The antitumor secondary metabolites identified from extremophilic and extremotolerant fungi are grouped according to their biological activity and type. It became evident that the significance of these compounds, with their medicinal properties and their potential application in cancer treatment, is tremendous. Furthermore, the utilization of omics tools, analysis, and genome mining technology to identify the novel metabolites for targeted treatments is discussed. Through this review, we tried to accentuate the invaluable importance of fungi grown in extreme environments and the necessity of innovative research in discovering naturally occurring bioactive compounds for the development of novel cancer treatments.
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Affiliation(s)
- Attila Kiss
- Agro-Food Science Techtransfer and Innovation Centre, Faculty for Agro, Food and Environmental Science, Debrecen University, 4032 Debrecen, Hungary;
| | - Farhad Hariri Akbari
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Andrey Marchev
- Laboratory of Metabolomics, Department of Biotechnology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 4000 Plovdiv, Bulgaria
| | - Viktor Papp
- Department of Botany, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Hungary;
| | - Iman Mirmazloum
- Department of Plant Physiology and Plant Ecology, Institute of Agronomy, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Hungary
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Zhgun AA. Fungal BGCs for Production of Secondary Metabolites: Main Types, Central Roles in Strain Improvement, and Regulation According to the Piano Principle. Int J Mol Sci 2023; 24:11184. [PMID: 37446362 PMCID: PMC10342363 DOI: 10.3390/ijms241311184] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Filamentous fungi are one of the most important producers of secondary metabolites. Some of them can have a toxic effect on the human body, leading to diseases. On the other hand, they are widely used as pharmaceutically significant drugs, such as antibiotics, statins, and immunosuppressants. A single fungus species in response to various signals can produce 100 or more secondary metabolites. Such signaling is possible due to the coordinated regulation of several dozen biosynthetic gene clusters (BGCs), which are mosaically localized in different regions of fungal chromosomes. Their regulation includes several levels, from pathway-specific regulators, whose genes are localized inside BGCs, to global regulators of the cell (taking into account changes in pH, carbon consumption, etc.) and global regulators of secondary metabolism (affecting epigenetic changes driven by velvet family proteins, LaeA, etc.). In addition, various low-molecular-weight substances can have a mediating effect on such regulatory processes. This review is devoted to a critical analysis of the available data on the "turning on" and "off" of the biosynthesis of secondary metabolites in response to signals in filamentous fungi. To describe the ongoing processes, the model of "piano regulation" is proposed, whereby pressing a certain key (signal) leads to the extraction of a certain sound from the "musical instrument of the fungus cell", which is expressed in the production of a specific secondary metabolite.
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Affiliation(s)
- Alexander A Zhgun
- Group of Fungal Genetic Engineering, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky Prosp. 33-2, 119071 Moscow, Russia
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13
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Toppo P, Kagatay LL, Gurung A, Singla P, Chakraborty R, Roy S, Mathur P. Endophytic fungi mediates production of bioactive secondary metabolites via modulation of genes involved in key metabolic pathways and their contribution in different biotechnological sector. 3 Biotech 2023; 13:191. [PMID: 37197561 PMCID: PMC10183385 DOI: 10.1007/s13205-023-03605-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 05/03/2023] [Indexed: 05/19/2023] Open
Abstract
Endophytic fungi stimulate the production of an enormous number of bioactive metabolites in medicinal plants and affect the different steps of biosynthetic pathways of these secondary metabolites. Endophytic fungi possess a number of biosynthetic gene clusters that possess genes for various enzymes, transcription factors, etc., in their genome responsible for the production of secondary metabolites. Additionally, endophytic fungi also modulate the expression of various genes responsible for the synthesis of key enzymes involved in metabolic pathways of such as HMGR, DXR, etc. involved in the production of a large number of phenolic compounds as well as regulate the expression of genes involved in the production of alkaloids and terpenoids in different plants. This review aims to provide a comprehensive overview of gene expression related to endophytes and their impact on metabolic pathways. Additionally, this review will emphasize the studies done to isolate these secondary metabolites from endophytic fungi in large quantities and assess their bioactivity. Due to ease in synthesis of secondary metabolites and their huge application in the medical industry, these bioactive metabolites are now being extracted from strains of these endophytic fungi commercially. Apart from their application in the pharmaceutical industry, most of these metabolites extracted from endophytic fungi also possess plant growth-promoting ability, bioremediation potential, novel bio control agents, sources of anti-oxidants, etc. The review will comprehensively shed a light on the biotechnological application of these fungal metabolites at the industrial level.
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Affiliation(s)
- Prabha Toppo
- Microbiology Laboratory, Department of Botany, University of North Bengal, Rajarammohunpur, Dist. Darjeeling, Siliguri, West Bengal India
| | - Lahasang Lamu Kagatay
- Microbiology Laboratory, Department of Botany, University of North Bengal, Rajarammohunpur, Dist. Darjeeling, Siliguri, West Bengal India
| | - Ankita Gurung
- Microbiology Laboratory, Department of Botany, University of North Bengal, Rajarammohunpur, Dist. Darjeeling, Siliguri, West Bengal India
| | - Priyanka Singla
- Department of Botany, Mount Carmel College, Bengaluru, Karnataka India
| | - Rakhi Chakraborty
- Department of Botany, Acharya Prafulla Chandra Roy Government College, Dist. Darjeeling, Siliguri, West Bengal India
| | - Swarnendu Roy
- Plant Biochemistry Laboratory, Department of Botany, University of North Bengal, Rajarammohunpur, Dist. Darjeeling, Siliguri, West Bengal India
| | - Piyush Mathur
- Microbiology Laboratory, Department of Botany, University of North Bengal, Rajarammohunpur, Dist. Darjeeling, Siliguri, West Bengal India
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14
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Makhwitine JP, Kumalo HM, Ndlovu SI, Mkhwanazi NP. Epigenetic Induction of Secondary Metabolites Production in Endophytic Fungi Penicillium chrysogenum and GC-MS Analysis of Crude Metabolites with Anti-HIV-1 Activity. Microorganisms 2023; 11:1404. [PMID: 37374906 DOI: 10.3390/microorganisms11061404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
The continuous burden of human immunodeficiency virus-1 in Sub-Saharan Africa, coupled with the inability of antiretroviral agents to eradicate HIV-1 from viral reservoirs, the potential risks of drug resistance development, and the development of adverse effects, emphasizes the need to develop a new class of HIV-1 inhibitors. Here, we cultivated four endophytic fungal isolates from a medicinal plant, Albizia adianthifolia with the addition of small epigenetic modifiers, sodium butyrate, and valproic acid, to induce the expression of biosynthetic gene clusters encoding active secondary metabolites with probable anti-HIV activities. We identified a non-toxic crude extract of the endophytic fungus Penicillium chrysogenum treated with sodium butyrate to possess significantly greater anti-HIV activity than the untreated extracts. Penicillium chrysogenum P03MB2 showed anti-HIV activity with an IC50 of 0.6024 µg/mL compared to untreated fungal crude extract (IC50 5.053 µg/mL) when treated with sodium butyrate. The profile of secondary metabolite compounds from the bioactive, partially purified extracts were identified by gas chromatography-mass spectrometry (GC-MS), and more bioactive compounds were detected in treated P. chrysogenum P03MB2 fractions than in untreated fractions. Pyrrolo[1,2-a]pyrazine-1,4-dione, hexahydro (13.64%), cyclotrisiloxane, hexamethyl (8.18%), cyclotetrasiloxane, octamethyl (7.23%), cyclopentasiloxane, decamethyl (6.36%), quinoline, 1,2-dihydro-2,24-trimethyl (5.45%), propanenitrile (4.55%), deca-6,9-diene (4.55%), dibutyl phthalate (4.55%), and silane[1,1-dimethyl-2-propenyl)oxy]dimethyl (2.73%) were the most abundant compounds. These results indicate that treatment of endophytic fungi with small epigenetic modifiers enhances the secretion of secondary metabolites with stronger anti-HIV-1 properties, acknowledging the feasibility of epigenetic modification as an innovative approach for the discovery of cryptic fungal metabolites which can be developed into therapeutic compounds.
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Affiliation(s)
- John P Makhwitine
- Discipline of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Hezekiel M Kumalo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Sizwe I Ndlovu
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Johannesburg 2028, South Africa
| | - Nompumelelo P Mkhwanazi
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
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15
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Chávez R, Vaca I, García-Estrada C. Secondary Metabolites Produced by the Blue-Cheese Ripening Mold Penicillium roqueforti; Biosynthesis and Regulation Mechanisms. J Fungi (Basel) 2023; 9:jof9040459. [PMID: 37108913 PMCID: PMC10144355 DOI: 10.3390/jof9040459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/29/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Filamentous fungi are an important source of natural products. The mold Penicillium roqueforti, which is well-known for being responsible for the characteristic texture, blue-green spots, and aroma of the so-called blue-veined cheeses (French Bleu, Roquefort, Gorgonzola, Stilton, Cabrales, and Valdeón, among others), is able to synthesize different secondary metabolites, including andrastins and mycophenolic acid, as well as several mycotoxins, such as Roquefortines C and D, PR-toxin and eremofortins, Isofumigaclavines A and B, festuclavine, and Annullatins D and F. This review provides a detailed description of the biosynthetic gene clusters and pathways of the main secondary metabolites produced by P. roqueforti, as well as an overview of the regulatory mechanisms controlling secondary metabolism in this filamentous fungus.
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Affiliation(s)
- Renato Chávez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile
| | - Inmaculada Vaca
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Carlos García-Estrada
- Departamento de Ciencias Biomédicas, Facultad de Veterinaria, Campus de Vegazana, Universidad de León, 24071 León, Spain
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16
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Alanzi A, Elhawary EA, Ashour ML, Moussa AY. Aspergillus co-cultures: A recent insight into their secondary metabolites and microbial interactions. Arch Pharm Res 2023; 46:273-298. [PMID: 37032397 DOI: 10.1007/s12272-023-01442-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 02/28/2023] [Indexed: 04/11/2023]
Abstract
There is an urgent need for novel antibiotics to combat emerging resistant microbial strains. One of the most pressing resources is Aspergillus microbial cocultures. The genome of Aspergillus species comprises a far larger number of novel gene clusters than previously expected, and novel strategies and approaches are essential to exploit this potential source of new drugs and pharmacological agents. This is the first review consulting recent developments and chemical diversity of Aspergillus cocultures and highlighting its untapped richness. The analyzed data revealed that cocultivation of several Aspergillus species with other microorganisms, including bacteria, plants, and fungi, is a source of novel bioactive natural products. Various vital chemical skeleton leads were newly produced or augmented in Aspergillus cocultures, among which were taxol, cytochalasans, notamides, pentapeptides, silibinin, and allianthrones. The possibility of mycotoxin production or complete elimination in cocultivations was detected, which pave the way for better decontamination strategies. Most cocultures revealed a remarkable improvement in their antimicrobial or cytotoxic behavior due to their produced chemical patterns; for instance, weldone and asperterrin whose antitumor and antibacterial activities, respectively, were superior. Microbial cocultivation elicited the upregulation or production of specific metabolites whose importance and significance are yet to be revealed. With more than 155 compounds isolated from Aspergillus cocultures in the last 10 years, showing overproduction, reduction, or complete suppression under the optimized coculture circumstances, this study filled a gap for medicinal chemists searching for new lead sources or bioactive molecules as anticancer agents or antimicrobials.
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Affiliation(s)
- Abdullah Alanzi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Esraa A Elhawary
- Department of Pharmacognosy, Faculty of Pharmacy, Ain shams University, Cairo, 11566, Egypt
| | - Mohamed L Ashour
- Department of Pharmacognosy, Faculty of Pharmacy, Ain shams University, Cairo, 11566, Egypt
- Pharmacy Program, Department of Pharmaceutical Science, Batterjee Medical College, 21442, Jeddah, Saudi Arabia
| | - Ashaimaa Y Moussa
- Department of Pharmacognosy, Faculty of Pharmacy, Ain shams University, Cairo, 11566, Egypt.
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17
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Advances and Challenges in CRISPR/Cas-Based Fungal Genome Engineering for Secondary Metabolite Production: A Review. J Fungi (Basel) 2023; 9:jof9030362. [PMID: 36983530 PMCID: PMC10058990 DOI: 10.3390/jof9030362] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/10/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
Fungi represent an important source of bioactive secondary metabolites (SMs), which have wide applications in many fields, including medicine, agriculture, human health, and many other industries. The genes involved in SM biosynthesis are usually clustered adjacent to each other into a region known as a biosynthetic gene cluster (BGC). The recent advent of a diversity of genetic and genomic technologies has facilitated the identification of many cryptic or uncharacterized BGCs and their associated SMs. However, there are still many challenges that hamper the broader exploration of industrially important secondary metabolites. The recent advanced CRISPR/Cas system has revolutionized fungal genetic engineering and enabled the discovery of novel bioactive compounds. In this review, we firstly introduce fungal BGCs and their relationships with associated SMs, followed by a brief summary of the conventional strategies for fungal genetic engineering. Next, we introduce a range of state-of-the-art CRISPR/Cas-based tools that have been developed and review recent applications of these methods in fungi for research on the biosynthesis of SMs. Finally, the challenges and limitations of these CRISPR/Cas-based systems are discussed and directions for future research are proposed in order to expand their applications and improve efficiency for fungal genetic engineering.
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18
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Jenkinson CB, Podgorny AR, Zhong C, Oakley BR. Computer-aided, resistance gene-guided genome mining for proteasome and HMG-CoA reductase inhibitors. J Ind Microbiol Biotechnol 2023; 50:kuad045. [PMID: 38061800 PMCID: PMC10734572 DOI: 10.1093/jimb/kuad045] [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: 06/09/2023] [Accepted: 12/06/2023] [Indexed: 12/22/2023]
Abstract
Secondary metabolites (SMs) are biologically active small molecules, many of which are medically valuable. Fungal genomes contain vast numbers of SM biosynthetic gene clusters (BGCs) with unknown products, suggesting that huge numbers of valuable SMs remain to be discovered. It is challenging, however, to identify SM BGCs, among the millions present in fungi, that produce useful compounds. One solution is resistance gene-guided genome mining, which takes advantage of the fact that some BGCs contain a gene encoding a resistant version of the protein targeted by the compound produced by the BGC. The bioinformatic signature of such BGCs is that they contain an allele of an essential gene with no SM biosynthetic function, and there is a second allele elsewhere in the genome. We have developed a computer-assisted approach to resistance gene-guided genome mining that allows users to query large databases for BGCs that putatively make compounds that have targets of therapeutic interest. Working with the MycoCosm genome database, we have applied this approach to look for SM BGCs that target the proteasome β6 subunit, the target of the proteasome inhibitor fellutamide B, or HMG-CoA reductase, the target of cholesterol reducing therapeutics such as lovastatin. Our approach proved effective, finding known fellutamide and lovastatin BGCs as well as fellutamide- and lovastatin-related BGCs with variations in the SM genes that suggest they may produce structural variants of fellutamides and lovastatin. Gratifyingly, we also found BGCs that are not closely related to lovastatin BGCs but putatively produce novel HMG-CoA reductase inhibitors. ONE-SENTENCE SUMMARY A new computer-assisted approach to resistance gene-directed genome mining is reported along with its use to identify fungal biosynthetic gene clusters that putatively produce proteasome and HMG-CoA reductase inhibitors.
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Affiliation(s)
- Cory B Jenkinson
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045,USA
| | - Adam R Podgorny
- Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS 66045,USA
| | - Cuncong Zhong
- Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS 66045,USA
| | - Berl R Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045,USA
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Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability. Mater Today Bio 2023; 19:100560. [PMID: 36756210 PMCID: PMC9900623 DOI: 10.1016/j.mtbio.2023.100560] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/22/2023] Open
Abstract
Filamentous fungi drive carbon and nutrient cycling across our global ecosystems, through its interactions with growing and decaying flora and their constituent microbiomes. The remarkable metabolic diversity, secretion ability, and fiber-like mycelial structure that have evolved in filamentous fungi have been increasingly exploited in commercial operations. The industrial potential of mycelial fermentation ranges from the discovery and bioproduction of enzymes and bioactive compounds, the decarbonization of food and material production, to environmental remediation and enhanced agricultural production. Despite its fundamental impact in ecology and biotechnology, molds and mushrooms have not, to-date, significantly intersected with synthetic biology in ways comparable to other industrial cell factories (e.g. Escherichia coli,Saccharomyces cerevisiae, and Komagataella phaffii). In this review, we summarize a suite of synthetic biology and computational tools for the mining, engineering and optimization of filamentous fungi as a bioproduction chassis. A combination of methods across genetic engineering, mutagenesis, experimental evolution, and computational modeling can be used to address strain development bottlenecks in established and emerging industries. These include slow mycelium growth rate, low production yields, non-optimal growth in alternative feedstocks, and difficulties in downstream purification. In the scope of biomanufacturing, we then detail previous efforts in improving key bottlenecks by targeting protein processing and secretion pathways, hyphae morphogenesis, and transcriptional control. Bringing synthetic biology practices into the hidden world of molds and mushrooms will serve to expand the limited panel of host organisms that allow for commercially-feasible and environmentally-sustainable bioproduction of enzymes, chemicals, therapeutics, foods, and materials of the future.
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de Medeiros LS, de Araújo Júnior MB, Peres EG, da Silva JCI, Bassicheto MC, Di Gioia G, Veiga TAM, Koolen HHF. Discovering New Natural Products Using Metabolomics-Based Approaches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1439:185-224. [PMID: 37843810 DOI: 10.1007/978-3-031-41741-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
The incessant search for new natural molecules with biological activities has forced researchers in the field of chemistry of natural products to seek different approaches for their prospection studies. In particular, researchers around the world are turning to approaches in metabolomics to avoid high rates of re-isolation of certain compounds, something recurrent in this branch of science. Thanks to the development of new technologies in the analytical instrumentation of spectroscopic and spectrometric techniques, as well as the advance in the computational processing modes of the results, metabolomics has been gaining more and more space in studies that involve the prospection of natural products. Thus, this chapter summarizes the precepts and good practices in the metabolomics of microbial natural products using mass spectrometry and nuclear magnetic resonance spectroscopy, and also summarizes several examples where this approach has been applied in the discovery of bioactive molecules.
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Affiliation(s)
- Lívia Soman de Medeiros
- Grupo de Pesquisas LaBiORG - Laboratório de Química Bio-orgânica Otto Richard Gottlieb, Universidade Federal de São Paulo, Diadema, Brazil.
| | - Moysés B de Araújo Júnior
- Grupo de Pesquisa em Metabolômica e Espectrometria de Massas, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Eldrinei G Peres
- Grupo de Pesquisa em Metabolômica e Espectrometria de Massas, Universidade do Estado do Amazonas, Manaus, Brazil
| | | | - Milena Costa Bassicheto
- Grupo de Pesquisas LaBiORG - Laboratório de Química Bio-orgânica Otto Richard Gottlieb, Universidade Federal de São Paulo, Diadema, Brazil
| | - Giordanno Di Gioia
- Grupo de Pesquisas LaBiORG - Laboratório de Química Bio-orgânica Otto Richard Gottlieb, Universidade Federal de São Paulo, Diadema, Brazil
| | - Thiago André Moura Veiga
- Grupo de Pesquisas LaBiORG - Laboratório de Química Bio-orgânica Otto Richard Gottlieb, Universidade Federal de São Paulo, Diadema, Brazil
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21
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Shi X, Sun Y, Liu J, Liu W, Xing Y, Xiu Z, Dong Y. Metabolomic Strategy to Characterize the Profile of Secondary Metabolites in Aspergillus aculeatus DL1011 Regulated by Chemical Epigenetic Agents. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010218. [PMID: 36615412 PMCID: PMC9821969 DOI: 10.3390/molecules28010218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/06/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022]
Abstract
Chemical epigenetic regulation (CER) is an effective method to activate the silent pathway of fungal secondary metabolite synthesis. However, conventional methods for CER study are laborious and time-consuming. In the meantime, the overall profile of the secondary metabolites in the fungi treated by the CER reagent is not well characterized. In this study, suberohydroxamic acid (SBHA), a histone deacetylase inhibitor, was added to a culture of Aspergillus aculeatus DL1011 and a new strategy based on LC-MS/MS analysis integrated with various metabolomic tools (MetaboAnalyst, MS-DIAL, SIRIUS and GNPS) was developed to characterize the profile of induced metabolites. As a result, 13.6%, 29.5% and 27.2% of metabolites were identified as newly biosynthesized, increasing and decreasing in abundance by CER, respectively. The structures of the 18 newly induced secondary metabolites were further identified by the new strategy to demonstrate that 72.2% of them (1 novel compound and 12 known compounds) were first discovered in A. aculeatus upon SBHA treatment. The accuracy of the new approach was confirmed by purification and NMR data analysis of major newly biosynthesized secondary metabolites. The bioassay showed that the newly biosynthesized compounds, roseopurpurin analogues, showed selective activities against DPPH scavenging, cytotoxicity and SHP1 inhibition. Our research demonstrated that CER was beneficial for changing the secondary metabolic profile of fungi and was an effective means of increasing the diversity of active metabolites. Our work also supplied a metabolomic strategy to characterize the profile changes and determine the newly induced compounds in the secondary metabolites of fungi treated with the chemical epigenetic regulator.
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Affiliation(s)
- Xuan Shi
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Yu Sun
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Junhui Liu
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Wencai Liu
- Shandong Provincial Engineering Laboratory of Protein Pharmaceutical, Shandong New Time Pharmaceutical Co., Ltd., Linyi 273400, China
| | - Yan Xing
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Zhilong Xiu
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Yuesheng Dong
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
- Correspondence:
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Complementary Strategies to Unlock Biosynthesis Gene Clusters Encoding Secondary Metabolites in the Filamentous Fungus Podospora anserina. J Fungi (Basel) 2022; 9:jof9010009. [PMID: 36675830 PMCID: PMC9864250 DOI: 10.3390/jof9010009] [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: 11/08/2022] [Revised: 12/09/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
The coprophilous ascomycete Podospora anserina is known to have a high potential to synthesize a wide array of secondary metabolites (SMs). However, to date, the characterization of SMs in this species, as in other filamentous fungal species, is far less than expected by the functional prediction through genome mining, likely due to the inactivity of most SMs biosynthesis gene clusters (BGCs) under standard conditions. In this work, our main objective was to compare the global strategies usually used to deregulate SM gene clusters in P. anserina, including the variation of culture conditions and the modification of the chromatin state either by genetic manipulation or by chemical treatment, and to show the complementarity of the approaches between them. In this way, we showed that the metabolomics-driven comparative analysis unveils the unexpected diversity of metabolic changes in P. anserina and that the integrated strategies have a mutual complementary effect on the expression of the fungal metabolome. Then, our results demonstrate that metabolite production is significantly influenced by varied cultivation states and epigenetic modifications. We believe that the strategy described in this study will facilitate the discovery of fungal metabolites of interest and will improve the ability to prioritize the production of specific fungal SMs with an optimized treatment.
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23
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Almeida H, Tsang A, Diallo AB. Improving candidate Biosynthetic Gene Clusters in fungi through reinforcement learning. Bioinformatics 2022; 38:3984-3991. [PMID: 35762945 PMCID: PMC9364373 DOI: 10.1093/bioinformatics/btac420] [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: 09/02/2021] [Revised: 05/17/2022] [Accepted: 06/23/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Precise identification of Biosynthetic Gene Clusters (BGCs) is a challenging task. Performance of BGC discovery tools is limited by their capacity to accurately predict components belonging to candidate BGCs, often overestimating cluster boundaries. To support optimizing the composition and boundaries of candidate BGCs, we propose reinforcement learning approach relying on protein domains and functional annotations from expert curated BGCs. RESULTS The proposed reinforcement learning method aims to improve candidate BGCs obtained with state-of-the-art tools. It was evaluated on candidate BGCs obtained for two fungal genomes, Aspergillus niger and Aspergillus nidulans. The results highlight an improvement of the gene precision by above 15% for TOUCAN, fungiSMASH and DeepBGC; and cluster precision by above 25% for fungiSMASH and DeepBCG, allowing these tools to obtain almost perfect precision in cluster prediction. This can pave the way of optimizing current prediction of candidate BGCs in fungi, while minimizing the curation effort required by domain experts. AVAILABILITY AND IMPLEMENTATION https://github.com/bioinfoUQAM/RL-bgc-components. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hayda Almeida
- Departement d’Informatique, UQAM, Montréal, QC H2X 3Y7, Canada,Centre for Structural and Functional Genomics, Concordia University, Montréal, QC H4B 1R6, Canada,Laboratoire d’Algèbre, de Combinatoire, et d’Informatique Mathématique (LACIM), UQAM, Montréal, QC H2X 3Y, Canada
| | - Adrian Tsang
- Departement d’Informatique, UQAM, Montréal, QC H2X 3Y7, Canada,Centre for Structural and Functional Genomics, Concordia University, Montréal, QC H4B 1R6, Canada
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24
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Gakuubi MM, Ching KC, Munusamy M, Wibowo M, Liang ZX, Kanagasundaram Y, Ng SB. Enhancing the Discovery of Bioactive Secondary Metabolites From Fungal Endophytes Using Chemical Elicitation and Variation of Fermentation Media. Front Microbiol 2022; 13:898976. [PMID: 35733953 PMCID: PMC9207341 DOI: 10.3389/fmicb.2022.898976] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/05/2022] [Indexed: 11/26/2022] Open
Abstract
Endophytic microorganisms are an important source of bioactive secondary metabolites. In this study, fungal endophytes obtained from A*STAR’s Natural Product Library (NPL) and previously isolated from different habitats of Singapore were investigated for their diversity, antimicrobial, and cytotoxic activities. A total of 222 fungal strains were identified on the basis of sequence analysis of ITS region of the rDNA gene. The identified fungal strains belong to 59 genera distributed in 20 orders. Majority of the identified strains (99%; 219 strains) belong to the phylum Ascomycota, while two strains belonged to the phylum Basidiomycota, and only one strain was from Mucoromycota phylum. The most dominant genus was Colletotrichum accounting for 27% of all the identified strains. Chemical elicitation using 5-azacytidine and suberoylanilide hydroxamic acid (SAHA) and variation of fermentation media resulted in the discovery of more bioactive strains. Bioassay-guided isolation and structure elucidation of active constituents from three prioritized fungal strains: Lophiotrema sp. F6932, Muyocopron laterale F5912, and Colletotrichum tropicicola F10154, led to the isolation of a known compound; palmarumycin C8 and five novel compounds; palmarumycin CP30, muyocopronol A-C and tropicicolide. Tropicicolide displayed the strongest antifungal activity against Aspergillus fumigatus with an IC50 value of 1.8 μg/ml but with a weaker activity against the Candida albicans presenting an IC50 of 7.1 μg/ml. Palmarumycin C8 revealed the best antiproliferative activity with IC50 values of 1.1 and 2.1 μg/ml against MIA PaCa-2 and PANC-1 cells, respectively.
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Affiliation(s)
- Martin Muthee Gakuubi
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kuan Chieh Ching
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Madhaiyan Munusamy
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Mario Wibowo
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yoganathan Kanagasundaram
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- *Correspondence: Siew Bee Ng,
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25
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Courtial J, Helesbeux JJ, Oudart H, Aligon S, Bahut M, Hamon B, N'Guyen G, Pigné S, Hussain AG, Pascouau C, Bataillé-Simoneau N, Collemare J, Berruyer R, Poupard P. Characterization of NRPS and PKS genes involved in the biosynthesis of SMs in Alternaria dauci including the phytotoxic polyketide aldaulactone. Sci Rep 2022; 12:8155. [PMID: 35581239 PMCID: PMC9114375 DOI: 10.1038/s41598-022-11896-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/25/2022] [Indexed: 11/17/2022] Open
Abstract
Alternaria dauci is a Dothideomycete fungus, causal agent of carrot leaf blight. As a member of the Alternaria genus, known to produce a lot of secondary metabolite toxins, A. dauci is also supposed to synthetize host specific and non-host specific toxins playing a crucial role in pathogenicity. This study provides the first reviewing of secondary metabolism genetic basis in the Alternaria genus by prediction of 55 different putative core genes. Interestingly, aldaulactone, a phytotoxic benzenediol lactone from A. dauci, was demonstrated as important in pathogenicity and in carrot partial resistance to this fungus. As nothing is known about aldaulactone biosynthesis, bioinformatic analyses on a publicly available A. dauci genome data set that were reassembled, thanks to a transcriptome data set described here, allowed to identify 19 putative secondary metabolism clusters. We exploited phylogeny to pinpoint cluster 8 as a candidate in aldaulactone biosynthesis. This cluster contains AdPKS7 and AdPKS8, homologs with genes encoding a reducing and a non-reducing polyketide synthase. Clusters containing such a pair of PKS genes have been identified in the biosynthesis of resorcylic acid lactones or dihydroxyphenylacetic acid lactones. AdPKS7 and AdPKS8 gene expression patterns correlated with aldaulactone production in different experimental conditions. The present results highly suggest that both genes are responsible for aldaulactone biosynthesis.
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Affiliation(s)
- Julia Courtial
- Univ Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France
| | - Jean-Jacques Helesbeux
- Substances d'Origine Naturelle et Analogues Structuraux, SFR4207 QUASAV, Université d'Angers, Angers, France
| | - Hugo Oudart
- Univ Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France
| | - Sophie Aligon
- Univ Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France
| | | | - Bruno Hamon
- Univ Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France
| | - Guillaume N'Guyen
- Univ Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France
| | - Sandrine Pigné
- Univ Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France
| | - Ahmed G Hussain
- Univ Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France.,Laboratory of Virology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Claire Pascouau
- Univ Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France
| | | | - Jérôme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
| | - Romain Berruyer
- Univ Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France.
| | - Pascal Poupard
- Univ Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France
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26
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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.
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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.
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27
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Tamizi AA, Mat-Amin N, Weaver JA, Olumakaiye RT, Akbar MA, Jin S, Bunawan H, Alberti F. Genome Sequencing and Analysis of Trichoderma (Hypocreaceae) Isolates Exhibiting Antagonistic Activity against the Papaya Dieback Pathogen, Erwinia mallotivora. J Fungi (Basel) 2022; 8:jof8030246. [PMID: 35330248 PMCID: PMC8949440 DOI: 10.3390/jof8030246] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/25/2022] [Accepted: 02/26/2022] [Indexed: 01/13/2023] Open
Abstract
Erwinia mallotivora, the causal agent of papaya dieback disease, is a devastating pathogen that has caused a tremendous decrease in Malaysian papaya export and affected papaya crops in neighbouring countries. A few studies on bacterial species capable of suppressing E. mallotivora have been reported, but the availability of antagonistic fungi remains unknown. In this study, mycelial suspensions from five rhizospheric Trichoderma isolates of Malaysian origin were found to exhibit notable antagonisms against E. mallotivora during co-cultivation. We further characterised three isolates, Trichoderma koningiopsis UKM-M-UW RA5, UKM-M-UW RA6, and UKM-M-UW RA3a, that showed significant growth inhibition zones on plate-based inhibition assays. A study of the genomes of the three strains through a combination of Oxford nanopore and Illumina sequencing technologies highlighted potential secondary metabolite pathways that might underpin their antimicrobial properties. Based on these findings, the fungal isolates are proven to be useful as potential biological control agents against E. mallotivora, and the genomic data opens possibilities to further explore the underlying molecular mechanisms behind their antimicrobial activity, with potential synthetic biology applications.
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Affiliation(s)
- Amin-Asyraf Tamizi
- Agri-Omics and Bioinformatics Programme, Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute Headquarters (MARDI), Serdang 43400, Selangor, Malaysia; (A.-A.T.); (N.M.-A.)
| | - Noriha Mat-Amin
- Agri-Omics and Bioinformatics Programme, Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute Headquarters (MARDI), Serdang 43400, Selangor, Malaysia; (A.-A.T.); (N.M.-A.)
| | - Jack A. Weaver
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK; (J.A.W.); (R.T.O.); (S.J.)
| | - Richard T. Olumakaiye
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK; (J.A.W.); (R.T.O.); (S.J.)
| | - Muhamad Afiq Akbar
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia;
| | - Sophie Jin
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK; (J.A.W.); (R.T.O.); (S.J.)
| | - Hamidun Bunawan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia;
- Correspondence: (H.B.); (F.A.)
| | - Fabrizio Alberti
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK; (J.A.W.); (R.T.O.); (S.J.)
- Correspondence: (H.B.); (F.A.)
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28
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Guo X, Chen F, Liu J, Shao Y, Wang X, Zhou Y. Genome Mining and Analysis of PKS Genes in Eurotium cristatum E1 Isolated from Fuzhuan Brick Tea. J Fungi (Basel) 2022; 8:jof8020193. [PMID: 35205947 PMCID: PMC8874483 DOI: 10.3390/jof8020193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 12/04/2022] Open
Abstract
Eurotium cristatum as the dominant fungi species of Fuzhuan brick tea in China, can produce multitudinous secondary metabolites (SMs) with various bioactivities. Polyketides are a very important class of SMs found in E. cristatum and have gained extensive attention in recent years due to their remarkable diversity of structures and multiple functions. Therefore, it is necessary to explore the polyketides produced by E. cristatum at the genomic level to enhance its application value. In this paper, 12 polyketide synthase (PKS) genes were found in the whole genome of E. cristatum E1 isolated from Fuzhuan brick tea. In addition, the qRT-PCR results further demonstrated that these genes were expressed. Moreover, metabolic analysis demonstrated E. cristatum E1 can produce a variety of polyketides, including citreorosein, emodin, physcion, isoaspergin, dihydroauroglaucin, iso-dihydroauroglaucin, aspergin, flavoglaucin and auroglaucin. Furthermore, based on genomic analysis, the putative secondary metabolites clusters for emodin and flavoglaucin were proposed. The results reported here will lay a good basis for systematically mining SMs resources of E. cristatum and broadening its application fields.
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Affiliation(s)
- Xiaoxiao Guo
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.G.); (F.C.); (Y.S.)
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Fusheng Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.G.); (F.C.); (Y.S.)
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiao Liu
- Institute of Agricultural Quality Standards and Testing Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China;
- Hubei Key Laboratory of Nutritional Quality and Safety of Agro Products, Wuhan 430064, China
| | - Yanchun Shao
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.G.); (F.C.); (Y.S.)
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaohong Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.G.); (F.C.); (Y.S.)
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: (X.W.); (Y.Z.); Tel./Fax: +86-27-87282111 (X.W.); +86-27-87389465 (Y.Z.)
| | - Youxiang Zhou
- Institute of Agricultural Quality Standards and Testing Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China;
- Hubei Key Laboratory of Nutritional Quality and Safety of Agro Products, Wuhan 430064, China
- Correspondence: (X.W.); (Y.Z.); Tel./Fax: +86-27-87282111 (X.W.); +86-27-87389465 (Y.Z.)
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29
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Biosynthetic potential of the endophytic fungus Helotiales sp. BL73 revealed via compound identification and genome mining. Appl Environ Microbiol 2022; 88:e0251021. [PMID: 35108081 DOI: 10.1128/aem.02510-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Endophytic fungi have been recognized as prolific producers of chemically diverse secondary metabolites. In this work, we describe a new representative of the order Helotiales isolated from the medicinal plant Bergenia pacumbis. Several bioactive secondary metabolites were produced by this Helotiales sp. BL 73 isolate grown on rice medium, including cochlioquinones and isofusidienols. Sequencing and analysis of the approx. 59 Mb genome revealed at least 77 secondary metabolite biosynthesis gene clusters, several of which could be associated with detected compounds or linked to previously reported molecules. Four terpene synthase genes identified in the BL73 genome were codon-optimized and expressed, together with farnesyl-, geranyl- and geranylgeranyl-pyrophosphate synthases, in Streptomyces spp. Analysis of recombinant strains revealed production of linalool and its oxidized form, terpenoids typically associated with plants, as well as a yet unidentified terpenoid. This study demonstrates the importance of a complex approach to the investigation of the biosynthetic potential of endophytic fungi using both conventional methods and genome mining. Importance Endophytic fungi represent as yet underexplored source of secondary metabolites, some of which may have industrial and medical applications. We isolated a slow-growing fungus belonging to the order Helotiales from the traditional medicinal plant Bergenia pacumbis and characterized its potential to biosynthesize secondary metabolites. We used both cultivation of the isolate with subsequent analysis of compounds produced, bioinformatics-based mining of the genome, and heterologous expression of several terpene synthase genes. Our study revealed enormous potential of this Helotiales isolate to produce structurally diverse natural products, including polyketides, non-ribosomally synthesized peptides, terpenoids and RiPPs. Identification of meroterpenoids and xanthones, along with establishing a link between these molecules and their putative biosynthetic genes sets a stage for investigation of the respective biosynthetic pathways. Heterologous production of terpenoids suggests that this approach can be used for the discovery of new compounds belonging to this chemical class using Streptomyces bacteria as hosts.
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30
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Pedersen TB, Nielsen MR, Kristensen SB, Spedtsberg EML, Sørensen T, Petersen C, Muff J, Sondergaard TE, Nielsen KL, Wimmer R, Gardiner DM, Sørensen JL. Speed dating for enzymes! Finding the perfect phosphopantetheinyl transferase partner for your polyketide synthase. Microb Cell Fact 2022; 21:9. [PMID: 35012550 PMCID: PMC8751348 DOI: 10.1186/s12934-021-01734-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/29/2021] [Indexed: 11/24/2022] Open
Abstract
The biosynthetic pathways for the fungal polyketides bikaverin and bostrycoidin, from Fusarium verticillioides and Fusarium solani respectively, were reconstructed and heterologously expressed in S. cerevisiae alongside seven different phosphopantetheinyl transferases (PPTases) from a variety of origins spanning bacterial, yeast and fungal origins. In order to gauge the efficiency of the interaction between the ACP-domains of the polyketide synthases (PKS) and PPTases, each were co-expressed individually and the resulting production of target polyketides were determined after 48 h of growth. In co-expression with both biosynthetic pathways, the PPTase from Fusarium verticillioides (FvPPT1) proved most efficient at producing both bikaverin and bostrycoidin, at 1.4 mg/L and 5.9 mg/L respectively. Furthermore, the remaining PPTases showed the ability to interact with both PKS's, except for a single PKS-PPTase combination. The results indicate that it is possible to boost the production of a target polyketide, simply by utilizing a more optimal PPTase partner, instead of the commonly used PPTases; NpgA, Gsp and Sfp, from Aspergillus nidulans, Brevibacillus brevis and Bacillus subtilis respectively.
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Affiliation(s)
- Tobias Bruun Pedersen
- Department of Chemistry and Bioscience, Aalborg University Esbjerg, Niels Bohrs Vej 8, 6700, Esbjerg, Denmark
| | - Mikkel Rank Nielsen
- Department of Chemistry and Bioscience, Aalborg University Esbjerg, Niels Bohrs Vej 8, 6700, Esbjerg, Denmark
| | | | - Eva Mie Lang Spedtsberg
- Department of Chemistry and Bioscience, Aalborg University Esbjerg, Niels Bohrs Vej 8, 6700, Esbjerg, Denmark
| | - Trine Sørensen
- Department of Chemistry and Bioscience, Aalborg University Aalborg, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Celine Petersen
- Department of Chemistry and Bioscience, Aalborg University Aalborg, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Jens Muff
- Department of Chemistry and Bioscience, Aalborg University Esbjerg, Niels Bohrs Vej 8, 6700, Esbjerg, Denmark
| | - Teis Esben Sondergaard
- Department of Chemistry and Bioscience, Aalborg University Aalborg, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Kåre Lehmann Nielsen
- Department of Chemistry and Bioscience, Aalborg University Aalborg, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Reinhard Wimmer
- Department of Chemistry and Bioscience, Aalborg University Aalborg, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Donald Max Gardiner
- The University of Queensland, 306 Carmody Rd, St Lucia, Brisbane, QLD, 4072, Australia
| | - Jens Laurids Sørensen
- Department of Chemistry and Bioscience, Aalborg University Esbjerg, Niels Bohrs Vej 8, 6700, Esbjerg, Denmark.
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31
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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.
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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.
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32
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Roux I, Chooi YH. Heterologous Expression of Fungal Biosynthetic Pathways in Aspergillus nidulans Using Episomal Vectors. Methods Mol Biol 2022; 2489:75-92. [PMID: 35524046 DOI: 10.1007/978-1-0716-2273-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Filamentous fungi produce a wide diversity of secondary metabolites, whose biosynthesis is encoded in biosynthetic gene clusters (BGCs). As novel BGCs are often found in fungal species that are genetically intractable or difficult to cultivate, heterologous expression is increasingly being used for compound discovery. In addition, heterologous expression is a useful strategy to elucidate the function of the genes within a BGC and shed light on their enzymatic mechanisms. Here, we describe a method for BGC elucidation using multi-marker AMA1-based pYFAC vectors for episomal expression in the fungal host Aspergillus nidulans. The pYFAC vectors have the advantage of high transformation efficiency and support high compound production. In addition, different pathway intermediates can be easily evaluated by testing different vector combinations. This protocol encompasses different AMA1-based strategies for BGC expression such as cloning of a BGC native sequence, promoter exchange or transcription factor overexpression. We also describe procedures for A. nidulans protoplasting, transformation, and small-scale culture analysis of strains containing AMA1 vectors.
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Affiliation(s)
- Indra Roux
- School of Molecular Sciences, University of Western Australia, Perth, WA, Australia
| | - Yit Heng Chooi
- School of Molecular Sciences, University of Western Australia, Perth, WA, Australia.
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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: 29] [Impact Index Per Article: 9.7] [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.
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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.
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Diale MO, Kayitesi E, Serepa-Dlamini MH. Genome In Silico and In Vitro Analysis of the Probiotic Properties of a Bacterial Endophyte, Bacillus Paranthracis Strain MHSD3. Front Genet 2021; 12:672149. [PMID: 34858466 PMCID: PMC8631869 DOI: 10.3389/fgene.2021.672149] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 10/11/2021] [Indexed: 01/25/2023] Open
Abstract
Spore-forming Bacillus species are gaining interest in human health recently, due to their ability to withstand the harsh environment of the gastrointestinal tract. The present study explores probiotic features of Bacillus paranthracis strain MHSD3 through genomic analysis and in vitro probiotic assays. The draft genome of strain MHSD3 contained genes associated with tolerance to gastrointestinal stress and adhesion. Cluster genes responsible for the synthesis of antimicrobial non-ribosomal peptide synthetases, bacteriocins, and linear azole-containing peptides were identified. Additionally, strain MHSD3 was able to survive in an acidic environment, had the tolerance to bile salt, and exhibited the capability to tolerate gastric juices. Moreover, the isolate was found to possess strong cell surface traits such as high auto-aggregation and hydrophobicity indices of 79 and 54%, respectively. Gas chromatography-mass spectrometry analysis showed that the strain produced secondary metabolites such as amino acids, phenolic compounds, and organic acid, known to exert health-promoting properties, including the improvement of gastrointestinal tract health.
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Affiliation(s)
- Mamonokane Olga Diale
- Department of Biotechnology and Food Technology, University of Johannesburg, Johannesburg, South Africa
| | - Eugenie Kayitesi
- Department of Consumer and Food Science, University of Pretoria, Pretoria, South Africa
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Bhagwat AC, Patil AM, Saroj SD. CRISPR/Cas 9-Based Editing in the Production of Bioactive Molecules. Mol Biotechnol 2021; 64:245-251. [PMID: 34643870 DOI: 10.1007/s12033-021-00418-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/10/2021] [Indexed: 11/28/2022]
Abstract
Plants, fungi, and bacteria synthesize a wide range of secondary metabolites that exhibit diverse biological activities. These bioactives, due to their potential benefits in research and therapeutics, have gained immense industrial importance. There is a need to synthesize these bioactives at significantly higher concentrations using cost-effective measures to be economically viable. However, the broader study of industrially important secondary metabolites has been hindered, thus, far due to a shortage of reliable, comparatively easy, and highly effective gene manipulation techniques. With the advent of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas), there is a revolution in the field of genetic engineering. CRISPR/Cas system, due to its simplicity and ease of use. This has widened its application in plant breeding, strain improvement, and engineering the metabolic pathways involved in the biochemical synthesis of industrially valuable bioactive. This review briefly introduces the CRISPR/Cas9 system and summarizes the applications of CRISPR/Cas9-mediated editing tools for the production of plant and fungal-derived bioactives.
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Affiliation(s)
- Amrita C Bhagwat
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune, Maharashtra, India
| | - Amrita M Patil
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune, Maharashtra, India
| | - Sunil D Saroj
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune, Maharashtra, India.
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Li Y, Zhuo L, Li X, Zhu Y, Wu S, Shen T, Hu W, Li YZ, Wu C. Myxadazoles, Myxobacterium-Derived Isoxazole-Benzimidazole Hybrids with Cardiovascular Activities. Angew Chem Int Ed Engl 2021; 60:21679-21684. [PMID: 34314077 DOI: 10.1002/anie.202106275] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/05/2021] [Indexed: 12/14/2022]
Abstract
There is a continuous need for novel microbial natural products to fill the drying-up drug development pipeline. Herein, we report myxadazoles from Myxococcus sp. SDU36, a family of novel chimeric small molecules that consist of N-ribityl 5,6-dimethylbenzimidazole and a linear fatty acid chain endowed with an isoxazole ring. The experiments of genome sequencing, gene insertion mutation, isotope labelling, and precursor feeding demonstrated that the fatty acid chain was encoded by a non-canonical PKS/NRPS gene cluster, whereas the origin of N-ribityl 5,6-dimethylbenzimidazole was related to the vitamin B12 metabolism. The convergence of these two distinct biosynthetic pathways through a C-N coupling led to the unique chemical framework of myxadazoles, which is an unprecedented hybridization mode in the paradigm of natural products. Myxadazoles exhibited potent vasculogenesis promotion effect and moderate antithrombotic activity, underscoring their potential usage for the treatment of cardiovascular diseases.
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Affiliation(s)
- Yuelan Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72 Binhai Avenue, Qingdao, 266237, P. R. China
| | - Li Zhuo
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72 Binhai Avenue, Qingdao, 266237, P. R. China
| | - Xiaobin Li
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), No. 28789 Jingshi Dong Road, Jinan, 250103, P. R. China
| | - Yongqiang Zhu
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), No. 28789 Jingshi Dong Road, Jinan, 250103, P. R. China
| | - Shuge Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72 Binhai Avenue, Qingdao, 266237, P. R. China
| | - Tao Shen
- Key Lab of Chemical Biology (MOE), School of Pharmaceutical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, 250012, P. R. China
| | - Wei Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72 Binhai Avenue, Qingdao, 266237, P. R. China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72 Binhai Avenue, Qingdao, 266237, P. R. China
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72 Binhai Avenue, Qingdao, 266237, P. R. China
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Li Y, Zhuo L, Li X, Zhu Y, Wu S, Shen T, Hu W, Li Y, Wu C. Myxadazoles, Myxobacterium‐Derived Isoxazole–Benzimidazole Hybrids with Cardiovascular Activities. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yuelan Li
- State Key Laboratory of Microbial Technology Institute of Microbial Technology Shandong University No. 72 Binhai Avenue Qingdao 266237 P. R. China
| | - Li Zhuo
- State Key Laboratory of Microbial Technology Institute of Microbial Technology Shandong University No. 72 Binhai Avenue Qingdao 266237 P. R. China
| | - Xiaobin Li
- Biology Institute Qilu University of Technology (Shandong Academy of Sciences) No. 28789 Jingshi Dong Road Jinan 250103 P. R. China
| | - Yongqiang Zhu
- Biology Institute Qilu University of Technology (Shandong Academy of Sciences) No. 28789 Jingshi Dong Road Jinan 250103 P. R. China
| | - Shuge Wu
- State Key Laboratory of Microbial Technology Institute of Microbial Technology Shandong University No. 72 Binhai Avenue Qingdao 266237 P. R. China
| | - Tao Shen
- Key Lab of Chemical Biology (MOE) School of Pharmaceutical Sciences Shandong University No. 44 West Wenhua Road Jinan 250012 P. R. China
| | - Wei Hu
- State Key Laboratory of Microbial Technology Institute of Microbial Technology Shandong University No. 72 Binhai Avenue Qingdao 266237 P. R. China
| | - Yue‐Zhong Li
- State Key Laboratory of Microbial Technology Institute of Microbial Technology Shandong University No. 72 Binhai Avenue Qingdao 266237 P. R. China
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology Institute of Microbial Technology Shandong University No. 72 Binhai Avenue Qingdao 266237 P. R. China
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Mishra S, Sahu PK, Agarwal V, Singh N. Exploiting endophytic microbes as micro-factories for plant secondary metabolite production. Appl Microbiol Biotechnol 2021; 105:6579-6596. [PMID: 34463800 DOI: 10.1007/s00253-021-11527-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/12/2021] [Accepted: 08/15/2021] [Indexed: 01/19/2023]
Abstract
Plant secondary metabolites have significant potential applications in a wide range of pharmaceutical, food, and cosmetic industries by providing new chemistries and compounds. However, direct isolation of such compounds from plants has resulted in over-harvesting and loss of biodiversity, currently threatening several medicinal plant species to extinction. With the breakthrough report of taxol production by an endophytic fungus of Taxus brevifolia, a new era in natural product research was established. Since then, the ability of endophytic microbes to produce metabolites similar to those produced by their host plants has been discovered. The plant "endosphere" represents a rich and unique biological niche inhabited by organisms capable of producing a range of desired compounds. In addition, plants growing in diverse habitats and adverse environmental conditions represent a valuable reservoir for obtaining rare microbes with potential applications. Despite being an attractive and sustainable approach for obtaining economically important metabolites, the industrial exploitation of microbial endophytes for the production and isolation of plant secondary metabolites remains in its infancy. The present review provides an updated overview of the prospects, challenges, and possible solutions for using microbial endophytes as micro-factories for obtaining commercially important plant metabolites.Key points• Some "plant" metabolites are rather synthesized by the associated endophytes.• Challenges: Attenuation, silencing of BGCs, unculturability, complex cross-talk.• Solutions: Simulation of in planta habitat, advanced characterization methods.
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Affiliation(s)
- Sushma Mishra
- Plant Biotechnology Laboratory, Dayalbagh Educational Institute (Deemed-to-be-University), Agra, Uttar Pradesh, 282005, India.
| | - Pramod Kumar Sahu
- ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan, Uttar Pradesh, 275103, India
| | - Vishad Agarwal
- Plant Biotechnology Laboratory, Dayalbagh Educational Institute (Deemed-to-be-University), Agra, Uttar Pradesh, 282005, India
| | - Namrata Singh
- Plant Biotechnology Laboratory, Dayalbagh Educational Institute (Deemed-to-be-University), Agra, Uttar Pradesh, 282005, India
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Palmer JM, Wiemann P, Greco C, Chiang YM, Wang CCC, Lindner DL, Keller NP. The sexual spore pigment asperthecin is required for normal ascospore production and protection from UV light in Aspergillus nidulans. J Ind Microbiol Biotechnol 2021; 48:6355442. [PMID: 34415047 PMCID: PMC8762651 DOI: 10.1093/jimb/kuab055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/03/2021] [Indexed: 11/12/2022]
Abstract
Many fungi develop both asexual and sexual spores that serve as propagules for dissemination and/or recombination of genetic traits. Asexual spores are often heavily pigmented and this pigmentation provides protection from UV light. However, little is known about any purpose pigmentation may serve for sexual spores. The model Ascomycete Aspergillus nidulans produces both green pigmented asexual spores (conidia) and red pigmented sexual spores (ascospores). Here we find that the previously characterized red pigment, asperthecin, is the A. nidulans ascospore pigment. The asperthecin biosynthetic gene cluster is composed of three genes, aptA, aptB, and aptC where deletion of either aptA (encoding a polyketide synthase) or aptB (encoding a thioesterase) yields small, mishappen hyaline ascospores while deletion of aptC (encoding a monooxygenase) yields morphologically normal but purple ascospores. ∆aptA and ∆aptB but not ∆aptC or WT ascospores are extremely sensitive to UV light. We find that two historical ascospore color mutants, clA6 and clB1, possess mutations in aptA and aptB sequences respectively.
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Affiliation(s)
- Jonathan M Palmer
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA.,Center for Forest Mycology Research, Northern Research Station, US Forest Service, Madison, WI 53726, USA
| | - Philipp Wiemann
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Claudio Greco
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yi Ming Chiang
- Departments of Chemistry and Pharmacology & Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Clay C C Wang
- Departments of Chemistry and Pharmacology & Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Daniel L Lindner
- Center for Forest Mycology Research, Northern Research Station, US Forest Service, Madison, WI 53726, USA
| | - Nancy P Keller
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
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Wang W, Yu Y, Keller NP, Wang P. Presence, Mode of Action, and Application of Pathway Specific Transcription Factors in Aspergillus Biosynthetic Gene Clusters. Int J Mol Sci 2021; 22:ijms22168709. [PMID: 34445420 PMCID: PMC8395729 DOI: 10.3390/ijms22168709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/10/2021] [Accepted: 08/10/2021] [Indexed: 01/21/2023] Open
Abstract
Fungal secondary metabolites are renowned toxins as well as valuable sources of antibiotics, cholesterol-lowering drugs, and immunosuppressants; hence, great efforts were levied to understand how these compounds are genetically regulated. The genes encoding for the enzymes required for synthesizing secondary metabolites are arranged in biosynthetic gene clusters (BGCs). Often, BGCs contain a pathway specific transcription factor (PSTF), a valuable tool in shutting down or turning up production of the BGC product. In this review, we present an in-depth view of PSTFs by examining over 40 characterized BGCs in the well-studied fungal species Aspergillus nidulans and Aspergillus fumigatus. Herein, we find BGC size is a predictor for presence of PSTFs, consider the number and the relative location of PSTF in regard to the cluster(s) regulated, discuss the function and the evolution of PSTFs, and present application strategies for pathway specific activation of cryptic BGCs.
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Affiliation(s)
- Wenjie Wang
- Ocean College, Zhejiang University, Zhoushan 316021, China; (W.W.); (Y.Y.)
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yuchao Yu
- Ocean College, Zhejiang University, Zhoushan 316021, China; (W.W.); (Y.Y.)
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Correspondence: (N.P.K.); (P.W.)
| | - Pinmei Wang
- Ocean College, Zhejiang University, Zhoushan 316021, China; (W.W.); (Y.Y.)
- Correspondence: (N.P.K.); (P.W.)
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Abstract
The fungal kingdom has provided advances in our ability to identify biosynthetic gene clusters (BGCs) and to examine how gene composition of BGCs evolves across species and genera. However, little is known about the evolution of specific BGC regulators that mediate how BGCs produce secondary metabolites (SMs). A bioinformatics search for conservation of the Aspergillus fumigatus xanthocillin BGC revealed an evolutionary trail of xan-like BGCs across Eurotiales species. Although the critical regulatory and enzymatic genes were conserved in Penicillium expansum, overexpression (OE) of the conserved xan BGC transcription factor (TF) gene, PexanC, failed to activate the putative xan BGC transcription or xanthocillin production in P. expansum, in contrast to the role of AfXanC in A. fumigatus. Surprisingly, OE::PexanC was instead found to promote citrinin synthesis in P. expansum via trans induction of the cit pathway-specific TF, ctnA, as determined by cit BGC expression and chemical profiling of ctnA deletion and OE::PexanC single and double mutants. OE::AfxanC results in significant increases of xan gene expression and metabolite synthesis in A. fumigatus but had no effect on either xanthocillin or citrinin production in P. expansum. Bioinformatics and promoter mutation analysis led to the identification of an AfXanC binding site, 5'-AGTCAGCA-3', in promoter regions of the A. fumigatus xan BGC genes. This motif was not in the ctnA promoter, suggesting a different binding site of PeXanC. A compilation of a bioinformatics examination of XanC orthologs and the presence/absence of the 5'-AGTCAGCA-3' binding motif in xan BGCs in multiple Aspergillus and Penicillium spp. supports an evolutionary divergence of XanC regulatory targets that we speculate reflects an exaptation event in the Eurotiales. IMPORTANCE Fungal secondary metabolites (SMs) are an important source of pharmaceuticals on one hand and toxins on the other. Efforts to identify the biosynthetic gene clusters (BGCs) that synthesize SMs have yielded significant insights into how variation in the genes that compose BGCs may impact subsequent metabolite production within and between species. However, the role of regulatory genes in BGC activation is less well understood. Our finding that the bZIP transcription factor XanC, located in the xanthocillin BGC of both Aspergillus fumigatus and Penicillium expansum, has functionally diverged to regulate different BGCs in these two species emphasizes that the diversification of BGC regulatory elements may sometimes occur through exaptation, which is the co-option of a gene that evolved for one function to a novel function. Furthermore, this work suggests that the loss/gain of transcription factor binding site targets may be an important mediator in the evolution of secondary-metabolism regulatory elements.
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Ortega HE, Torres-Mendoza D, Caballero E. Z, Cubilla-Rios L. Structurally Uncommon Secondary Metabolites Derived from Endophytic Fungi. J Fungi (Basel) 2021; 7:570. [PMID: 34356949 PMCID: PMC8308102 DOI: 10.3390/jof7070570] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 01/25/2023] Open
Abstract
Among microorganisms, endophytic fungi are the least studied, but they have attracted attention due to their high biological diversity and ability to produce novel and bioactive secondary metabolites to protect their host plant against biotic and abiotic stress. These compounds belong to different structural classes, such as alkaloids, peptides, terpenoids, polyketides, and steroids, which could present significant biological activities that are useful for pharmacological or medical applications. Recent reviews on endophytic fungi have mainly focused on the production of novel bioactive compounds. Here, we focus on compounds produced by endophytic fungi, reported with uncommon bioactive structures, establishing the neighbor net and diversity of endophytic fungi. The review includes compounds published from January 2015 to December 2020 that were catalogued as unprecedented, rare, uncommon, or possessing novel structural skeletons from more than 39 different genera, with Aspergillus and Penicillium being the most mentioned. They were reported as displaying cytotoxic, antitumor, antimicrobial, antiviral, or anti-inflammatory activity. The solid culture, using rice as a carbon source, was the most common medium utilized in the fermentation process when this type of compound was isolated.
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Affiliation(s)
- Humberto E. Ortega
- Laboratory of Tropical Bioorganic Chemistry, Faculty of Natural, Exact Sciences and Technology, University of Panama, Panama City 0824, Panama; (H.E.O.); (D.T.-M.)
- Department of Organic Chemistry, Faculty of Natural, Exact Sciences and Technology, University of Panama, Panama City 0824, Panama
| | - Daniel Torres-Mendoza
- Laboratory of Tropical Bioorganic Chemistry, Faculty of Natural, Exact Sciences and Technology, University of Panama, Panama City 0824, Panama; (H.E.O.); (D.T.-M.)
- Department of Organic Chemistry, Faculty of Natural, Exact Sciences and Technology, University of Panama, Panama City 0824, Panama
- Vicerrectoría de Investigación y Postgrado, Universidad de Panamá, Panama City 0824, Panama
| | - Zuleima Caballero E.
- Center of Cellular and Molecular Biology of Diseases, Institute for Scientific Research and Technology Services (INDICASAT-AIP), Clayton 0843-01103, Panama;
| | - Luis Cubilla-Rios
- Laboratory of Tropical Bioorganic Chemistry, Faculty of Natural, Exact Sciences and Technology, University of Panama, Panama City 0824, Panama; (H.E.O.); (D.T.-M.)
- Department of Organic Chemistry, Faculty of Natural, Exact Sciences and Technology, University of Panama, Panama City 0824, Panama
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Futyma ME, Guo Y, Hoeck C, Hoof JB, Gotfredsen CH, Mortensen UH, Larsen TO. Genetic origin of homopyrones, a rare type of hybrid phenylpropanoid- and polyketide-derived yellow pigments from Aspergillus homomorphus. Appl Microbiol Biotechnol 2021; 105:5113-5121. [PMID: 34106309 DOI: 10.1007/s00253-021-11379-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 04/11/2021] [Accepted: 05/27/2021] [Indexed: 10/21/2022]
Abstract
In recent years, there has been an increasing demand for the replacement of synthetic food colorants with naturally derived alternatives. Filamentous fungi are prolific producers of secondary metabolites including polyketide-derived pigments, many of which have not been fully characterized yet. During our ongoing investigations of black aspergilli, we noticed that Aspergillus homomorphus turned yellow when cultivated on malt extract agar plates. Chemical discovery guided by UV and MS led to the isolation of two novel yellow natural products, and their structures were elucidated as aromatic α-pyrones homopyrones A (1) and B (2) by HRMS and NMR. Combined investigations including retro-biosynthesis, genome mining, and gene deletions successfully linked both compounds to their related biosynthetic gene clusters. This demonstrated that homopyrones are biosynthesized by using cinnamoyl-CoA as the starter unit, followed by extension with three malonyl-CoA units, and lactonization to give the core hybrid backbone structure. The polyketide synthase AhpA includes a C-methylation domain, which however seems to be promiscuous since only 2 is C-methylated. Altogether, the homopyrones represent a rare case of hybrid phenylpropanoid- and polyketide-derived natural products in filamentous fungi. KEY POINTS: • Homopyrones represent a rare type of fungal polyketides synthesized from cinnamic-CoA. • CRISPR/Cas9 technology has been firstly applied in Aspergillus homomorphus.
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Affiliation(s)
- Malgorzata E Futyma
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800, Kgs. Lyngby, Denmark.,CHRETO, Lejrvej 17, 3500, Værløse, Denmark
| | - Yaojie Guo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800, Kgs. Lyngby, Denmark
| | - Casper Hoeck
- Department of Chemistry, Technical University of Denmark, Kemitorvet B207, DK-2800, Kgs. Lyngby, Denmark.,Novo Nordisk A/S, Smørmosevej 10-12, 2880, Bagsværd, Denmark
| | - Jakob B Hoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800, Kgs. Lyngby, Denmark
| | - Charlotte H Gotfredsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet B207, DK-2800, Kgs. Lyngby, Denmark
| | - Uffe H Mortensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800, Kgs. Lyngby, Denmark.
| | - Thomas O Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800, Kgs. Lyngby, Denmark.
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Sbaraini N, Hu J, Roux I, Phan CS, Motta H, Rezaee H, Schrank A, Chooi YH, Staats CC. Polyketides produced by the entomopathogenic fungus Metarhizium anisopliae induce Candida albicans growth. Fungal Genet Biol 2021; 152:103568. [PMID: 33991663 DOI: 10.1016/j.fgb.2021.103568] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 03/16/2021] [Accepted: 04/18/2021] [Indexed: 11/15/2022]
Abstract
Metarhizium anisopliae is an important entomopathogenic species and model for arthropod-fungus interaction studies. This fungus harbors a diverse arsenal of unexplored secondary metabolite biosynthetic gene clusters, which are suggested to perform diverse roles during host interaction and soil subsistence as a saprophytic species. Here we explored an unusual carnitine acyltransferase domain-containing highly reducing polyketide synthase found in the genome of M. anisopliae. Employing heterologous expression in Aspergillus nidulans, two new polyketides were obtained, named BAA and BAB, as well as one known polyketide [(2Z,4E,6E)-octa-2,4,6-trienedioic acid]. Intra-hemocoel injection of the most abundant compound (BAA) in the model-arthropod Galleria mellonella larvae did not induce mortality or noticeable alterations, suggesting that this compound may not harbor insecticidal activity. Also, the potential role of such molecules in polymicrobial interactions was evaluated. Determination of minimum inhibitory concentration assays using distinct fungal species revealed that BAA and BAB did not alter Cryptococcus neoformans growth, while BAA exhibited weak antifungal activity against Saccharomyces cerevisiae. Unexpectedly, these compounds increased Candida albicans growth compared to control conditions. Furthermore, BAA can mitigate the fungicidal effects of fluconazole over C. albicans. Although the exact role of these compounds on the M. anisopliae life cycle is elusive, the described results add up to the complexity of secondary metabolites produced by Metarhizium spp. Moreover, up to our knowledge, these are the first polyketides isolated from filamentous fungi that can boost the growth of another fungal species.
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Affiliation(s)
- Nicolau Sbaraini
- Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Jinyu Hu
- 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
| | - Chin-Soon Phan
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Heryk Motta
- Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Hamideh Rezaee
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Augusto Schrank
- Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| | - Charley Christian Staats
- Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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Mishra AK, Baek KH. Salicylic Acid Biosynthesis and Metabolism: A Divergent Pathway for Plants and Bacteria. Biomolecules 2021; 11:705. [PMID: 34065121 PMCID: PMC8150894 DOI: 10.3390/biom11050705] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/06/2021] [Accepted: 05/06/2021] [Indexed: 01/24/2023] Open
Abstract
Salicylic acid (SA) is an active secondary metabolite that occurs in bacteria, fungi, and plants. SA and its derivatives (collectively called salicylates) are synthesized from chorismate (derived from shikimate pathway). SA is considered an important phytohormone that regulates various aspects of plant growth, environmental stress, and defense responses against pathogens. Besides plants, a large number of bacterial species, such as Pseudomonas, Bacillus, Azospirillum, Salmonella, Achromobacter, Vibrio, Yersinia, and Mycobacteria, have been reported to synthesize salicylates through the NRPS/PKS biosynthetic gene clusters. This bacterial salicylate production is often linked to the biosynthesis of small ferric-ion-chelating molecules, salicyl-derived siderophores (known as catecholate) under iron-limited conditions. Although bacteria possess entirely different biosynthetic pathways from plants, they share one common biosynthetic enzyme, isochorismate synthase, which converts chorismate to isochorismate, a common precursor for synthesizing SA. Additionally, SA in plants and bacteria can undergo several modifications to carry out their specific functions. In this review, we will systematically focus on the plant and bacterial salicylate biosynthesis and its metabolism.
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Affiliation(s)
| | - Kwang-Hyun Baek
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Korea;
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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.
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Sagita R, Quax WJ, Haslinger K. Current State and Future Directions of Genetics and Genomics of Endophytic Fungi for Bioprospecting Efforts. Front Bioeng Biotechnol 2021; 9:649906. [PMID: 33791289 PMCID: PMC8005728 DOI: 10.3389/fbioe.2021.649906] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/16/2021] [Indexed: 12/16/2022] Open
Abstract
The bioprospecting of secondary metabolites from endophytic fungi received great attention in the 1990s and 2000s, when the controversy around taxol production from Taxus spp. endophytes was at its height. Since then, hundreds of reports have described the isolation and characterization of putative secondary metabolites from endophytic fungi. However, only very few studies also report the genetic basis for these phenotypic observations. With low sequencing cost and fast sample turnaround, genetics- and genomics-based approaches have risen to become comprehensive approaches to study natural products from a wide-range of organisms, especially to elucidate underlying biosynthetic pathways. However, in the field of fungal endophyte biology, elucidation of biosynthetic pathways is still a major challenge. As a relatively poorly investigated group of microorganisms, even in the light of recent efforts to sequence more fungal genomes, such as the 1000 Fungal Genomes Project at the Joint Genome Institute (JGI), the basis for bioprospecting of enzymes and pathways from endophytic fungi is still rather slim. In this review we want to discuss the current approaches and tools used to associate phenotype and genotype to elucidate biosynthetic pathways of secondary metabolites in endophytic fungi through the lens of bioprospecting. This review will point out the reported successes and shortcomings, and discuss future directions in sampling, and genetics and genomics of endophytic fungi. Identifying responsible biosynthetic genes for the numerous secondary metabolites isolated from endophytic fungi opens the opportunity to explore the genetic potential of producer strains to discover novel secondary metabolites and enhance secondary metabolite production by metabolic engineering resulting in novel and more affordable medicines and food additives.
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Affiliation(s)
| | | | - Kristina Haslinger
- Groningen Institute of Pharmacy, Chemical and Pharmaceutical Biology, University of Groningen, Groningen, Netherlands
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Jiang C, Lv G, Tu Y, Cheng X, Duan Y, Zeng B, He B. Applications of CRISPR/Cas9 in the Synthesis of Secondary Metabolites in Filamentous Fungi. Front Microbiol 2021; 12:638096. [PMID: 33643273 PMCID: PMC7905030 DOI: 10.3389/fmicb.2021.638096] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/18/2021] [Indexed: 12/19/2022] Open
Abstract
Filamentous fungi possess the capacity to produce a wide array of secondary metabolites with diverse biological activities and structures, such as lovastatin and swainsonine. With the advent of the post-genomic era, increasing amounts of cryptic or uncharacterized secondary metabolite biosynthetic gene clusters are continually being discovered. However, owing to the longstanding lack of versatile, comparatively simple, and highly efficient genetic manipulation techniques, the broader exploration of industrially important secondary metabolites has been hampered thus far. With the emergence of CRISPR/Cas9-based genome editing technology, this dilemma may be alleviated, as this advanced technique has revolutionized genetic research and enabled the exploitation and discovery of new bioactive compounds from filamentous fungi. In this review, we introduce the CRISPR/Cas9 system in detail and summarize the latest applications of CRISPR/Cas9-mediated genome editing in filamentous fungi. We also briefly introduce the specific applications of the CRISPR/Cas9 system and CRISPRa in the improvement of secondary metabolite contents and discovery of novel biologically active compounds in filamentous fungi, with specific examples noted. Additionally, we highlight and discuss some of the challenges and deficiencies of using the CRISPR/Cas9-based genome editing technology in research on the biosynthesis of secondary metabolites as well as future application of CRISPR/Cas9 strategy in filamentous fungi are highlighted and discussed.
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Affiliation(s)
- Chunmiao Jiang
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Gongbo Lv
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Yayi Tu
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Xiaojie Cheng
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Yitian Duan
- School of Information, Renmin University of China, Beijing, China
| | - Bin Zeng
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China.,College of Pharmacy, Shenzhen Technology University, Shenzhen, China
| | - Bin He
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
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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.
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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
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50
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Shenouda ML, Cox RJ. Molecular methods unravel the biosynthetic potential of Trichoderma species. RSC Adv 2021; 11:3622-3635. [PMID: 35424278 PMCID: PMC8694227 DOI: 10.1039/d0ra09627j] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/10/2021] [Indexed: 12/14/2022] Open
Abstract
Members of the genus Trichoderma are a well-established and studied group of fungi, mainly due to their efficient protein production capabilities and their biocontrol activities. Despite the immense interest in the use of different members of this species as biopesticides and biofertilizers, the study of their active metabolites and their biosynthetic gene clusters has not gained significant attention until recently. Here we review the challenges and opportunities in exploiting the full potential of Trichoderma spp. for the production of natural products and new metabolic engineering strategies used to overcome some of these challenges.
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Affiliation(s)
- Mary L Shenouda
- OCI, BMWZ, Leibniz University of Hannover Schneiderberg 38 30167 Hannover Germany
- Department of Pharmacognosy, Faculty of Pharmacy, Alexandria University 21521 Egypt
| | - Russell J Cox
- OCI, BMWZ, Leibniz University of Hannover Schneiderberg 38 30167 Hannover Germany
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