1
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Steenwyk JL, Knowles S, Bastos RW, Balamurugan C, Rinker D, Mead ME, Roberts CD, Raja HA, Li Y, Colabardini AC, de Castro PA, Dos Reis TF, Gumilang A, Almagro-Molto M, Alanio A, Garcia-Hermoso D, Delbaje E, Pontes L, Pinzan CF, Schreiber AZ, Canóvas D, Sanchez Luperini R, Lagrou K, Torrado E, Rodrigues F, Oberlies NH, Zhou X, Goldman GH, Rokas A. Evolutionary origin and population diversity of a cryptic hybrid pathogen. Nat Commun 2024; 15:8412. [PMID: 39333551 PMCID: PMC11436853 DOI: 10.1038/s41467-024-52639-1] [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: 06/25/2024] [Accepted: 09/16/2024] [Indexed: 09/29/2024] Open
Abstract
Cryptic fungal pathogens pose disease management challenges due to their morphological resemblance to known pathogens. Here, we investigated the genomes and phenotypes of 53 globally distributed isolates of Aspergillus section Nidulantes fungi and found 30 clinical isolates-including four isolated from COVID-19 patients-were A. latus, a cryptic pathogen that originated via allodiploid hybridization. Notably, all A. latus isolates were misidentified. A. latus hybrids likely originated via a single hybridization event during the Miocene and harbor substantial genetic diversity. Transcriptome profiling of a clinical isolate revealed that both parental subgenomes are actively expressed and respond to environmental stimuli. Characterizing infection-relevant traits-such as drug resistance and growth under oxidative stress-revealed distinct phenotypic profiles among A. latus hybrids compared to parental and closely related species. Moreover, we identified four features that could aid A. latus taxonomic identification. Together, these findings deepen our understanding of the origin of cryptic pathogens.
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Affiliation(s)
- Jacob L Steenwyk
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, USA
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, USA
| | - Sonja Knowles
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, USA
| | - Rafael W Bastos
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
- Department of Microbiology and Parasitology, Bioscience Center, Federal University of Rio Grande do Norte, Natal-RN, Brazil
| | - Charu Balamurugan
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, USA
| | - David Rinker
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, USA
| | - Matthew E Mead
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, USA
- Ginkgo Bioworks, 27 Drydock Avenue, 8th Floor, Boston, USA
| | - Christopher D Roberts
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, USA
| | - Huzefa A Raja
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, USA
| | - Yuanning Li
- Institute of Marine Science and Technology, Shandong University, 72 Binhai Road, Qingdao, China
| | - Ana Cristina Colabardini
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Patrícia Alves de Castro
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Thaila Fernanda Dos Reis
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Adiyantara Gumilang
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, USA
| | - María Almagro-Molto
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Faculty of Medicine, Ludwig Maximilian University, Munich, Germany
| | - Alexandre Alanio
- Institut Pasteur, Paris Cité University, National Reference Center for Invasives Mycoses and Antifungals, Translational Mycology Research Group, Mycology Department, Paris, France
- Laboratoire de parasitologie-mycologie, AP-HP, Hôpital Saint-Louis, Paris, France
| | - Dea Garcia-Hermoso
- Institut Pasteur, Paris Cité University, National Reference Center for Invasives Mycoses and Antifungals, Translational Mycology Research Group, Mycology Department, Paris, France
| | - Endrews Delbaje
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Laís Pontes
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Camila Figueiredo Pinzan
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | | | - David Canóvas
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
- Clinical Microbiology Unit. Synlab Laboratory at Viamed Sta. Ángela de la Cruz Hospital, Seville, Spain
| | - Rafael Sanchez Luperini
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Katrien Lagrou
- Department of Microbiology, Immunology and Transplantation, Katholieke Universiteit Leuven, Leuven, Belgium
- Department of Laboratory Medicine and National Reference Centre for Mycosis, University Hospitals Leuven, Leuven, Belgium
| | - Egídio Torrado
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4715-495 Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga, Portugal
| | - Fernando Rodrigues
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4715-495 Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga, Portugal
| | - Nicholas H Oberlies
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, USA
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Gustavo H Goldman
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil.
- National Institute of Science and Technology in Human Pathogenic, Fungi, Brazil.
| | - Antonis Rokas
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, USA.
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, USA.
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2
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Huang X, He Y, Zhang K, Shi Y, Zhao H, Lai D, Lin H, Wang X, Yang Z, Xiao Y, Li W, Ouyang Y, Woo SH, Quinet M, Georgiev MI, Fernie AR, Liu X, Zhou M. Evolution and Domestication of a Novel Biosynthetic Gene Cluster Contributing to the Flavonoid Metabolism and High-Altitude Adaptability of Plants in the Fagopyrum Genus. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403603. [PMID: 39312476 DOI: 10.1002/advs.202403603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 08/15/2024] [Indexed: 09/25/2024]
Abstract
The diversity of secondary metabolites is an important means for plants to cope with the complex and ever-changing terrestrial environment. Plant biosynthetic gene clusters (BGCs) are crucial for the biosynthesis of secondary metabolites. The domestication and evolution of BGCs and how they affect plant secondary metabolites biosynthesis and environmental adaptation are still not fully understood. Buckwheat exhibits strong resistance and abundant secondary metabolites, especially flavonoids, allowing it to thrive in harsh environments. A non-canonical BGC named UFGT3 cluster is identified, which comprises a phosphorylase kinase (PAK), two transcription factors (MADS1/2), and a glycosyltransferase (UFGT3), forming a complete molecular regulatory module involved in flavonoid biosynthesis. This cluster is selected during Tartary buckwheat domestication and is widely present in species of the Fagopyrum genus. In wild relatives of cultivated buckwheat, a gene encoding anthocyanin glycosyltransferase (AGT), which glycosylates pelargonidin into pelargonidin-3-O-glucoside, is found inserted into this cluster. The pelargonidin-3-O-glucoside can help plants resist UV stress, endowing wild relatives with stronger high-altitude adaptability. This study provides a new research paradigm for the evolutionary dynamics of plant BGCs, and offers new perspectives for exploring the mechanism of plant ecological adaptability driven by environmental stress through the synthesis of secondary metabolites.
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Affiliation(s)
- Xu Huang
- National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuqi He
- National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Kaixuan Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yaliang Shi
- National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | | | - Dili Lai
- National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hao Lin
- National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiangru Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhimin Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yawen Xiao
- National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Li
- National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yinan Ouyang
- National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Sun Hee Woo
- Department of Agronomy, Chungbuk National University, Cheongju, 28644, South Korea
| | - Muriel Quinet
- Groupe de Recherche en Physiologie Végétale (GRPV), Earth and Life Institute-Agronomy (ELI-A), Université Catholique de Louvain, Croix du Sud 45, boîte L7.07.13, Louvain-la-Neuve, B-1348, Belgium
| | - Milen I Georgiev
- Laboratory of Metabolomics, Institute of Microbiology, Bulgarian Academy of Sciences, Plovdiv, 4000, Bulgaria
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Alisdair R Fernie
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
| | - Xu Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Meiliang Zhou
- National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Konkel Z, Kubatko L, Slot JC. CLOCI: unveiling cryptic fungal gene clusters with generalized detection. Nucleic Acids Res 2024; 52:e75. [PMID: 39016185 PMCID: PMC11381361 DOI: 10.1093/nar/gkae625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 07/01/2024] [Accepted: 07/10/2024] [Indexed: 07/18/2024] Open
Abstract
Gene clusters are genomic loci that contain multiple genes that are functionally and genetically linked. Gene clusters collectively encode diverse functions, including small molecule biosynthesis, nutrient assimilation, metabolite degradation, and production of proteins essential for growth and development. Identifying gene clusters is a powerful tool for small molecule discovery and provides insight into the ecology and evolution of organisms. Current detection algorithms focus on canonical 'core' biosynthetic functions many gene clusters encode, while overlooking uncommon or unknown cluster classes. These overlooked clusters are a potential source of novel natural products and comprise an untold portion of overall gene cluster repertoires. Unbiased, function-agnostic detection algorithms therefore provide an opportunity to reveal novel classes of gene clusters and more precisely define genome organization. We present CLOCI (Co-occurrence Locus and Orthologous Cluster Identifier), an algorithm that identifies gene clusters using multiple proxies of selection for coordinated gene evolution. Our approach generalizes gene cluster detection and gene cluster family circumscription, improves detection of multiple known functional classes, and unveils non-canonical gene clusters. CLOCI is suitable for genome-enabled small molecule mining, and presents an easily tunable approach for delineating gene cluster families and homologous loci.
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Affiliation(s)
- Zachary Konkel
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Laura Kubatko
- Department of Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Statistics, The Ohio State University, Columbus, OH 43210, USA
| | - Jason C Slot
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH 43210, USA
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4
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Rinker DC, Sauters TJC, Steffen K, Gumilang A, Raja HA, Rangel-Grimaldo M, Pinzan CF, de Castro PA, Dos Reis TF, Delbaje E, Houbraken J, Goldman GH, Oberlies NH, Rokas A. Strain heterogeneity in a non-pathogenic Aspergillus fungus highlights factors associated with virulence. Commun Biol 2024; 7:1082. [PMID: 39232082 PMCID: PMC11374809 DOI: 10.1038/s42003-024-06756-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 08/20/2024] [Indexed: 09/06/2024] Open
Abstract
Fungal pathogens exhibit extensive strain heterogeneity, including variation in virulence. Whether closely related non-pathogenic species also exhibit strain heterogeneity remains unknown. Here, we comprehensively characterized the pathogenic potentials (i.e., the ability to cause morbidity and mortality) of 16 diverse strains of Aspergillus fischeri, a non-pathogenic close relative of the major pathogen Aspergillus fumigatus. In vitro immune response assays and in vivo virulence assays using a mouse model of pulmonary aspergillosis showed that A. fischeri strains varied widely in their pathogenic potential. Furthermore, pangenome analyses suggest that A. fischeri genomic and phenotypic diversity is even greater. Genomic, transcriptomic, and metabolic profiling identified several pathways and secondary metabolites associated with variation in virulence. Notably, strain virulence was associated with the simultaneous presence of the secondary metabolites hexadehydroastechrome and gliotoxin. We submit that examining the pathogenic potentials of non-pathogenic close relatives is key for understanding the origins of fungal pathogenicity.
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Affiliation(s)
- David C Rinker
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Thomas J C Sauters
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Karin Steffen
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Adiyantara Gumilang
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Huzefa A Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Manuel Rangel-Grimaldo
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Camila Figueiredo Pinzan
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Patrícia Alves de Castro
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Thaila Fernanda Dos Reis
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Endrews Delbaje
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Jos Houbraken
- Food and Indoor Mycology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Gustavo H Goldman
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil.
| | - Nicholas H Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA.
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Perrier M, Barber AE. Unraveling the genomic diversity and virulence of human fungal pathogens through pangenomics. PLoS Pathog 2024; 20:e1012313. [PMID: 38990800 PMCID: PMC11238998 DOI: 10.1371/journal.ppat.1012313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024] Open
Affiliation(s)
- Marion Perrier
- Junior Research Group Fungal Informatics, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany
| | - Amelia E Barber
- Junior Research Group Fungal Informatics, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany
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6
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Gluck-Thaler E, Forsythe A, Puerner C, Stajich JE, Croll D, Cramer RA, Vogan AA. Giant transposons promote strain heterogeneity in a major fungal pathogen. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601215. [PMID: 38979181 PMCID: PMC11230402 DOI: 10.1101/2024.06.28.601215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Fungal infections are difficult to prevent and treat in large part due to heterogeneity in clinically relevant phenotypes. However, the genetic mechanisms driving pathogen variation remain poorly understood. Here, we determined the extent to which Starships -giant transposons capable of mobilizing numerous fungal genes-generate genetic and phenotypic variability in the human pathogen Aspergillus fumigatus . We analyzed 519 diverse strains, including 12 newly sequenced with long-read technology, to reveal 20 distinct Starships that generate genomic heterogeneity over timescales impacting experimental reproducibility. Starship -mobilized genes encode diverse functions, including biofilm-related virulence factors and biosynthetic gene clusters, and many are differentially expressed during infection and antifungal exposure in a strain-specific manner. These findings support a new model of fungal pathogenesis wherein Starships mediate variation in virulence-related gene content and expression. Together, our results demonstrate that Starships are a foundational mechanism generating disease-relevant genotypic and, in turn, phenotypic heterogeneity in a major human fungal pathogen.
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Wang WH, Li CR, Qin XJ, Yang XQ, Xie SD, Jiang Q, Zou LH, Zhang YJ, Zhu GL, Zhao P. Novel Alkaloids from Aspergillus fumigatus VDL36, an Endophytic Fungus Associated with Vaccinium dunalianum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10970-10980. [PMID: 38708787 DOI: 10.1021/acs.jafc.4c00371] [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: 05/07/2024]
Abstract
Eleven alkaloids (1-11) including seven new ones, 1-7, were isolated from the solid fermentation of Aspergillus fumigatus VDL36, an endophytic fungus isolated from the leaves of Vaccinium dunalianum Wight (Ericaceae), a perennial evergreen shrub distributed across the Southwest regions of China, Myanmar, and Vietnam. Their structures were elucidated on the basis of extensive spectroscopic methods. The isolates were evaluated for in vitro antifungal activities against five phytopathogenic fungi (Fusarium oxysporum, Coriolus versicolor, Fusarium solani, Botrytis cinerea, Fusarium graminearum). As a result, the new compounds fumigaclavine I (1), 13-ethoxycyclotryprostatin A (5), 13-dehydroxycyclotryprostatin A (6), and 12β-hydroxy-13-oxofumitremorgin C (7) exhibited antifungal activities with MIC values of 7.8-62.5 μg/mL which were comparable to the two positive controls ketoconazole (MIC = 7.8-31.25 μg/mL) and carbendazim (MIC = 1.95-7.8 μg/mL). Furthermore, compounds 1 and 5 demonstrated potent protective and curative effects against the tomato gray mold in vivo. Preliminary structure-activity relationships of the tested indole diketopiperazine alkaloids indicate that the introduction of a substituent group at position C-13 enhances their biological activities.
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Affiliation(s)
- Wei-Hua Wang
- Key Laboratory of State Forestry and Grassland Administration on Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Southwest Forestry University, Kunming 650224, P. R. China
- Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University, Zhaotong 657000, Yunnan, P. R. China
| | - Chu-Ran Li
- Key Laboratory of State Forestry and Grassland Administration on Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Southwest Forestry University, Kunming 650224, P. R. China
| | - Xu-Jie Qin
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, P. R. China
| | - Xiao-Qin Yang
- Key Laboratory of State Forestry and Grassland Administration on Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Southwest Forestry University, Kunming 650224, P. R. China
| | - Si-Da Xie
- Key Laboratory of State Forestry and Grassland Administration on Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Southwest Forestry University, Kunming 650224, P. R. China
| | - Qian Jiang
- Key Laboratory of State Forestry and Grassland Administration on Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Southwest Forestry University, Kunming 650224, P. R. China
| | - Li-Hua Zou
- Key Laboratory of State Forestry and Grassland Administration on Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Southwest Forestry University, Kunming 650224, P. R. China
| | - Ying-Jun Zhang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, P. R. China
| | - Guo-Lei Zhu
- Key Laboratory of State Forestry and Grassland Administration on Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Southwest Forestry University, Kunming 650224, P. R. China
| | - Ping Zhao
- Key Laboratory of State Forestry and Grassland Administration on Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Southwest Forestry University, Kunming 650224, P. R. China
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Na H, Zheng YY, Jia Y, Feng J, Huang J, Huang J, Wang CY, Yao G. Screening and genetic engineering of marine-derived Aspergillus terreus for high-efficient production of lovastatin. Microb Cell Fact 2024; 23:134. [PMID: 38724934 PMCID: PMC11084141 DOI: 10.1186/s12934-024-02396-z] [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: 01/18/2024] [Accepted: 04/17/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Lovastatin has widespread applications thanks to its multiple pharmacological effects. Fermentation by filamentous fungi represents the major way of lovastatin production. However, the current lovastatin productivity by fungal fermentation is limited and needs to be improved. RESULTS In this study, the lovastatin-producing strains of Aspergillus terreus from marine environment were screened, and their lovastatin productions were further improved by genetic engineering. Five strains of A. terreus were isolated from various marine environments. Their secondary metabolites were profiled by metabolomics analysis using Ultra Performance Liquid Chromatography-Mass spectrometry (UPLC-MS) with Global Natural Products Social Molecular Networking (GNPS), revealing that the production of secondary metabolites was variable among different strains. Remarkably, the strain of A. terreus MJ106 could principally biosynthesize the target drug lovastatin, which was confirmed by High Performance Liquid Chromatography (HPLC) and gene expression analysis. By one-factor experiment, lactose was found to be the best carbon source for A. terreus MJ106 to produce lovastatin. To improve the lovastatin titer in A. terreus MJ106, genetic engineering was applied to this strain. Firstly, a series of strong promoters was identified by transcriptomic and green fluorescent protein reporter analysis. Then, three selected strong promoters were used to overexpress the transcription factor gene lovE encoding the major transactivator for lov gene cluster expression. The results revealed that compared to A. terreus MJ106, all lovE over-expression mutants exhibited significantly more production of lovastatin and higher gene expression. One of them, LovE-b19, showed the highest lovastatin productivity at a titer of 1512 mg/L, which represents the highest production level reported in A. terreus. CONCLUSION Our data suggested that combination of strain screen and genetic engineering represents a powerful tool for improving the productivity of fungal secondary metabolites, which could be adopted for large-scale production of lovastatin in marine-derived A. terreus.
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Affiliation(s)
- Han Na
- Key Laboratory of Marine Drugs and Key Laboratory of Evolution and Marine Biodiversity (the Ministry of Education of China), Institute of Evolution & Marine Biodiversity, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Yao-Yao Zheng
- Key Laboratory of Marine Drugs and Key Laboratory of Evolution and Marine Biodiversity (the Ministry of Education of China), Institute of Evolution & Marine Biodiversity, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yaoning Jia
- Key Laboratory of Marine Drugs and Key Laboratory of Evolution and Marine Biodiversity (the Ministry of Education of China), Institute of Evolution & Marine Biodiversity, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Jingzhao Feng
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jizi Huang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
- School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jihao Huang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Chang-Yun Wang
- Key Laboratory of Marine Drugs and Key Laboratory of Evolution and Marine Biodiversity (the Ministry of Education of China), Institute of Evolution & Marine Biodiversity, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Guangshan Yao
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Institute of Oceanography, Minjiang University, Fuzhou, 350108, China.
- School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China.
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Skellam E, Rajendran S, Li L. Combinatorial biosynthesis for the engineering of novel fungal natural products. Commun Chem 2024; 7:89. [PMID: 38637654 PMCID: PMC11026467 DOI: 10.1038/s42004-024-01172-9] [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: 01/21/2024] [Accepted: 04/08/2024] [Indexed: 04/20/2024] Open
Abstract
Natural products are small molecules synthesized by fungi, bacteria and plants, which historically have had a profound effect on human health and quality of life. These natural products have evolved over millions of years resulting in specific biological functions that may be of interest for pharmaceutical, agricultural, or nutraceutical use. Often natural products need to be structurally modified to make them suitable for specific applications. Combinatorial biosynthesis is a method to alter the composition of enzymes needed to synthesize a specific natural product resulting in structurally diversified molecules. In this review we discuss different approaches for combinatorial biosynthesis of natural products via engineering fungal enzymes and biosynthetic pathways. We highlight the biosynthetic knowledge gained from these studies and provide examples of new-to-nature bioactive molecules, including molecules synthesized using combinations of fungal and non-fungal enzymes.
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Affiliation(s)
- Elizabeth Skellam
- Department of Chemistry, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA.
- BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA.
- Department of Biological Sciences, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA.
| | - Sanjeevan Rajendran
- Department of Chemistry, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA
- BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA
| | - Lei Li
- Department of Chemistry, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA
- BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA
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10
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Rothchild KW, Hagar M, Berry D, Ryan KS. Two Iron(II), α-Ketoglutarate-Dependent Enzymes Encoded by the PPZ Gene Cluster of Metarhizium majus Enable Production of 8-Hydroxyperamine. J Am Chem Soc 2024; 146:10263-10267. [PMID: 38578094 DOI: 10.1021/jacs.4c01419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Entomopathogenic fungus Metarhizium majus contains the nine-gene PPZ cluster, with ppzA, encoding a peramine-producing nonribosomal peptide synthetase, as the central component. In this work, the roles of two α-ketoglutarate, iron-dependent oxygenases encoded by the PPZ genes ppzC and ppzD were elucidated. PpzD was found to produce both trans-4-hydroxy-l-proline and trans-3-hydroxy-l-proline in a 13.1:1 ratio, yielding a key precursor for peramine biosynthesis. PpzC was found to act directly on peramine, yielding the novel analogue 8-hydroxyperamine.
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Affiliation(s)
- Kristina W Rothchild
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Mostafa Hagar
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Daniel Berry
- Ferrier Research Institute, Victoria University of Wellington, Wellington, 6012, New Zealand
| | - Katherine S Ryan
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
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11
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Seo HW, Wassano NS, Amir Rawa MS, Nickles GR, Damasio A, Keller NP. A Timeline of Biosynthetic Gene Cluster Discovery in Aspergillus fumigatus: From Characterization to Future Perspectives. J Fungi (Basel) 2024; 10:266. [PMID: 38667937 PMCID: PMC11051388 DOI: 10.3390/jof10040266] [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: 03/08/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
In 1999, the first biosynthetic gene cluster (BGC), synthesizing the virulence factor DHN melanin, was characterized in Aspergillus fumigatus. Since then, 19 additional BGCs have been linked to specific secondary metabolites (SMs) in this species. Here, we provide a comprehensive timeline of A. fumigatus BGC discovery and find that initial advances centered around the commonly expressed SMs where chemical structure informed rationale identification of the producing BGC (e.g., gliotoxin, fumigaclavine, fumitremorgin, pseurotin A, helvolic acid, fumiquinazoline). Further advances followed the transcriptional profiling of a ΔlaeA mutant, which aided in the identification of endocrocin, fumagillin, hexadehydroastechrome, trypacidin, and fumisoquin BGCs. These SMs and their precursors are the commonly produced metabolites in most A. fumigatus studies. Characterization of other BGC/SM pairs required additional efforts, such as induction treatments, including co-culture with bacteria (fumicycline/neosartoricin, fumigermin) or growth under copper starvation (fumivaline, fumicicolin). Finally, four BGC/SM pairs were discovered via overexpression technologies, including the use of heterologous hosts (fumicycline/neosartoricin, fumihopaside, sphingofungin, and sartorypyrone). Initial analysis of the two most studied A. fumigatus isolates, Af293 and A1160, suggested that both harbored ca. 34-36 BGCs. However, an examination of 264 available genomes of A. fumigatus shows up to 20 additional BGCs, with some strains showing considerable variations in BGC number and composition. These new BGCs present a new frontier in the future of secondary metabolism characterization in this important species.
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Affiliation(s)
- Hye-Won Seo
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, USA; (H.-W.S.); (N.S.W.); (M.S.A.R.); (G.R.N.)
| | - Natalia S. Wassano
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, USA; (H.-W.S.); (N.S.W.); (M.S.A.R.); (G.R.N.)
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), São Paulo 13083-970, Brazil;
| | - Mira Syahfriena Amir Rawa
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, USA; (H.-W.S.); (N.S.W.); (M.S.A.R.); (G.R.N.)
| | - Grant R. Nickles
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, USA; (H.-W.S.); (N.S.W.); (M.S.A.R.); (G.R.N.)
| | - André Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), São Paulo 13083-970, Brazil;
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, USA; (H.-W.S.); (N.S.W.); (M.S.A.R.); (G.R.N.)
- Department of Plant Pathology, University of Wisconsin, Madison, WI 53706, USA
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12
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Rinker DC, Sauters TJC, Steffen K, Gumilang A, Raja HA, Rangel-Grimaldo M, Pinzan CF, de Castro PA, dos Reis TF, Delbaje E, Houbraken J, Goldman GH, Oberlies NH, Rokas A. Strain heterogeneity in a non-pathogenic fungus highlights factors contributing to virulence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.583994. [PMID: 38496489 PMCID: PMC10942418 DOI: 10.1101/2024.03.08.583994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Fungal pathogens exhibit extensive strain heterogeneity, including variation in virulence. Whether closely related non-pathogenic species also exhibit strain heterogeneity remains unknown. Here, we comprehensively characterized the pathogenic potentials (i.e., the ability to cause morbidity and mortality) of 16 diverse strains of Aspergillus fischeri, a non-pathogenic close relative of the major pathogen Aspergillus fumigatus. In vitro immune response assays and in vivo virulence assays using a mouse model of pulmonary aspergillosis showed that A. fischeri strains varied widely in their pathogenic potential. Furthermore, pangenome analyses suggest that A. fischeri genomic and phenotypic diversity is even greater. Genomic, transcriptomic, and metabolomic profiling identified several pathways and secondary metabolites associated with variation in virulence. Notably, strain virulence was associated with the simultaneous presence of the secondary metabolites hexadehydroastechrome and gliotoxin. We submit that examining the pathogenic potentials of non-pathogenic close relatives is key for understanding the origins of fungal pathogenicity.
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Affiliation(s)
- David C. Rinker
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Thomas J. C. Sauters
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Karin Steffen
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Adiyantara Gumilang
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Huzefa A. Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Manuel Rangel-Grimaldo
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Camila Figueiredo Pinzan
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Patrícia Alves de Castro
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Thaila Fernanda dos Reis
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Endrews Delbaje
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Jos Houbraken
- Food and Indoor Mycology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Gustavo H. Goldman
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Nicholas H. Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
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13
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Garcia JF, Morales-Cruz A, Cochetel N, Minio A, Figueroa-Balderas R, Rolshausen PE, Baumgartner K, Cantu D. Comparative Pangenomic Insights into the Distinct Evolution of Virulence Factors Among Grapevine Trunk Pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:127-142. [PMID: 37934016 DOI: 10.1094/mpmi-09-23-0129-r] [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: 11/08/2023]
Abstract
The permanent organs of grapevines (Vitis vinifera L.), like those of other woody perennials, are colonized by various unrelated pathogenic ascomycete fungi secreting cell wall-degrading enzymes and phytotoxic secondary metabolites that contribute to host damage and disease symptoms. Trunk pathogens differ in the symptoms they induce and the extent and speed of damage. Isolates of the same species often display a wide virulence range, even within the same vineyard. This study focuses on Eutypa lata, Neofusicoccum parvum, and Phaeoacremonium minimum, causal agents of Eutypa dieback, Botryosphaeria dieback, and Esca, respectively. We sequenced 50 isolates from viticulture regions worldwide and built nucleotide-level, reference-free pangenomes for each species. Through examination of genomic diversity and pangenome structure, we analyzed intraspecific conservation and variability of putative virulence factors, focusing on functions under positive selection and recent gene family dynamics of contraction and expansion. Our findings reveal contrasting distributions of putative virulence factors in the core, dispensable, and private genomes of each pangenome. For example, carbohydrate active enzymes (CAZymes) were prevalent in the core genomes of each pangenome, whereas biosynthetic gene clusters were prevalent in the dispensable genomes of E. lata and P. minimum. The dispensable fractions were also enriched in Gypsy transposable elements and virulence factors under positive selection (polyketide synthase genes in E. lata and P. minimum, glycosyltransferases in N. parvum). Our findings underscore the complexity of the genomic architecture in each species and provide insights into their adaptive strategies, enhancing our understanding of the underlying mechanisms of virulence. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Jadran F Garcia
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
| | - Abraham Morales-Cruz
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, CA, U.S.A
| | - Noé Cochetel
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
| | - Andrea Minio
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
| | - Philippe E Rolshausen
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, U.S.A
| | - Kendra Baumgartner
- Crops Pathology and Genetics Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Davis, CA, U.S.A
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
- Genome Center, University of California, Davis, Davis, CA, U.S.A
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14
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Pandey P, Tripathi A, Dwivedi S, Lal K, Jhang T. Deciphering the mechanisms, hormonal signaling, and potential applications of endophytic microbes to mediate stress tolerance in medicinal plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1250020. [PMID: 38034581 PMCID: PMC10684941 DOI: 10.3389/fpls.2023.1250020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023]
Abstract
The global healthcare market in the post-pandemic era emphasizes a constant pursuit of therapeutic, adaptogenic, and immune booster drugs. Medicinal plants are the only natural resource to meet this by supplying an array of bioactive secondary metabolites in an economic, greener and sustainable manner. Driven by the thrust in demand for natural immunity imparting nutraceutical and life-saving plant-derived drugs, the acreage for commercial cultivation of medicinal plants has dramatically increased in recent years. Limited resources of land and water, low productivity, poor soil fertility coupled with climate change, and biotic (bacteria, fungi, insects, viruses, nematodes) and abiotic (temperature, drought, salinity, waterlogging, and metal toxicity) stress necessitate medicinal plant productivity enhancement through sustainable strategies. Plants evolved intricate physiological (membrane integrity, organelle structural changes, osmotic adjustments, cell and tissue survival, reclamation, increased root-shoot ratio, antibiosis, hypersensitivity, etc.), biochemical (phytohormones synthesis, proline, protein levels, antioxidant enzymes accumulation, ion exclusion, generation of heat-shock proteins, synthesis of allelochemicals. etc.), and cellular (sensing of stress signals, signaling pathways, modulating expression of stress-responsive genes and proteins, etc.) mechanisms to combat stresses. Endophytes, colonizing in different plant tissues, synthesize novel bioactive compounds that medicinal plants can harness to mitigate environmental cues, thus making the agroecosystems self-sufficient toward green and sustainable approaches. Medicinal plants with a host set of metabolites and endophytes with another set of secondary metabolites interact in a highly complex manner involving adaptive mechanisms, including appropriate cellular responses triggered by stimuli received from the sensors situated on the cytoplasm and transmitting signals to the transcriptional machinery in the nucleus to withstand a stressful environment effectively. Signaling pathways serve as a crucial nexus for sensing stress and establishing plants' proper molecular and cellular responses. However, the underlying mechanisms and critical signaling pathways triggered by endophytic microbes are meager. This review comprehends the diversity of endophytes in medicinal plants and endophyte-mediated plant-microbe interactions for biotic and abiotic stress tolerance in medicinal plants by understanding complex adaptive physiological mechanisms and signaling cascades involving defined molecular and cellular responses. Leveraging this knowledge, researchers can design specific microbial formulations that optimize plant health, increase nutrient uptake, boost crop yields, and support a resilient, sustainable agricultural system.
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Affiliation(s)
- Praveen Pandey
- Microbial Technology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
- Division of Plant Breeding and Genetic Resource Conservation, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Arpita Tripathi
- Microbial Technology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
- Faculty of Education, Teerthanker Mahaveer University, Moradabad, India
| | - Shweta Dwivedi
- Division of Plant Breeding and Genetic Resource Conservation, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kanhaiya Lal
- Division of Plant Breeding and Genetic Resource Conservation, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Tripta Jhang
- Division of Plant Breeding and Genetic Resource Conservation, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
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15
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Nickles GR, Oestereicher B, Keller NP, Drott M. Mining for a new class of fungal natural products: the evolution, diversity, and distribution of isocyanide synthase biosynthetic gene clusters. Nucleic Acids Res 2023; 51:7220-7235. [PMID: 37427794 PMCID: PMC10415135 DOI: 10.1093/nar/gkad573] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/16/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023] Open
Abstract
The products of non-canonical isocyanide synthase (ICS) biosynthetic gene clusters (BGCs) mediate pathogenesis, microbial competition, and metal-homeostasis through metal-associated chemistry. We sought to enable research into this class of compounds by characterizing the biosynthetic potential and evolutionary history of these BGCs across the Fungal Kingdom. We amalgamated a pipeline of tools to predict BGCs based on shared promoter motifs and located 3800 ICS BGCs in 3300 genomes, making ICS BGCs the fifth largest class of specialized metabolites compared to canonical classes found by antiSMASH. ICS BGCs are not evenly distributed across fungi, with evidence of gene-family expansions in several Ascomycete families. We show that the ICS dit1/2 gene cluster family (GCF), which was prior only studied in yeast, is present in ∼30% of all Ascomycetes. The dit variety ICS exhibits greater similarity to bacterial ICS than other fungal ICS, suggesting a potential convergence of the ICS backbone domain. The evolutionary origins of the dit GCF in Ascomycota are ancient and these genes are diversifying in some lineages. Our results create a roadmap for future research into ICS BGCs. We developed a website (https://isocyanides.fungi.wisc.edu/) that facilitates the exploration and downloading of all identified fungal ICS BGCs and GCFs.
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Affiliation(s)
- Grant R Nickles
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, WI 53706, USA
| | | | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, WI 53706, USA
- Department of Plant Pathology, University of Wisconsin—Madison, Madison, WI 53706, USA
| | - Milton T Drott
- USDA-ARS Cereal Disease Lab (CDL), St. Paul, MN 55108, USA
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16
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Song X, Chen M, Zhao Y, Zhang M, Zhang L, Zhang D, Song C, Shang X, Tan Q. Multi-stage nuclear transcriptomic insights of morphogenesis and biparental role changes in Lentinula edodes. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12624-y. [PMID: 37439832 DOI: 10.1007/s00253-023-12624-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 07/14/2023]
Abstract
Based on six offspring with different mitochondrial (M) and parental nuclear (N) genotypes, the multi-stage morphological characteristics and nuclear transcriptomes of Lentinula edodes were compared to investigate morphogenesis mechanisms during cultivation, the key reason for cultivar resistance to genotype changes, and regulation related to biparental role changes. Six offspring had specific transcriptomic data and morphological characteristics that were mainly regulated by the two parental nuclei, followed by the cytoplasm, at different growth stages. Importing a wild N genotype easily leads to failure or instability of fruiting; however, importing wild M genotypes may improve cultivars. Major facilitator superfamily (MFS) transporter genes encoding specific metabolites in spawns may play crucial roles in fruiting body formation. Pellets from submerged cultivation and spawns from sawdust substrate cultivation showed different carbon metabolic pathways, especially in secondary metabolism, degradation of lignin, cellulose and hemicellulose, and plasma membrane transport (mainly MFS). When the stage of small young pileus (SYP) was formed on the surface of the bag, the spawns inside were mainly involved in nutrient accumulation. Just broken pileus (JBP) showed a different expression of plasma membrane transporter genes related to intracellular material transport compared to SYP and showed different ribosomal proteins and cytochrome P450 functioning in protein biosynthesis and metabolism than near spreading pileus (NSP). Biparental roles mainly regulate offspring metabolism, growth, and morphogenesis by differentially expressing specific genes during different vegetative growth stages. Additionally, some genes encoding glycine-rich RNA-binding proteins, F-box, and folliculin-interacting protein repeat-containing proteins may be related to multi-stage morphogenesis. KEY POINTS: • Replacement of nuclear genotype is not suitable for cultivar breeding of L. edodes. • Some genes show a biparental role-divergent expression at mycelial growth stage. • Transcriptomic changes of some sawdust substrate cultivation stages have been elucidated.
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Affiliation(s)
- Xiaoxia Song
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
| | - Mingjie Chen
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
| | - Yan Zhao
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
| | - Meiyan Zhang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
| | - Lujun Zhang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
| | - Dang Zhang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
| | - Chunyan Song
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China.
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
| | - Xiaodong Shang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
| | - Qi Tan
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
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17
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Steenwyk JL, Knowles S, Bastos RW, Balamurugan C, Rinker D, Mead ME, Roberts CD, Raja HA, Li Y, Colabardini AC, de Castro PA, dos Reis TF, Canóvas D, Sanchez RL, Lagrou K, Torrado E, Rodrigues F, Oberlies NH, Zhou X, Goldman GH, Rokas A. Evolutionary origin, population diversity, and diagnostics for a cryptic hybrid pathogen. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.03.547508. [PMID: 37461539 PMCID: PMC10350022 DOI: 10.1101/2023.07.03.547508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Cryptic fungal pathogens pose significant identification and disease management challenges due to their morphological resemblance to known pathogenic species while harboring genetic and (often) infectionrelevant trait differences. The cryptic fungal pathogen Aspergillus latus, an allodiploid hybrid originating from Aspergillus spinulosporus and an unknown close relative of Aspergillus quadrilineatus within section Nidulantes, remains poorly understood. The absence of accurate diagnostics for A. latus has led to misidentifications, hindering epidemiological studies and the design of effective treatment plans. We conducted an in-depth investigation of the genomes and phenotypes of 44 globally distributed isolates (41 clinical isolates and three type strains) from Aspergillus section Nidulantes. We found that 21 clinical isolates were A. latus; notably, standard methods of pathogen identification misidentified all A. latus isolates. The remaining isolates were identified as A. spinulosporus (8), A. quadrilineatus (1), or A. nidulans (11). Phylogenomic analyses shed light on the origin of A. latus, indicating one or two hybridization events gave rise to the species during the Miocene, approximately 15.4 to 8.8 million years ago. Characterizing the A. latus pangenome uncovered substantial genetic diversity within gene families and biosynthetic gene clusters. Transcriptomic analysis revealed that both parental genomes are actively expressed in nearly equal proportions and respond to environmental stimuli. Further investigation into infection-relevant chemical and physiological traits, including drug resistance profiles, growth under oxidative stress conditions, and secondary metabolite biosynthesis, highlight distinct phenotypic profiles of the hybrid A. latus compared to its parental and closely related species. Leveraging our comprehensive genomic and phenotypic analyses, we propose five genomic and phenotypic markers as diagnostics for A. latus species identification. These findings provide valuable insights into the evolutionary origin, genomic outcome, and phenotypic implications of hybridization in a cryptic fungal pathogen, thus enhancing our understanding of the underlying processes contributing to fungal pathogenesis. Furthermore, our study underscores the effectiveness of extensive genomic and phenotypic analyses as a promising approach for developing diagnostics applicable to future investigations of cryptic and emerging pathogens.
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Affiliation(s)
- Jacob L. Steenwyk
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Vanderbilt University, Department of Biological Sciences, VU Station B #35–1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Sonja Knowles
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Rafael W. Bastos
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
- Department of Microbiology and Parasitology, Bioscience Center, Federal University of Rio Grande do Norte, Natal-RN, Brazil
| | - Charu Balamurugan
- Vanderbilt University, Department of Biological Sciences, VU Station B #35–1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - David Rinker
- Vanderbilt University, Department of Biological Sciences, VU Station B #35–1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Matthew E. Mead
- Vanderbilt University, Department of Biological Sciences, VU Station B #35–1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Christopher D. Roberts
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Huzefa A. Raja
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Yuanning Li
- Institute of Marine Science and Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Ana Cristina Colabardini
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Patrícia Alves de Castro
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Thaila Fernanda dos Reis
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - David Canóvas
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Rafael Luperini Sanchez
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Katrien Lagrou
- Department of Microbiology, Immunology and Transplantation, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- Department of Laboratory Medicine and National Reference Centre for Mycosis, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Egídio Torrado
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4715-495 Braga, Portugal; ICVS/3B’s-PT Government Associate Laboratory, 4715-495 Braga, Portugal
| | - Fernando Rodrigues
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4715-495 Braga, Portugal; ICVS/3B’s-PT Government Associate Laboratory, 4715-495 Braga, Portugal
| | - Nicholas H. Oberlies
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Gustavo H. Goldman
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Antonis Rokas
- Vanderbilt University, Department of Biological Sciences, VU Station B #35–1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
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18
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Meyer M, Slot J. The evolution and ecology of psilocybin in nature. Fungal Genet Biol 2023; 167:103812. [PMID: 37210028 DOI: 10.1016/j.fgb.2023.103812] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/19/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023]
Abstract
Fungi produce diverse metabolites that can have antimicrobial, antifungal, antifeedant, or psychoactive properties. Among these metabolites are the tryptamine-derived compounds psilocybin, its precursors, and natural derivatives (collectively referred to as psiloids), which have played significant roles in human society and culture. The high allocation of nitrogen to psiloids in mushrooms, along with evidence of convergent evolution and horizontal transfer of psilocybin genes, suggest they provide a selective benefit to some fungi. However, no precise ecological roles of psilocybin have been experimentally determined. The structural and functional similarities of psiloids to serotonin, an essential neurotransmitter in animals, suggest that they may enhance the fitness of fungi through interference with serotonergic processes. However, other ecological mechanisms of psiloids have been proposed. Here, we review the literature pertinent to psilocybin ecology and propose potential adaptive advantages psiloids may confer to fungi.
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Affiliation(s)
- Matthew Meyer
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA; Environmental Science Graduate Program, The Ohio State University, Columbus, OH 43210, USA; Center for Psychedelic Drug Research and Education, The Ohio State University, Columbus, OH 43210, USA.
| | - Jason Slot
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA; Center for Psychedelic Drug Research and Education, The Ohio State University, Columbus, OH 43210, USA.
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19
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Ramírez-Villalobos JM, Gomez-Flores R, Velázquez-Flores PV, Morán-Santibáñez KS, Tamez-Guerra P, Pérez-González O, de la Garza-Ramos MA, Rodríguez-Padilla C, Romo-Sáenz CI. Effect of Culture Conditions of Lophocereus marginatus Endophytic Fungi on Yield and Anticancer and Antioxidant Activities. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:ijerph20053948. [PMID: 36900961 PMCID: PMC10001847 DOI: 10.3390/ijerph20053948] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 05/29/2023]
Abstract
Culture conditions affect the production of secondary metabolites in endophytic fungi. Therefore, the aim of the present study was to evaluate the yield and anticancer and antioxidant activity of endophytic fungi extracts from the cactus Lophocereus marginatus, under different culture conditions. The strains Penicillium citrinum, Aspergillus versicolor, Metarhizium anisopliae, and Cladosporium sp. were fermented in different culture media (potato dextrose agar, Czapeck broth, and malt broth), types of inoculums (spore or mycelium), and shaking conditions (150 rpm or static) for one week. Methanol extracts were obtained from mycelia, which was followed by determining their yields and evaluating their effect on L5178Y-R murine lymphoma cells growth and human peripheral blood mononuclear cells (PBMCs) viability, using the 3-[4,5dimethylthiazol-2-yl]2,5-diphenyl tetrazolium bromide reduction colorimetric assay. In addition, antioxidant activity was determined by the 2,2-diphenyl-1-picrylhydrazyl test. We determined the half-maximal inhibitory concentration (IC50) values of tumor cell growth inhibition, the selectivity index (SI), and the antioxidant activity, as compared with the healthy cells control. The best yields were obtained with the Czapeck broth medium in all the evaluated strains, reaching values of 50.3%. Of the 48 extracts evaluated, only seven significantly (p < 0.01) inhibited tumor cell growth (IC50 < 250 µg/mL). A. versicolor extract showed the highest anticancer activity, after culturing spores (IC50 = 49.62 µg/mL; SI = 15.8) or mycelium (IC50 = 69.67 µg/mL; SI = 12.2) in malt broth, under static conditions. Extracts did not present significant antioxidant activity. In conclusion, we showed that culture conditions influenced the anticancer activity of L. marginatus endophytic fungi.
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Affiliation(s)
- Jesica María Ramírez-Villalobos
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Mexico
| | - Ricardo Gomez-Flores
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Mexico
| | - Priscilla Viridiana Velázquez-Flores
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Mexico
| | - Karla Selene Morán-Santibáñez
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Mexico
| | - Patricia Tamez-Guerra
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Mexico
| | - Orquídea Pérez-González
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Mexico
| | - Myriam Angélica de la Garza-Ramos
- Centro de Investigación y Desarrollo en Ciencias de la Salud, Facultad de Odontología, Universidad Autónoma de Nuevo León Dr. Eduardo Aguirre Pequeño y Silao S/N, Colonia Mitras Centro, Monterrey 64460, Mexico
| | - Cristina Rodríguez-Padilla
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Mexico
| | - César Iván Romo-Sáenz
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Mexico
- Universidad Emiliano Zapata, Avenida Rodrigo Gómez, Sector Heroico S/N, Monterrey 64260, Mexico
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20
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Marszalek-Zenczak M, Satyr A, Wojciechowski P, Zenczak M, Sobieszczanska P, Brzezinski K, Iefimenko T, Figlerowicz M, Zmienko A. Analysis of Arabidopsis non-reference accessions reveals high diversity of metabolic gene clusters and discovers new candidate cluster members. FRONTIERS IN PLANT SCIENCE 2023; 14:1104303. [PMID: 36778696 PMCID: PMC9909608 DOI: 10.3389/fpls.2023.1104303] [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: 11/21/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Metabolic gene clusters (MGCs) are groups of genes involved in a common biosynthetic pathway. They are frequently formed in dynamic chromosomal regions, which may lead to intraspecies variation and cause phenotypic diversity. We examined copy number variations (CNVs) in four Arabidopsis thaliana MGCs in over one thousand accessions with experimental and bioinformatic approaches. Tirucalladienol and marneral gene clusters showed little variation, and the latter was fixed in the population. Thalianol and especially arabidiol/baruol gene clusters displayed substantial diversity. The compact version of the thalianol gene cluster was predominant and more conserved than the noncontiguous version. In the arabidiol/baruol cluster, we found a large genomic insertion containing divergent duplicates of the CYP705A2 and BARS1 genes. The BARS1 paralog, which we named BARS2, encoded a novel oxidosqualene synthase. The expression of the entire arabidiol/baruol gene cluster was altered in the accessions with the duplication. Moreover, they presented different root growth dynamics and were associated with warmer climates compared to the reference-like accessions. In the entire genome, paired genes encoding terpene synthases and cytochrome P450 oxidases were more variable than their nonpaired counterparts. Our study highlights the role of dynamically evolving MGCs in plant adaptation and phenotypic diversity.
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Affiliation(s)
| | - Anastasiia Satyr
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Pawel Wojciechowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Institute of Computing Science, Faculty of Computing and Telecommunications, Poznan University of Technology, Poznan, Poland
| | - Michal Zenczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | | | | | - Tetiana Iefimenko
- Department of Biology, National University of Kyiv-Mohyla Academy, Kyiv, Ukraine
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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21
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Llewellyn T, Nowell RW, Aptroot A, Temina M, Prescott TAK, Barraclough TG, Gaya E. Metagenomics Shines Light on the Evolution of "Sunscreen" Pigment Metabolism in the Teloschistales (Lichen-Forming Ascomycota). Genome Biol Evol 2023; 15:6986375. [PMID: 36634008 PMCID: PMC9907504 DOI: 10.1093/gbe/evad002] [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: 09/26/2022] [Revised: 11/25/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Fungi produce a vast number of secondary metabolites that shape their interactions with other organisms and the environment. Characterizing the genes underpinning metabolite synthesis is therefore key to understanding fungal evolution and adaptation. Lichenized fungi represent almost one-third of Ascomycota diversity and boast impressive secondary metabolites repertoires. However, most lichen biosynthetic genes have not been linked to their metabolite products. Here we used metagenomic sequencing to survey gene families associated with production of anthraquinones, UV-protectant secondary metabolites present in various fungi, but especially abundant in a diverse order of lichens, the Teloschistales (class Lecanoromycetes, phylum Ascomycota). We successfully assembled 24 new, high-quality lichenized-fungal genomes de novo and combined them with publicly available Lecanoromycetes genomes from taxa with diverse secondary chemistry to produce a whole-genome tree. Secondary metabolite biosynthetic gene cluster (BGC) analysis showed that whilst lichen BGCs are numerous and highly dissimilar, core enzyme genes are generally conserved across taxa. This suggests metabolite diversification occurs via re-shuffling existing enzyme genes with novel accessory genes rather than BGC gains/losses or de novo gene evolution. We identified putative anthraquinone BGCs in our lichen dataset that appear homologous to anthraquinone clusters from non-lichenized fungi, suggesting these genes were present in the common ancestor of the subphylum Pezizomycotina. Finally, we identified unique transporter genes in Teloschistales anthraquinone BGCs that may explain why these metabolites are so abundant and ubiquitous in these lichens. Our results support the importance of metagenomics for understanding the secondary metabolism of non-model fungi such as lichens.
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Affiliation(s)
| | - Reuben W Nowell
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK,Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Andre Aptroot
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Avenida Costa e Silva s/n Bairro Universitário, Campo Grande, Mato Grosso do Sul CEP 79070-900, Brazil
| | - Marina Temina
- Institute of Evolution, University of Haifa, 199 Aba Khoushy Ave, Mount Carmel, Haifa, 3498838, Israel
| | - Thomas A K Prescott
- Comparative Fungal Biology, Royal Botanic Gardens, Kew, Jodrell Laboratory, Richmond, TW9 3DS, UK
| | - Timothy G Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK,Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Ester Gaya
- Comparative Fungal Biology, Royal Botanic Gardens, Kew, Jodrell Laboratory, Richmond, TW9 3DS, UK
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22
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Whole genome sequence characterization of Aspergillus terreus ATCC 20541 and genome comparison of the fungi A. terreus. Sci Rep 2023; 13:194. [PMID: 36604572 PMCID: PMC9814666 DOI: 10.1038/s41598-022-27311-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Aspergillus terreus is well-known for lovastatin and itaconic acid production with biomedical and commercial importance. The mechanisms of metabolite formation have been extensively studied to improve their yield through genetic engineering. However, the combined repertoire of carbohydrate-active enzymes (CAZymes), cytochrome P450s (CYP) enzymes, and secondary metabolites (SMs) in the different A. terreus strains has not been well studied yet, especially with respect to the presence of biosynthetic gene clusters (BGCs). Here we present a 30 Mb whole genome sequence of A. terreus ATCC 20541 in which we predicted 10,410 protein-coding genes. We compared the CAZymes, CYPs enzyme, and SMs across eleven A. terreus strains, and the results indicate that all strains have rich pectin degradation enzyme and CYP52 families. The lovastatin BGC of lovI was linked with lovF in A. terreus ATCC 20541, and the phenomenon was not found in the other strains. A. terreus ATCC 20541 lacked a non-ribosomal peptide synthetase (AnaPS) participating in acetylaszonalenin production, which was a conserved protein in the ten other strains. Our results present a comprehensive analysis of CAZymes, CYPs enzyme, and SM diversities in A. terreus strains and will facilitate further research in the function of BGCs associated with valuable SMs.
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23
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Zhao S, Martin-Vicente A, Colabardini AC, Pereira Silva L, Rinker DC, Fortwendel JR, Goldman GH, Gibbons JG. Genomic and Molecular Identification of Genes Contributing to the Caspofungin Paradoxical Effect in Aspergillus fumigatus. Microbiol Spectr 2022; 10:e0051922. [PMID: 36094204 PMCID: PMC9603777 DOI: 10.1128/spectrum.00519-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 08/17/2022] [Indexed: 11/25/2022] Open
Abstract
Aspergillus fumigatus is a deadly opportunistic fungal pathogen responsible for ~100,000 annual deaths. Azoles are the first line antifungal agent used against A. fumigatus, but azole resistance has rapidly evolved making treatment challenging. Caspofungin is an important second-line therapy against invasive pulmonary aspergillosis, a severe A. fumigatus infection. Caspofungin functions by inhibiting β-1,3-glucan synthesis, a primary and essential component of the fungal cell wall. A phenomenon termed the caspofungin paradoxical effect (CPE) has been observed in several fungal species where at higher concentrations of caspofungin, chitin replaces β-1,3-glucan, morphology returns to normal, and growth rate increases. CPE appears to occur in vivo, and it is therefore clinically important to better understand the genetic contributors to CPE. We applied genomewide association (GWA) analysis and molecular genetics to identify and validate candidate genes involved in CPE. We quantified CPE across 67 clinical isolates and conducted three independent GWA analyses to identify genetic variants associated with CPE. We identified 48 single nucleotide polymorphisms (SNPs) associated with CPE. We used a CRISPR/Cas9 approach to generate gene deletion mutants for seven genes harboring candidate SNPs. Two null mutants, ΔAfu3g13230 and ΔAfu4g07080 (dscP), resulted in reduced basal growth rate and a loss of CPE. We further characterized the dscP phosphatase-null mutant and observed a significant reduction in conidia production and extremely high sensitivity to caspofungin at both low and high concentrations. Collectively, our work reveals the contribution of Afu3g13230 and dscP in CPE and sheds new light on the complex genetic interactions governing this phenotype. IMPORTANCE This is one of the first studies to apply genomewide association (GWA) analysis to identify genes involved in an Aspergillus fumigatus phenotype. A. fumigatus is an opportunistic fungal pathogen that causes hundreds of thousands of infections and ~100,000 deaths each year, and antifungal resistance has rapidly evolved in this species. A phenomenon called the caspofungin paradoxical effect (CPE) occurs in some isolates, where high concentrations of the drug lead to increased growth rate. There is clinical relevance in understanding the genetic basis of this phenotype, since caspofungin concentrations could lead to unintended adverse clinical outcomes in certain cases. Using GWA analysis, we identified several interesting candidate polymorphisms and genes and then generated gene deletion mutants to determine whether these genes were important for CPE. Two of these mutant strains (ΔAfu3g13230 and ΔAfu4g07080/ΔdscP) displayed a loss of the CPE. This study sheds light on the genes involved in clinically important phenotype CPE.
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Affiliation(s)
- Shu Zhao
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
| | - Adela Martin-Vicente
- Department of Clinical Pharmacy and Translational Science, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Ana Cristina Colabardini
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Lilian Pereira Silva
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - David C. Rinker
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Jarrod R. Fortwendel
- Department of Clinical Pharmacy and Translational Science, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Gustavo Henrique Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - John G. Gibbons
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
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24
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Schüller A, Studt-Reinhold L, Strauss J. How to Completely Squeeze a Fungus-Advanced Genome Mining Tools for Novel Bioactive Substances. Pharmaceutics 2022; 14:1837. [PMID: 36145585 PMCID: PMC9505985 DOI: 10.3390/pharmaceutics14091837] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/23/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
Fungal species have the capability of producing an overwhelming diversity of bioactive substances that can have beneficial but also detrimental effects on human health. These so-called secondary metabolites naturally serve as antimicrobial "weapon systems", signaling molecules or developmental effectors for fungi and hence are produced only under very specific environmental conditions or stages in their life cycle. However, as these complex conditions are difficult or even impossible to mimic in laboratory settings, only a small fraction of the true chemical diversity of fungi is known so far. This also implies that a large space for potentially new pharmaceuticals remains unexplored. We here present an overview on current developments in advanced methods that can be used to explore this chemical space. We focus on genetic and genomic methods, how to detect genes that harbor the blueprints for the production of these compounds (i.e., biosynthetic gene clusters, BGCs), and ways to activate these silent chromosomal regions. We provide an in-depth view of the chromatin-level regulation of BGCs and of the potential to use the CRISPR/Cas technology as an activation tool.
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Affiliation(s)
| | | | - Joseph Strauss
- Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, A-3430 Tulln/Donau, Austria
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25
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Horta MAC, Steenwyk JL, Mead ME, dos Santos LHB, Zhao S, Gibbons JG, Marcet-Houben M, Gabaldón T, Rokas A, Goldman GH. Examination of Genome-Wide Ortholog Variation in Clinical and Environmental Isolates of the Fungal Pathogen Aspergillus fumigatus. mBio 2022; 13:e0151922. [PMID: 35766381 PMCID: PMC9426589 DOI: 10.1128/mbio.01519-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 06/02/2022] [Indexed: 11/20/2022] Open
Abstract
Aspergillus fumigatus is both an environmental saprobe and an opportunistic human fungal pathogen. Knowledge of genomic variation across A. fumigatus isolates is essential for understanding the evolution of pathogenicity, virulence, and resistance to antifungal drugs. Here, we investigated 206 A. fumigatus isolates (133 clinical and 73 environmental isolates), aiming to identify genes with variable presence across isolates and test whether this variation was related to the clinical or environmental origin of isolates. The PanOrtho genome of A. fumigatus consists of 13,085 ortholog groups, of which 7,773 (59.4%) are shared by all isolates (core groups) and 5,312 (40.6%) vary in their gene presence across isolates (accessory groups plus singletons). Despite differences in the distribution of orthologs across all isolates, no significant differences were observed among clinical versus environmental isolates when phylogeny was accounted for. Orthologs that differ in their distribution across isolates tend to occur at low frequency and/or be restricted to specific isolates; thus, the degree of genomic conservation between orthologs of A. fumigatus is high. These results suggest that differences in the distribution of orthologs within A. fumigatus cannot be associated with the clinical or environmental origin of isolates. IMPORTANCE Aspergillus fumigatus is a cosmopolitan species of fungus responsible for thousands of cases of invasive disease annually. Clinical and environmental isolates of A. fumigatus exhibit extensive phenotypic differences, including differences related to virulence and antifungal drug resistance. A comprehensive survey of the genomic diversity present in A. fumigatus and its relationship to the clinical or environmental origin of isolates can contribute to the prediction of the mechanisms of evolution and infection of the species. Our results suggest that there is no significant variation in ortholog distribution between clinical and environmental isolates when accounting for evolutionary history. The work supports the hypothesis that environmental and clinical isolates of A. fumigatus do not differ in their gene contents.
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Affiliation(s)
- Maria Augusta C. Horta
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Jacob L. Steenwyk
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Matthew E. Mead
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | | | - Shu Zhao
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
| | - John G. Gibbons
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
| | - Marina Marcet-Houben
- Barcelona Supercomputing Centre, Barcelona, Spain
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre, Barcelona, Spain
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas, Barcelona, Spain
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
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26
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Sayari M, Dolatabadian A, El-Shetehy M, Rehal PK, Daayf F. Genome-Based Analysis of Verticillium Polyketide Synthase Gene Clusters. BIOLOGY 2022; 11:biology11091252. [PMID: 36138731 PMCID: PMC9495618 DOI: 10.3390/biology11091252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Fungi can produce many types of secondary metabolites, including mycotoxins. Poisonous mushrooms and mycotoxins that cause food spoilage have been known for a very long time. For example, Aspergillus flavus, which can grow on grains and nuts, produces highly toxic substances called Aflatoxins. Despite their menace to other living organisms, mycotoxins can be used for medicinal purposes, i.e., as antibiotics, growth-promoting compounds, and other kinds of drugs. These and other secondary metabolites produced by plant-pathogenic fungi may cause host plants to display disease symptoms and may play a substantial role in disease progression. Therefore, the identification and characterization of the genes involved in their biosynthesis are essential for understanding the molecular mechanism involved in their biosynthetic pathways and further promoting sustainable knowledge-based crop production. Abstract Polyketides are structurally diverse and physiologically active secondary metabolites produced by many organisms, including fungi. The biosynthesis of polyketides from acyl-CoA thioesters is catalyzed by polyketide synthases, PKSs. Polyketides play roles including in cell protection against oxidative stress, non-constitutive (toxic) roles in cell membranes, and promoting the survival of the host organisms. The genus Verticillium comprises many species that affect a wide range of organisms including plants, insects, and other fungi. Many are known as causal agents of Verticillium wilt diseases in plants. In this study, a comparative genomics approach involving several Verticillium species led us to evaluate the potential of Verticillium species for producing polyketides and to identify putative polyketide biosynthesis gene clusters. The next step was to characterize them and predict the types of polyketide compounds they might produce. We used publicly available sequences from ten species of Verticillium including V. dahliae, V. longisporum, V. nonalfalfae, V. alfalfae, V. nubilum, V. zaregamsianum, V. klebahnii, V. tricorpus, V. isaacii, and V. albo-atrum to identify and characterize PKS gene clusters by utilizing a range of bioinformatic and phylogenetic approaches. We found 32 putative PKS genes and possible clusters in the genomes of Verticillium species. All the clusters appear to be complete and functional. In addition, at least five clusters including putative DHN-melanin-, cytochalasin-, fusarielien-, fujikurin-, and lijiquinone-like compounds may belong to the active PKS repertoire of Verticillium. These results will pave the way for further functional studies to understand the role of these clusters.
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Affiliation(s)
- Mohammad Sayari
- Department of Plant Science, Faculty of Agricultural and Food Sciences, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2, Canada
| | - Aria Dolatabadian
- Department of Plant Science, Faculty of Agricultural and Food Sciences, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2, Canada
| | - Mohamed El-Shetehy
- Department of Plant Science, Faculty of Agricultural and Food Sciences, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2, Canada
- Department of Botany, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Pawanpuneet Kaur Rehal
- Department of Plant Science, Faculty of Agricultural and Food Sciences, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2, Canada
| | - Fouad Daayf
- Department of Plant Science, Faculty of Agricultural and Food Sciences, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2, Canada
- Correspondence:
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Wang L, Ge S, Liang W, Liao W, Li W, Jiao G, Wei X, Shao G, Xie L, Sheng Z, Hu S, Tang S, Hu P. Genome-Wide Characterization Reveals Variation Potentially Involved in Pathogenicity and Mycotoxins Biosynthesis of Fusarium proliferatum Causing Spikelet Rot Disease in Rice. Toxins (Basel) 2022; 14:toxins14080568. [PMID: 36006230 PMCID: PMC9414198 DOI: 10.3390/toxins14080568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/04/2022] [Accepted: 08/17/2022] [Indexed: 12/12/2022] Open
Abstract
Fusarium proliferatum is the primary cause of spikelet rot disease in rice (Oryza sativa L.) in China. The pathogen not only infects a wide range of cereals, causing severe yield losses but also contaminates grains by producing various mycotoxins that are hazardous to humans and animals. Here, we firstly reported the whole-genome sequence of F. proliferatum strain Fp9 isolated from the rice spikelet. The genome was approximately 43.9 Mb with an average GC content of 48.28%, and it was assembled into 12 scaffolds with an N50 length of 4,402,342 bp. There is a close phylogenetic relationship between F. proliferatum and Fusarium fujikuroi, the causal agent of the bakanae disease of rice. The expansion of genes encoding cell wall-degrading enzymes and major facilitator superfamily (MFS) transporters was observed in F. proliferatum relative to other fungi with different nutritional lifestyles. Species-specific genes responsible for mycotoxins biosynthesis were identified among F. proliferatum and other Fusarium species. The expanded and unique genes were supposed to promote F. proliferatum adaptation and the rapid response to the host's infection. The high-quality genome of F. proliferatum strain Fp9 provides a valuable resource for deciphering the mechanisms of pathogenicity and secondary metabolism, and therefore shed light on development of the disease management strategies and detoxification of mycotoxins contamination for spikelet rot disease in rice.
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Rivera-Chávez J, Ceapă CD, Figueroa M. Biological Dark Matter Exploration using Data Mining for the Discovery of Antimicrobial Natural Products. PLANTA MEDICA 2022; 88:702-720. [PMID: 35697058 DOI: 10.1055/a-1795-0562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The discovery of novel antimicrobials has significantly slowed down over the last three decades. At the same time, humans rely increasingly on antimicrobials because of the progressive antimicrobial resistance in medical practices, human communities, and the environment. Data mining is currently considered a promising option in the discovery of new antibiotics. Some of the advantages of data mining are the ability to predict chemical structures from sequence data, anticipation of the presence of novel metabolites, the understanding of gene evolution, and the corroboration of data from multiple omics technologies. This review analyzes the state-of-the-art for data mining in the fields of bacteria, fungi, and plant genomic data, as well as metabologenomics. It also summarizes some of the most recent research accomplishments in the field, all pinpointing to innovation through uncovering and implementing the next generation of antimicrobials.
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Affiliation(s)
- José Rivera-Chávez
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Corina-Diana Ceapă
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Mario Figueroa
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
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Kuhnert E, Collemare J. A genomic journey in the secondary metabolite diversity of fungal plant and insect pathogens: from functional to population genomics. Curr Opin Microbiol 2022; 69:102178. [PMID: 35870224 DOI: 10.1016/j.mib.2022.102178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/01/2022] [Accepted: 06/23/2022] [Indexed: 11/03/2022]
Abstract
Fungal pathogens produce a broad array of secondary metabolites (SMs), which allow the fungus to thrive in its natural habitat and gain competitive advantage. Analysis of the genetically encoded blueprints for SM assembly highlighted that only a small portion of the SMs these fungi are capable of producing are known, and even fewer have been investigated for their natural function. Using molecular tools, a lot of progress has been made recently in identifying the blueprint products and linking them to their ecological purpose such as the peptide virulence factor fusaoctaxin A released by Fusarium graminearum during infection of wheat or the F. oxysporum polyketide bikaverin that provides competitive advantage against bacteria in tomato. In addition, population genomics have given particularly important insights into the species-specific plasticity of the SM blueprint arsenal, showcasing the ongoing evolution and adaptation of fungal pathogens. This approach holds promise in inferring roles in pathogenicity of many more fungal SMs.
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Affiliation(s)
- Eric Kuhnert
- Centre of Biomolecular Drug Research (BMWZ), Institute for Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany.
| | - Jérôme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
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Ilyukhin E, Markovskaja S, Elgorban AM, Al-Rejaie SS, Maharachchikumbura SS. Genomic Characteristics and Comparative Genomics Analysis of Parafenestella ontariensis sp. nov. J Fungi (Basel) 2022; 8:jof8070732. [PMID: 35887487 PMCID: PMC9318755 DOI: 10.3390/jof8070732] [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: 06/04/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
A new ascomycetous species of Parafenestella was isolated from Acer negundo during the survey of diseased trees in Southern Ontario, Canada. The species is morphologically similar to other taxa of Cucurbitariacea (Pleosporales). The new species is different from the extant species in the morphology of ascospores, culture characteristics and molecular data. The novel species is described as Parafenestella ontariensis sp. nov. based on morphological and multi-gene phylogenetic analyses using a combined set of ITS, LSU, tef1 and tub2 loci. Additionally, the genome of P. ontariensis was sequenced and analyzed. The phylogenomic analysis confirmed the close relationship of the species to the fenestelloid clades of Cucurbitariaceae. The comparative genomics analysis revealed that the species lifestyle appears to be multitrophic (necrotrophic or hemi-biotrophic) with a capability to turn pathogenic on a corresponding plant host.
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Affiliation(s)
- Evgeny Ilyukhin
- Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada
- Correspondence: or
| | | | - Abdallah M. Elgorban
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Salim S. Al-Rejaie
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Sajeewa S.N. Maharachchikumbura
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China;
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Wu D, Jiang B, Ye CY, Timko MP, Fan L. Horizontal transfer and evolution of the biosynthetic gene cluster for benzoxazinoids in plants. PLANT COMMUNICATIONS 2022; 3:100320. [PMID: 35576160 PMCID: PMC9251436 DOI: 10.1016/j.xplc.2022.100320] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/07/2022] [Accepted: 03/23/2022] [Indexed: 05/11/2023]
Abstract
Benzoxazinoids are a class of protective and allelopathic plant secondary metabolites that have been identified in multiple grass species and are encoded by the Bx biosynthetic gene cluster (BGC) in maize. Data mining of 41 high-quality grass genomes identified complete Bx clusters (containing genes Bx1-Bx5 and Bx8) in three genera (Zea, Echinochloa, and Dichanthelium) of Panicoideae and partial clusters in Triticeae. The Bx cluster probably originated from gene duplication and chromosomal translocation of native homologs of Bx genes. An ancient Bx cluster that included additional Bx genes (e.g., Bx6) is presumed to have been present in ancestral Panicoideae. The ancient Bx cluster was putatively gained by the Triticeae ancestor via horizontal transfer (HT) from the ancestral Panicoideae and later separated into multiple segments on different chromosomes. Bx6 appears to have been under less constrained selection compared with the Bx cluster during the evolution of Panicoideae, as evidenced by the fact that it was translocated away from the Bx cluster in Zea mays, moved to other chromosomes in Echinochloa, and even lost in Dichanthelium. Further investigations indicate that purifying selection and polyploidization have shaped the evolutionary trajectory of Bx clusters in the grass family. This study provides the first candidate case of HT of a BGC between plants and sheds new light on the evolution of BGCs.
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Affiliation(s)
- Dongya Wu
- Hainan Institute of Zhejiang University, Yonyou Industrial Park, Sanya 572025, China; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Bowen Jiang
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Chu-Yu Ye
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Longjiang Fan
- Hainan Institute of Zhejiang University, Yonyou Industrial Park, Sanya 572025, China; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.
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Henriksen NNSE, Lindqvist LL, Wibowo M, Sonnenschein EC, Bentzon-Tilia M, Gram L. Role is in the eye of the beholder-the multiple functions of the antibacterial compound tropodithietic acid produced by marine Rhodobacteraceae. FEMS Microbiol Rev 2022; 46:fuac007. [PMID: 35099011 PMCID: PMC9075582 DOI: 10.1093/femsre/fuac007] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 11/13/2022] Open
Abstract
Many microbial secondary metabolites have been studied for decades primarily because of their antimicrobial properties. However, several of these metabolites also possess nonantimicrobial functions, both influencing the physiology of the producer and their ecological neighbors. An example of a versatile bacterial secondary metabolite with multiple functions is the tropone derivative tropodithietic acid (TDA). TDA is a broad-spectrum antimicrobial compound produced by several members of the Rhodobacteraceae family, a major marine bacterial lineage, within the genera Phaeobacter, Tritonibacter, and Pseudovibrio. The production of TDA is governed by the mode of growth and influenced by the availability of nutrient sources. The antibacterial effect of TDA is caused by disruption of the proton motive force of target microorganisms and, potentially, by its iron-chelating properties. TDA also acts as a signaling molecule, affecting gene expression in other bacteria, and altering phenotypic traits such as motility, biofilm formation, and antibiotic production in the producer. In microbial communities, TDA-producing bacteria cause a reduction of the relative abundance of closely related species and some fast-growing heterotrophic bacteria. Here, we summarize the current understanding of the chemical ecology of TDA, including the environmental niches of TDA-producing bacteria, and the molecular mechanisms governing the function and regulation of TDA.
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Affiliation(s)
- Nathalie N S E Henriksen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
| | - Laura L Lindqvist
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
| | - Mario Wibowo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
| | - Eva C Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
| | - Mikkel Bentzon-Tilia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
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Brown DW, Kim HS, McGovern A, Probyn C, Proctor RH. Genus-wide analysis of Fusarium polyketide synthases reveals broad chemical potential. Fungal Genet Biol 2022; 160:103696. [DOI: 10.1016/j.fgb.2022.103696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/25/2022] [Accepted: 04/18/2022] [Indexed: 11/27/2022]
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Phylogenetic Comparison of Swainsonine Biosynthetic Gene Clusters among Fungi. J Fungi (Basel) 2022; 8:jof8040359. [PMID: 35448590 PMCID: PMC9030584 DOI: 10.3390/jof8040359] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/18/2022] [Accepted: 03/26/2022] [Indexed: 02/01/2023] Open
Abstract
Swainsonine is a cytotoxic alkaloid produced by fungi. Genome sequence analyses revealed that these fungi share an orthologous gene cluster, SWN, necessary for swainsonine biosynthesis. To investigate the SWN cluster, the gene sequences and intergenic regions were assessed in organisms containing swnK, which is conserved across all fungi that produce swainsonine. The orders of fungi which contained orthologous swainsonine genes included Pleosporales, Onygenales, Hypocreales, Chaetothyriales, Xylariales, Capnodiales, Microthyriales, Caliciales, Patellariales, Eurotiales, and a species of the Leotiomycetes. SwnK and swnH2 genes were conserved across all fungi containing the SWN cluster; in contrast, swnT and swnA were found in a limited number of fungi containing the SWN cluster. The phylogenetic data suggest that in some orders that the SWN cluster was gained once from a common ancestor while in other orders it was likely gained several times from one or more common ancestors. The data also show that rearrangements and inversions of the SWN cluster happened within a genus as species diverged. Analysis of the intergenic regions revealed different combinations and inversions of open reading frames, as well as absence of genes. These results provide evidence of a complex evolutionary history of the SWN cluster in fungi.
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Colabardini AC, Wang F, Dong Z, Pardeshi L, Rocha MC, Costa JH, dos Reis TF, Brown A, Jaber QZ, Fridman M, Fill T, Rokas A, Malavazi I, Wong KH, Goldman GH. Heterogeneity in the transcriptional response of the human pathogen Aspergillus fumigatus to the antifungal agent caspofungin. Genetics 2022; 220:iyab183. [PMID: 34718550 PMCID: PMC8733440 DOI: 10.1093/genetics/iyab183] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/07/2021] [Indexed: 01/11/2023] Open
Abstract
Aspergillus fumigatus is the main causative agent of invasive pulmonary aspergillosis (IPA), a severe disease that affects immunosuppressed patients worldwide. The fungistatic drug caspofungin (CSP) is the second line of therapy against IPA but has increasingly been used against clinical strains that are resistant to azoles, the first line antifungal therapy. In high concentrations, CSP induces a tolerance phenotype with partial reestablishment of fungal growth called CSP paradoxical effect (CPE), resulting from a change in the composition of the cell wall. An increasing number of studies has shown that different isolates of A. fumigatus exhibit phenotypic heterogeneity, including heterogeneity in their CPE response. To gain insights into the underlying molecular mechanisms of CPE response heterogeneity, we analyzed the transcriptomes of two A. fumigatus reference strains, Af293 and CEA17, exposed to low and high CSP concentrations. We found that there is a core transcriptional response that involves genes related to cell wall remodeling processes, mitochondrial function, transmembrane transport, and amino acid and ergosterol metabolism, and a variable response related to secondary metabolite (SM) biosynthesis and iron homeostasis. Specifically, we show here that the overexpression of a SM pathway that works as an iron chelator extinguishes the CPE in both backgrounds, whereas iron depletion is detrimental for the CPE in Af293 but not in CEA17. We next investigated the function of the transcription factor CrzA, whose deletion was previously shown to result in heterogeneity in the CPE response of the Af293 and CEA17 strains. We found that CrzA constitutively binds to and modulates the expression of several genes related to processes involved in CSP tolerance and that crzA deletion differentially impacts the SM production and growth of Af293 and CEA17. As opposed to the ΔcrzACEA17 mutant, the ΔcrzAAf293 mutant fails to activate cell wall remodeling genes upon CSP exposure, which most likely severely affects its macrostructure and extinguishes its CPE. This study describes how heterogeneity in the response to an antifungal agent between A. fumigatus strains stems from heterogeneity in the function of a transcription factor and its downstream target genes.
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Affiliation(s)
- Ana Cristina Colabardini
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo CEP 14040-903, Brazil
- Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Fang Wang
- Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Zhiqiang Dong
- Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Lakhansing Pardeshi
- Faculty of Health Sciences, University of Macau, Macau 999078, China
- Genomics, Bioinformatics and Single Cell Analysis Core, Faculty of Health Sciences, University of Macau, Macau, 999078, China
| | - Marina Campos Rocha
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos CEP 13565-905, Brazil
| | - Jonas Henrique Costa
- Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo CEP 13083-970, Brazil
| | - Thaila Fernanda dos Reis
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo CEP 14040-903, Brazil
| | - Alec Brown
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Qais Z Jaber
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Micha Fridman
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Taicia Fill
- Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo CEP 13083-970, Brazil
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Iran Malavazi
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos CEP 13565-905, Brazil
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Macau 999078, China
- Faculty of Health Sciences, Institute of Translational Medicine, University of Macau, Macau 999078, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Macau 999078, China
| | - Gustavo Henrique Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo CEP 14040-903, Brazil
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de Castro PA, Colabardini AC, Moraes M, Horta MAC, Knowles SL, Raja HA, Oberlies NH, Koyama Y, Ogawa M, Gomi K, Steenwyk JL, Rokas A, Gonçales RA, Duarte-Oliveira C, Carvalho A, Ries LNA, Goldman GH. Regulation of gliotoxin biosynthesis and protection in Aspergillus species. PLoS Genet 2022; 18:e1009965. [PMID: 35041649 PMCID: PMC8797188 DOI: 10.1371/journal.pgen.1009965] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/28/2022] [Accepted: 01/04/2022] [Indexed: 02/07/2023] Open
Abstract
Aspergillus fumigatus causes a range of human and animal diseases collectively known as aspergillosis. A. fumigatus possesses and expresses a range of genetic determinants of virulence, which facilitate colonisation and disease progression, including the secretion of mycotoxins. Gliotoxin (GT) is the best studied A. fumigatus mycotoxin with a wide range of known toxic effects that impair human immune cell function. GT is also highly toxic to A. fumigatus and this fungus has evolved self-protection mechanisms that include (i) the GT efflux pump GliA, (ii) the GT neutralising enzyme GliT, and (iii) the negative regulation of GT biosynthesis by the bis-thiomethyltransferase GtmA. The transcription factor (TF) RglT is the main regulator of GliT and this GT protection mechanism also occurs in the non-GT producing fungus A. nidulans. However, the A. nidulans genome does not encode GtmA and GliA. This work aimed at analysing the transcriptional response to exogenous GT in A. fumigatus and A. nidulans, two distantly related Aspergillus species, and to identify additional components required for GT protection. RNA-sequencing shows a highly different transcriptional response to exogenous GT with the RglT-dependent regulon also significantly differing between A. fumigatus and A. nidulans. However, we were able to observe homologs whose expression pattern was similar in both species (43 RglT-independent and 11 RglT-dependent). Based on this approach, we identified a novel RglT-dependent methyltranferase, MtrA, involved in GT protection. Taking into consideration the occurrence of RglT-independent modulated genes, we screened an A. fumigatus deletion library of 484 transcription factors (TFs) for sensitivity to GT and identified 15 TFs important for GT self-protection. Of these, the TF KojR, which is essential for kojic acid biosynthesis in Aspergillus oryzae, was also essential for virulence and GT biosynthesis in A. fumigatus, and for GT protection in A. fumigatus, A. nidulans, and A. oryzae. KojR regulates rglT, gliT, gliJ expression and sulfur metabolism in Aspergillus species. Together, this study identified conserved components required for GT protection in Aspergillus species. A. fumigatus secretes mycotoxins that are essential for its virulence and pathogenicity. Gliotoxin (GT) is a sulfur-containing mycotoxin, which is known to impair several aspects of the human immune response. GT is also toxic to different fungal species, which have evolved several GT protection strategies. To further decipher these responses, we used transcriptional profiling aiming to compare the response to GT in the GT producer A. fumigatus and the GT non-producer A. nidulans. This analysis allowed us to identify additional genes with a potential role in GT protection. We also identified 15 transcription factors (TFs) encoded in the A. fumigatus genome that are important for conferring resistance to exogenous gliotoxin. One of these TFs, KojR, which is essential for A. oryzae kojic acid production, is also important for virulence in A. fumigatus and GT protection in A. fumigatus, A. nidulans and A. oryzae. KojR regulates the expression of genes important for gliotoxin biosynthesis and protection, and sulfur metabolism. Together, this work identified conserved components required for gliotoxin protection in Aspergillus species.
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Affiliation(s)
- Patrícia Alves de Castro
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Ana Cristina Colabardini
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Maísa Moraes
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | | | - Sonja L. Knowles
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, North Carolina United States of America
| | - Huzefa A. Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, North Carolina United States of America
| | - Nicholas H. Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, North Carolina United States of America
| | - Yasuji Koyama
- Noda Institute for Scientific Research, 338 Noda, Chiba, Japan
| | - Masahiro Ogawa
- Noda Institute for Scientific Research, 338 Noda, Chiba, Japan
| | - Katsuya Gomi
- Department of Bioindustrial Informatics and Genomics, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Relber A. Gonçales
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Cláudio Duarte-Oliveira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Agostinho Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Laure N. A. Ries
- MRC Centre for Medical Mycology at the University of Exeter, Geoffrey Pope Building, Exeter, United Kingdom
- * E-mail: (LNAR); (GHG)
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- * E-mail: (LNAR); (GHG)
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37
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Colabardini AC, Wang F, Miao Z, Pardeshi L, Valero C, de Castro PA, Akiyama DY, Tan K, Nora LC, Silva-Rocha R, Marcet-Houben M, Gabaldón T, Fill T, Wong KH, Goldman GH. Chromatin profiling reveals heterogeneity in clinical isolates of the human pathogen Aspergillus fumigatus. PLoS Genet 2022; 18:e1010001. [PMID: 35007279 PMCID: PMC8782537 DOI: 10.1371/journal.pgen.1010001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 01/21/2022] [Accepted: 12/17/2021] [Indexed: 12/21/2022] Open
Abstract
Invasive Pulmonary Aspergillosis, which is caused by the filamentous fungus Aspergillus fumigatus, is a life-threatening infection for immunosuppressed patients. Chromatin structure regulation is important for genome stability maintenance and has the potential to drive genome rearrangements and affect virulence and pathogenesis of pathogens. Here, we performed the first A. fumigatus global chromatin profiling of two histone modifications, H3K4me3 and H3K9me3, focusing on the two most investigated A. fumigatus clinical isolates, Af293 and CEA17. In eukaryotes, H3K4me3 is associated with active transcription, while H3K9me3 often marks silent genes, DNA repeats, and transposons. We found that H3K4me3 deposition is similar between the two isolates, while H3K9me3 is more variable and does not always represent transcriptional silencing. Our work uncovered striking differences in the number, locations, and expression of transposable elements between Af293 and CEA17, and the differences are correlated with H3K9me3 modifications and higher genomic variations among strains of Af293 background. Moreover, we further showed that the Af293 strains from different laboratories actually differ in their genome contents and found a frequently lost region in chromosome VIII. For one such Af293 variant, we identified the chromosomal changes and demonstrated their impacts on its secondary metabolites production, growth and virulence. Overall, our findings not only emphasize the influence of genome heterogeneity on A. fumigatus fitness, but also caution about unnoticed chromosomal variations among common laboratory strains.
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Affiliation(s)
- Ana Cristina Colabardini
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
- Faculty of Health Sciences, University of Macau, Macau SAR of China
| | - Fang Wang
- Faculty of Health Sciences, University of Macau, Macau SAR of China
- Intensive Care Unit, Biomedical Research Center, Shenzhen Institute of Translational Medicine, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Zhengqiang Miao
- Faculty of Health Sciences, University of Macau, Macau SAR of China
| | - Lakhansing Pardeshi
- Faculty of Health Sciences, University of Macau, Macau SAR of China
- Genomics, Bioinformatics and Single Cell Analysis Core, Faculty of Health Sciences, University of Macau, Macau SAR of China
| | - Clara Valero
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Patrícia Alves de Castro
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Daniel Yuri Akiyama
- Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Kaeling Tan
- Faculty of Health Sciences, University of Macau, Macau SAR of China
- Genomics, Bioinformatics and Single Cell Analysis Core, Faculty of Health Sciences, University of Macau, Macau SAR of China
| | - Luisa Czamanski Nora
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Rafael Silva-Rocha
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Marina Marcet-Houben
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Taicia Fill
- Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Macau SAR of China
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau SAR of China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR of China
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
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Vertical Inheritance Facilitates Interspecies Diversification in Biosynthetic Gene Clusters and Specialized Metabolites. mBio 2021; 12:e0270021. [PMID: 34809466 PMCID: PMC8609351 DOI: 10.1128/mbio.02700-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
While specialized metabolites are thought to mediate ecological interactions, the evolutionary processes driving chemical diversification, particularly among closely related lineages, remain poorly understood. Here, we examine the evolutionary dynamics governing the distribution of natural product biosynthetic gene clusters (BGCs) among 118 strains representing all nine currently named species of the marine actinobacterial genus Salinispora. While much attention has been given to the role of horizontal gene transfer (HGT) in structuring BGC distributions, we find that vertical descent facilitates interspecies BGC diversification over evolutionary timescales. Moreover, we identified a distinct phylogenetic signal among Salinispora species at both the BGC and metabolite level, indicating that specialized metabolism represents a conserved phylogenetic trait. Using a combination of genomic analyses and liquid chromatography–high-resolution tandem mass spectrometry (LC-MS/MS) targeting nine experimentally characterized BGCs and their small molecule products, we identified gene gain/loss events, constrained interspecies recombination, and other evolutionary processes associated with vertical inheritance as major contributors to BGC diversification. These evolutionary dynamics had direct consequences for the compounds produced, as exemplified by species-level differences in salinosporamide production. Together, our results support the concept that specialized metabolites, and their cognate BGCs, can represent phylogenetically conserved functional traits with chemical diversification proceeding in species-specific patterns over evolutionary time frames.
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Barber AE, Sae-Ong T, Kang K, Seelbinder B, Li J, Walther G, Panagiotou G, Kurzai O. Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection. Nat Microbiol 2021; 6:1526-1536. [PMID: 34819642 DOI: 10.1038/s41564-021-00993-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 10/08/2021] [Indexed: 12/25/2022]
Abstract
Aspergillus fumigatus is an environmental saprobe and opportunistic human fungal pathogen. Despite an estimated annual occurrence of more than 300,000 cases of invasive disease worldwide, a comprehensive survey of the genomic diversity present in A. fumigatus-including the relationship between clinical and environmental isolates and how this genetic diversity contributes to virulence and antifungal drug resistance-has been lacking. In this study we define the pan-genome of A. fumigatus using a collection of 300 globally sampled genomes (83 clinical and 217 environmental isolates). We found that 7,563 of the 10,907 unique orthogroups (69%) are core and present in all isolates and the remaining 3,344 show presence/absence of variation, representing 16-22% of the genome of each isolate. Using this large genomic dataset of environmental and clinical samples, we found an enrichment for clinical isolates in a genetic cluster whose genomes also contain more accessory genes, including genes coding for transmembrane transporters and proteins with iron-binding activity, and genes involved in both carbohydrate and amino-acid metabolism. Finally, we leverage the power of genome-wide association studies to identify genomic variation associated with clinical isolates and triazole resistance as well as characterize genetic variation in known virulence factors. This characterization of the genomic diversity of A. fumigatus allows us to move away from a single reference genome that does not necessarily represent the species as a whole and better understand its pathogenic versatility, ultimately leading to better management of these infections.
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Affiliation(s)
- Amelia E Barber
- Research Group Fungal Septomics, Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany.,Junior Research Group Fungal Informatics, Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - Tongta Sae-Ong
- Research Group Systems Biology and Bioinformatics, Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - Kang Kang
- Research Group Systems Biology and Bioinformatics, Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - Bastian Seelbinder
- Research Group Systems Biology and Bioinformatics, Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China.,School of Data Science, City University of Hong Kong, Hong Kong, China
| | - Grit Walther
- National Reference Center for Invasive Fungal Infections (NRZMyk), Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - Gianni Panagiotou
- Research Group Systems Biology and Bioinformatics, Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany. .,Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong, China.
| | - Oliver Kurzai
- Research Group Fungal Septomics, Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany. .,National Reference Center for Invasive Fungal Infections (NRZMyk), Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany. .,Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany.
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Chevrette MG, Gavrilidou A, Mantri S, Selem-Mojica N, Ziemert N, Barona-Gómez F. The confluence of big data and evolutionary genome mining for the discovery of natural products. Nat Prod Rep 2021; 38:2024-2040. [PMID: 34787598 DOI: 10.1039/d1np00013f] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review covers literature between 2003-2021The development and application of genome mining tools has given rise to ever-growing genetic and chemical databases and propelled natural products research into the modern age of Big Data. Likewise, an explosion of evolutionary studies has unveiled genetic patterns of natural products biosynthesis and function that support Darwin's theory of natural selection and other theories of adaptation and diversification. In this review, we aim to highlight how Big Data and evolutionary thinking converge in the study of natural products, and how this has led to an emerging sub-discipline of evolutionary genome mining of natural products. First, we outline general principles to best utilize Big Data in natural products research, addressing key considerations needed to provide evolutionary context. We then highlight successful examples where Big Data and evolutionary analyses have been combined to provide bioinformatic resources and tools for the discovery of novel natural products and their biosynthetic enzymes. Rather than an exhaustive list of evolution-driven discoveries, we highlight examples where Big Data and evolutionary thinking have been embraced for the evolutionary genome mining of natural products. After reviewing the nascent history of this sub-discipline, we discuss the challenges and opportunities of genomic and metabolomic tools with evolutionary foundations and/or implications and provide a future outlook for this emerging and exciting field of natural product research.
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Affiliation(s)
- Marc G Chevrette
- Wisconsin Institute for Discovery, Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Athina Gavrilidou
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, Germany.
| | - Shrikant Mantri
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, Germany. .,Computational Biology Laboratory, National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Nelly Selem-Mojica
- Laboratorio de Evolución de la Diversidad Metabólica, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico.
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, Germany.
| | - Francisco Barona-Gómez
- Laboratorio de Evolución de la Diversidad Metabólica, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico.
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41
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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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42
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Roux I, Bowles S, Kalaitzis JA, Vuong D, Lacey E, Chooi YH, Piggott AM. Characterisation and heterologous biosynthesis of burnettiene A, a new polyene-decalin polyketide from Aspergillus burnettii. Org Biomol Chem 2021; 19:9506-9513. [PMID: 34714309 DOI: 10.1039/d1ob01766g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Chemical exploration of the recently described Australian fungus, Aspergillus burnettii, uncovered a new metabolite, burnettiene A. Here, we characterise the structure of burnettiene A as a polyene-decalin polyketide. Bioinformatic analysis of the genome of A. burnettii identified a putative biosynthetic gene cluster for burnettiene A (bue), consisting of eight genes and sharing similarity to the fusarielin gene cluster. Introduction of the reassembled bue gene cluster into Aspergillus nidulans for heterologous expression resulted in the production of burnettiene A under native promoters. Omission of bueE encoding a cytochrome P450 led to the production of preburnettiene A, confirming that BueE is responsible for catalysing the regiospecific multi-oxidation of terminal methyl groups to carboxylic acids. Similarly, bueF was shown to encode an ester-forming methyltransferase, with its omission resulting in the production of the tricarboxylic acid, preburnettiene B. Introduction of an additional copy of the transcription factor bueR under the regulation of the gpdA promoter significantly improved the heterologous production of the burnettienes. Burnettiene A displayed strong in vitro cytotoxicity against mouse myeloma NS-1 cells (MIC 0.8 μg mL-1).
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Affiliation(s)
- Indra Roux
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| | - Simon Bowles
- Microbial Screening Technologies Pty. Ltd, Smithfield, NSW 2164, Australia
| | - John A Kalaitzis
- Microbial Screening Technologies Pty. Ltd, Smithfield, NSW 2164, Australia
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Daniel Vuong
- Microbial Screening Technologies Pty. Ltd, Smithfield, NSW 2164, Australia
| | - Ernest Lacey
- Microbial Screening Technologies Pty. Ltd, Smithfield, NSW 2164, Australia
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| | - Andrew M Piggott
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
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43
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Anderson VM, Wendt KL, Najar FZ, McCall LI, Cichewicz RH. Building Natural Product Libraries Using Quantitative Clade-Based and Chemical Clustering Strategies. mSystems 2021; 6:e0064421. [PMID: 34698546 PMCID: PMC8547436 DOI: 10.1128/msystems.00644-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/16/2021] [Indexed: 12/01/2022] Open
Abstract
The success of natural product-based drug discovery is predicated on having chemical collections that offer broad coverage of metabolite diversity. We propose a simple set of tools combining genetic barcoding and metabolomics to help investigators build natural product libraries aimed at achieving predetermined levels of chemical coverage. It was found that such tools aided in identifying overlooked pockets of chemical diversity within taxa, which could be useful for refocusing collection strategies. We have used fungal isolates identified as Alternaria from a citizen-science-based soil collection to demonstrate the application of these tools for assessing and carrying out predictive measurements of chemical diversity in a natural product collection. Within Alternaria, different subclades were found to contain nonequivalent levels of chemical diversity. It was also determined that a surprisingly modest number of isolates (195 isolates) was sufficient to afford nearly 99% of Alternaria chemical features in the data set. However, this result must be considered in the context that 17.9% of chemical features appeared in single isolates, suggesting that fungi like Alternaria might be engaged in an ongoing process of actively exploring nature's metabolic landscape. Our results demonstrate that combining modest investments in securing internal transcribed spacer (ITS)-based sequence information (i.e., establishing gene-based clades) with data from liquid chromatography-mass spectrometry (i.e., generating feature accumulation curves) offers a useful route to obtaining actionable insights into chemical diversity coverage trends in a natural product library. It is anticipated that these outcomes could be used to improve opportunities for accessing bioactive molecules that serve as the cornerstone of natural product-based drug discovery. IMPORTANCE Natural product drug discovery efforts rely on libraries of organisms to provide access to diverse pools of compounds. Actionable strategies to rationally maximize chemical diversity, rather than relying on serendipity, can add value to such efforts. Readily implementable biological (i.e., ITS sequence analysis) and chemical (i.e., mass spectrometry-based feature and scaffold measurements) diversity assessment tools can be employed to monitor and adjust library development tactics in real time. In summary, metabolomics-driven technologies and simple gene-based specimen barcoding approaches have broad applicability to building chemically diverse natural product libraries.
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Affiliation(s)
- Victoria M. Anderson
- Natural Products Discovery Group, University of Oklahoma, Norman, Oklahoma, USA
- Institute for Natural Products Applications and Research Technologies, University of Oklahoma, Norman, Oklahoma, USA
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Karen L. Wendt
- Natural Products Discovery Group, University of Oklahoma, Norman, Oklahoma, USA
- Institute for Natural Products Applications and Research Technologies, University of Oklahoma, Norman, Oklahoma, USA
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Fares Z. Najar
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
- Chemistry and Biochemistry Bioinformatics Core, University of Oklahoma, Norman, Oklahoma, USA
| | - Laura-Isobel McCall
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma, USA
| | - Robert H. Cichewicz
- Natural Products Discovery Group, University of Oklahoma, Norman, Oklahoma, USA
- Institute for Natural Products Applications and Research Technologies, University of Oklahoma, Norman, Oklahoma, USA
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
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Depside and Depsidone Synthesis in Lichenized Fungi Comes into Focus through a Genome-Wide Comparison of the Olivetoric Acid and Physodic Acid Chemotypes of Pseudevernia furfuracea. Biomolecules 2021; 11:biom11101445. [PMID: 34680078 PMCID: PMC8533459 DOI: 10.3390/biom11101445] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/25/2021] [Accepted: 09/28/2021] [Indexed: 12/13/2022] Open
Abstract
Primary biosynthetic enzymes involved in the synthesis of lichen polyphenolic compounds depsides and depsidones are non-reducing polyketide synthases (NR-PKSs), and cytochrome P450s. However, for most depsides and depsidones the corresponding PKSs are unknown. Additionally, in non-lichenized fungi specific fatty acid synthases (FASs) provide starters to the PKSs. Yet, the presence of such FASs in lichenized fungi remains to be investigated. Here we implement comparative genomics and metatranscriptomics to identify the most likely PKS and FASs for olivetoric acid and physodic acid biosynthesis, the primary depside and depsidone defining the two chemotypes of the lichen Pseudevernia furfuracea. We propose that the gene cluster PF33-1_006185, found in both chemotypes, is the most likely candidate for the olivetoric acid and physodic acid biosynthesis. This is the first study to identify the gene cluster and the FAS likely responsible for olivetoric acid and physodic acid biosynthesis in a lichenized fungus. Our findings suggest that gene regulation and other epigenetic factors determine whether the mycobiont produces the depside or the depsidone, providing the first direct indication that chemotype diversity in lichens can arise through regulatory and not only through genetic diversity. Combining these results and existing literature, we propose a detailed scheme for depside/depsidone synthesis.
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Vignolle GA, Schaffer D, Zehetner L, Mach RL, Mach-Aigner AR, Derntl C. FunOrder: A robust and semi-automated method for the identification of essential biosynthetic genes through computational molecular co-evolution. PLoS Comput Biol 2021; 17:e1009372. [PMID: 34570757 PMCID: PMC8476034 DOI: 10.1371/journal.pcbi.1009372] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/23/2021] [Indexed: 11/24/2022] Open
Abstract
Secondary metabolites (SMs) are a vast group of compounds with different structures and properties that have been utilized as drugs, food additives, dyes, and as monomers for novel plastics. In many cases, the biosynthesis of SMs is catalysed by enzymes whose corresponding genes are co-localized in the genome in biosynthetic gene clusters (BGCs). Notably, BGCs may contain so-called gap genes, that are not involved in the biosynthesis of the SM. Current genome mining tools can identify BGCs, but they have problems with distinguishing essential genes from gap genes. This can and must be done by expensive, laborious, and time-consuming comparative genomic approaches or transcriptome analyses. In this study, we developed a method that allows semi-automated identification of essential genes in a BGC based on co-evolution analysis. To this end, the protein sequences of a BGC are blasted against a suitable proteome database. For each protein, a phylogenetic tree is created. The trees are compared by treeKO to detect co-evolution. The results of this comparison are visualized in different output formats, which are compared visually. Our results suggest that co-evolution is commonly occurring within BGCs, albeit not all, and that especially those genes that encode for enzymes of the biosynthetic pathway are co-evolutionary linked and can be identified with FunOrder. In light of the growing number of genomic data available, this will contribute to the studies of BGCs in native hosts and facilitate heterologous expression in other organisms with the aim of the discovery of novel SMs. The discovery and description of novel fungal secondary metabolites promises novel antibiotics, pharmaceuticals, and other useful compounds. A way to identify novel secondary metabolites is to express the corresponding genes in a suitable expression host. Consequently, a detailed knowledge or an accurate prediction of these genes is necessary. In fungi, the genes are co-localized in so-called biosynthetic gene clusters. Notably, the clusters may also contain genes that are not necessary for the biosynthesis of the secondary metabolites, so-called gap genes. We developed a method to detect co-evolved genes within the clusters and demonstrated that essential genes are co-evolving and can thus be differentiated from the gap genes. This adds an additional layer of information, which can support researchers with their decisions on which genes to study and express for the discovery of novel secondary metabolites.
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Affiliation(s)
- Gabriel A. Vignolle
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Denise Schaffer
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Leopold Zehetner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Robert L. Mach
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Astrid R. Mach-Aigner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Christian Derntl
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
- * E-mail:
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Pizarro D, Divakar PK, Grewe F, Crespo A, Dal Grande F, Lumbsch HT. Genome-Wide Analysis of Biosynthetic Gene Cluster Reveals Correlated Gene Loss with Absence of Usnic Acid in Lichen-Forming Fungi. Genome Biol Evol 2021; 12:1858-1868. [PMID: 33151307 PMCID: PMC7643366 DOI: 10.1093/gbe/evaa189] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2020] [Indexed: 12/04/2022] Open
Abstract
Lichen-forming fungi are known to produce a large number of secondary metabolites. Some metabolites are deposited in the cortical layer of the lichen thallus where they exert important ecological functions, such as UV filtering. The fact that closely related lineages of lichen-forming fungi can differ in cortical chemistry suggests that natural product biosynthesis in lichens can evolve independent from phylogenetic constraints. Usnic acid is one of the major cortical pigments in lichens. Here we used a comparative genomic approach on 46 lichen-forming fungal species of the Lecanoromycetes to elucidate the biosynthetic gene content and evolution of the gene cluster putatively responsible for the biosynthesis of usnic acid. Whole-genome sequences were gathered from taxa belonging to different orders and families of Lecanoromycetes, where Parmeliaceae is the most well-represented taxon, and analyzed with a variety of genomic tools. The highest number of biosynthetic gene clusters was found in Evernia prunastri, Pannoparmelia angustata, and Parmotrema austrosinense, respectively, and lowest in Canoparmelia nairobiensis, Bulbothrix sensibilis, and Hypotrachyna scytodes. We found that all studied species producing usnic acid contain the putative usnic acid biosynthetic gene cluster, whereas the cluster was absent in all genomes of species lacking usnic acid. The absence of the gene cluster was supported by an additional unsuccessful search for ß-ketoacylsynthase, the most conserved domain of the gene cluster, in the genomes of species lacking usnic acid. The domain architecture of this PKS cluster—homologous to the already known usnic acid PKS cluster (MPAS) and CYT450 (MPAO)—varies within the studied species, whereas the gene arrangement is highly similar in closely related taxa. We hypothesize that the ancestor of these lichen-forming fungi contained the putative usnic acid producing PKS cluster and that the gene cluster was lost repeatedly during the evolution of these groups. Our study provides insight into the genomic adaptations to the evolutionary success of these lichen-forming fungal species and sets a baseline for further exploration of biosynthetic gene content and its evolutionary significance.
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Affiliation(s)
- David Pizarro
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Pradeep K Divakar
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Felix Grewe
- Department of Science & Education, The Field Museum, Chicago, Illinois
| | - Ana Crespo
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main D-60325, Germany.,LOEWE Center for Translational Biodiversity Genomics, Frankfurt am Main D-60325, Germany
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47
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Steenwyk JL, Mead ME, de Castro PA, Valero C, Damasio A, dos Santos RAC, Labella AL, Li Y, Knowles SL, Raja HA, Oberlies NH, Zhou X, Cornely OA, Fuchs F, Koehler P, Goldman GH, Rokas A. Genomic and Phenotypic Analysis of COVID-19-Associated Pulmonary Aspergillosis Isolates of Aspergillus fumigatus. Microbiol Spectr 2021; 9:e0001021. [PMID: 34106569 PMCID: PMC8552514 DOI: 10.1128/spectrum.00010-21] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 04/08/2021] [Indexed: 02/06/2023] Open
Abstract
The ongoing global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for coronavirus disease 2019 (COVID-19), first described in Wuhan, China. A subset of COVID-19 patients has been reported to have acquired secondary infections by microbial pathogens, such as opportunistic fungal pathogens from the genus Aspergillus. To gain insight into COVID-19-associated pulmonary aspergillosis (CAPA), we analyzed the genomes and characterized the phenotypic profiles of four CAPA isolates of Aspergillus fumigatus obtained from patients treated in the area of North Rhine-Westphalia, Germany. By examining the mutational spectrum of single nucleotide polymorphisms, insertion-deletion polymorphisms, and copy number variants among 206 genes known to modulate A. fumigatus virulence, we found that CAPA isolate genomes do not exhibit significant differences from the genome of the Af293 reference strain. By examining a number of factors, including virulence in an invertebrate moth model, growth in the presence of osmotic, cell wall, and oxidative stressors, secondary metabolite biosynthesis, and the MIC of antifungal drugs, we found that CAPA isolates were generally, but not always, similar to A. fumigatus reference strains Af293 and CEA17. Notably, CAPA isolate D had more putative loss-of-function mutations in genes known to increase virulence when deleted. Moreover, CAPA isolate D was significantly more virulent than the other three CAPA isolates and the A. fumigatus reference strains Af293 and CEA17, but similarly virulent to two other clinical strains of A. fumigatus. These findings expand our understanding of the genomic and phenotypic characteristics of isolates that cause CAPA. IMPORTANCE The global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), has already killed millions of people. COVID-19 patient outcome can be further complicated by secondary infections, such as COVID-19-associated pulmonary aspergillosis (CAPA). CAPA is caused by Aspergillus fungal pathogens, but there is little information about the genomic and phenotypic characteristics of CAPA isolates. We conducted genome sequencing and extensive phenotyping of four CAPA isolates of Aspergillus fumigatus from Germany. We found that CAPA isolates were often, but not always, similar to other reference strains of A. fumigatus across 206 genetic determinants of infection-relevant phenotypes, including virulence. For example, CAPA isolate D was more virulent than other CAPA isolates and reference strains in an invertebrate model of fungal disease, but similarly virulent to two other clinical strains. These results expand our understanding of COVID-19-associated pulmonary aspergillosis.
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Affiliation(s)
- Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Matthew E. Mead
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Patrícia Alves de Castro
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Clara Valero
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - André Damasio
- Institute of Biology, University of Campinas (UNICAMP), Campinas-SP, Brazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas (UNICAMP), Campinas-SP, Brazil
| | - Renato A. C. dos Santos
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Abigail L. Labella
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Yuanning Li
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Sonja L. Knowles
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Huzefa A. Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Nicholas H. Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Oliver A. Cornely
- University of Cologne, Medical Faculty and University Hospital Cologne, Department I of Internal Medicine, Excellence Center for Medical Mycology (ECMM), Cologne, Germany
- University of Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
- ZKS Köln, Clinical Trials Centre Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn‐Cologne, Medical Faculty and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Frieder Fuchs
- Faculty of Medicine, Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Philipp Koehler
- University of Cologne, Medical Faculty and University Hospital Cologne, Department I of Internal Medicine, Excellence Center for Medical Mycology (ECMM), Cologne, Germany
- University of Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
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48
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Boysen JM, Saeed N, Hillmann F. Natural products in the predatory defence of the filamentous fungal pathogen Aspergillus fumigatus. Beilstein J Org Chem 2021; 17:1814-1827. [PMID: 34394757 PMCID: PMC8336654 DOI: 10.3762/bjoc.17.124] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 07/14/2021] [Indexed: 11/30/2022] Open
Abstract
The kingdom of fungi comprises a large and highly diverse group of organisms that thrive in diverse natural environments. One factor to successfully confront challenges in their natural habitats is the capability to synthesize defensive secondary metabolites. The genetic potential for the production of secondary metabolites in fungi is high and numerous potential secondary metabolite gene clusters have been identified in sequenced fungal genomes. Their production may well be regulated by specific ecological conditions, such as the presence of microbial competitors, symbionts or predators. Here we exemplarily summarize our current knowledge on identified secondary metabolites of the pathogenic fungus Aspergillus fumigatus and their defensive function against (microbial) predators.
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Affiliation(s)
- Jana M Boysen
- Junior Research Group Evolution of Microbial Interactions, Leibniz-Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Nauman Saeed
- Junior Research Group Evolution of Microbial Interactions, Leibniz-Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Falk Hillmann
- Junior Research Group Evolution of Microbial Interactions, Leibniz-Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
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49
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Chacón-Vargas K, McCarthy CO, Choi D, Wang L, Yu JH, Gibbons JG. Comparison of Two Aspergillus oryzae Genomes From Different Clades Reveals Independent Evolution of Alpha-Amylase Duplication, Variation in Secondary Metabolism Genes, and Differences in Primary Metabolism. Front Microbiol 2021; 12:691296. [PMID: 34326825 PMCID: PMC8313989 DOI: 10.3389/fmicb.2021.691296] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/22/2021] [Indexed: 12/02/2022] Open
Abstract
Microbes (bacteria, yeasts, molds), in addition to plants and animals, were domesticated for their roles in food preservation, nutrition and flavor. Aspergillus oryzae is a domesticated filamentous fungal species traditionally used during fermentation of Asian foods and beverage, such as sake, soy sauce, and miso. To date, little is known about the extent of genome and phenotypic variation of A. oryzae isolates from different clades. Here, we used long-read Oxford Nanopore and short-read Illumina sequencing to produce a highly accurate and contiguous genome assemble of A. oryzae 14160, an industrial strain from China. To understand the relationship of this isolate, we performed phylogenetic analysis with 90 A. oryzae isolates and 1 isolate of the A. oryzae progenitor, Aspergillus flavus. This analysis showed that A. oryzae 14160 is a member of clade A, in comparison to the RIB 40 type strain, which is a member of clade F. To explore genome variation between isolates from distinct A. oryzae clades, we compared the A. oryzae 14160 genome with the complete RIB 40 genome. Our results provide evidence of independent evolution of the alpha-amylase gene duplication, which is one of the major adaptive mutations resulting from domestication. Synteny analysis revealed that both genomes have three copies of the alpha-amylase gene, but only one copy on chromosome 2 was conserved. While the RIB 40 genome had additional copies of the alpha-amylase gene on chromosomes III, and V, 14160 had a second copy on chromosome II and an third copy on chromosome VI. Additionally, we identified hundreds of lineage specific genes, and putative high impact mutations in genes involved in secondary metabolism, including several of the core biosynthetic genes. Finally, to examine the functional effects of genome variation between strains, we measured amylase activity, proteolytic activity, and growth rate on several different substrates. RIB 40 produced significantly higher levels of amylase compared to 14160 when grown on rice and starch. Accordingly, RIB 40 grew faster on rice, while 14160 grew faster on soy. Taken together, our analyses reveal substantial genome and phenotypic variation within A. oryzae.
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Affiliation(s)
- Katherine Chacón-Vargas
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, United States.,Department of Food Science, University of Massachusetts, Amherst, MA, United States
| | - Colin O McCarthy
- Department of Food Science, University of Massachusetts, Amherst, MA, United States
| | - Dasol Choi
- Deapertment of Food Science, University of Wisconsin-Madison, Madison, WI, United States.,Department of Bacteriology, and Food Research Institute, University of Wisconsin-Madison, Madison, WI, United States
| | - Long Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jae-Hyuk Yu
- Department of Bacteriology, and Food Research Institute, University of Wisconsin-Madison, Madison, WI, United States.,Department of Systems Biotechnology, Konkuk University, Seoul, South Korea
| | - John G Gibbons
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, United States.,Department of Food Science, University of Massachusetts, Amherst, MA, United States.,Organismic & Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA, United States
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50
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Keizer EM, Valdes ID, Forn-Cuni G, Klijn E, Meijer AH, Hillman F, Wösten HAB, de Cock H. Variation of virulence of five Aspergillus fumigatus isolates in four different infection models. PLoS One 2021; 16:e0252948. [PMID: 34242260 PMCID: PMC8270121 DOI: 10.1371/journal.pone.0252948] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 05/25/2021] [Indexed: 11/19/2022] Open
Abstract
Conidia of Aspergillus fumigatus are inhaled by humans on daily basis. As a consequence, these conidia can cause infections that differ in severity ranging from allergic bronchopulmonary aspergillosis to invasive aspergillosis. In this study we compared virulence of five A. fumigatus isolates in four different infection models to address the predictive value of different model systems. Two of the A. fumigatus strains were isolated from dogs with a non-invasive sino-nasal aspergillosis (DTO271-B5 and DTO303-F3), while three strains were isolated from human patients with invasive aspergillosis (Af293, ATCC46645 and CEA10). Infection models used encompassed cultured type II A549 lung epithelial cells, Protostelium aurantium amoeba, Galleria melonella larvae and zebrafish embryos. No major differences in virulence between these five strains were observed in the lung epithelial cell model. In contrast, strain ATCC46645 was most virulent in the amoeba and zebrafish model, whereas it was much less virulent in the Galleria infection model. DTO303-F3 was most virulent in the latter model. In general, reference strain Af293 was less virulent as compared to the other strains. Genome sequence analysis showed that this latter strain differed from the other four strains in 136 SNPs in virulence-related genes. Together, our results show that virulence of individual A. fumigatus strains show significant differences between infection models. We conclude that the predictive value of different model systems varies since the relative virulence across fungal strains does not hold up across different infection model systems.
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Affiliation(s)
- E. M. Keizer
- Microbiology, Department of Biology, Utrecht University, Utrecht, The Netherlands
- Institute of Biomembranes, Utrecht University, Utrecht, The Netherlands
| | - I. D. Valdes
- Microbiology, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - G. Forn-Cuni
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - E. Klijn
- Microbiology, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - A. H. Meijer
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - F. Hillman
- Junior Research Group Evolution of Microbial Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany
| | - H. A. B. Wösten
- Microbiology, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - H. de Cock
- Microbiology, Department of Biology, Utrecht University, Utrecht, The Netherlands
- Institute of Biomembranes, Utrecht University, Utrecht, The Netherlands
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