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Konkel Z, Kubatko L, Slot JC. CLOCI: unveiling cryptic fungal gene clusters with generalized detection. Nucleic Acids Res 2024:gkae625. [PMID: 39016185 DOI: 10.1093/nar/gkae625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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Hayakawa I, Isogai T, Takanishi J, Asai S, Ando C, Tsutsumi T, Watanabe K, Sakakura A, Tsunematsu Y. Synthesis and biological evaluation of coprinoferrin, an acylated tripeptide hydroxamate siderophore. Org Biomol Chem 2024; 22:831-837. [PMID: 38175167 DOI: 10.1039/d3ob01850d] [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: 01/05/2024]
Abstract
Coprinoferrin (CPF), originally isolated from a genetically engineered strain (ΔlaeA) of the mushroom fungus Coprinopsis cinerea, is an acylated tripeptide hydroxamate consisting of tandem aligned N5-hexanoyl-N5-hydroxy-L-ornithine with modifications of N-acetyl and C-carboxamide. These unique chemical properties make CPF an iron(III) binder (siderophore), which helps in iron acquisition from the environment and promotes hyphal growth as well as fruiting body formation in C. cinerea. However, CPF's detailed mode of action remains enigmatic. In this study, we have accomplished the synthesis of CPF from N-Boc-L-glutamic acid 5-benzyl ester. The physicochemical characteristics, spectroscopic features, and biological activity observed in the synthetic CPF closely match those of natural CPF. This alignment provides unequivocal confirmation of the proposed chemical structure, facilitating a deeper understanding of its physiological role in nature, particularly in fruiting body formation.
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Affiliation(s)
- Ichiro Hayakawa
- Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo 156-8550, Japan.
| | - Tomoki Isogai
- Division of Applied Chemistry, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan.
| | - Jun Takanishi
- Department of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan.
| | - Shihori Asai
- Department of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan.
| | - Chika Ando
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi, 464-8601, Japan.
| | - Tomohiro Tsutsumi
- Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo 156-8550, Japan.
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan.
| | - Akira Sakakura
- Division of Applied Chemistry, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan.
| | - Yuta Tsunematsu
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi, 464-8601, Japan.
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3
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Narh Mensah DL, Wingfield BD, Coetzee MPA. Two distinct non-ribosomal peptide synthetase-independent siderophore synthetase gene clusters identified in Armillaria and other species in the Physalacriaceae. G3 (BETHESDA, MD.) 2023; 13:jkad205. [PMID: 37843963 PMCID: PMC10700112 DOI: 10.1093/g3journal/jkad205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/28/2023] [Indexed: 10/18/2023]
Abstract
Siderophores are important for ferric iron solubilization, sequestration, transportation, and storage, especially under iron-limiting conditions such as aerobic conditions at high pH. Siderophores are mainly produced by non-ribosomal peptide synthetase-dependent siderophore pathway, non-ribosomal peptide synthetase-independent siderophore synthetase pathway, or the hybrid non-ribosomal peptide synthetases/non-ribosomal peptide synthetases-independent siderophore pathway. Outcompeting or inhibition of plant pathogens, alteration of host defense mechanisms, and alteration of plant-fungal interactions have been associated with fungal siderophores. To understand these mechanisms in fungi, studies have been conducted on siderophore biosynthesis by ascomycetes with limited focus on the basidiomycetes. Armillaria includes several species that are pathogens of woody plants and trees important to agriculture, horticulture, and forestry. The aim of this study was to investigate the presence of non-ribosomal peptide synthetases-independent siderophore synthetase gene cluster(s) in genomes of Armillaria species using a comparative genomics approach. Iron-dependent growth and siderophore biosynthesis in strains of selected Armillaria spp. were also evaluated in vitro. Two distinct non-ribosomal peptide synthetases-independent siderophore synthetase gene clusters were identified in all the genomes. All non-ribosomal peptide synthetases-independent siderophore synthetase genes identified putatively encode Type A' non-ribosomal peptide synthetases-independent siderophore synthetases, most of which have IucA_IucC and FhuF-like transporter domains at their N- and C-terminals, respectively. The effect of iron on culture growth varied among the strains studied. Bioassays using the CAS assay on selected Armillaria spp. revealed in vitro siderophore biosynthesis by all strains irrespective of added FeCl3 concentration. This study highlights some of the tools that Armillaria species allocate to iron homeostasis. The information generated from this study may in future aid in developing molecular based methods to control these phytopathogens.
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Affiliation(s)
- Deborah L Narh Mensah
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa
- CSIR—Food Research Institute, Microbiology and Mushroom Research Division, P. O. Box, M20, Accra, Ghana
| | - Brenda D Wingfield
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa
| | - Martin P A Coetzee
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa
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Shen Y, Zhao J, Zou X, Shi Z, Liao Y, He Y, Wang H, Chen Q, Yang P, Li M. Differential Responses of Bacterial and Fungal Communities to Siderophore Supplementation in Soil Affected by Tobacco Bacterial Wilt ( Ralstonia solanacearum). Microorganisms 2023; 11:1535. [PMID: 37375037 DOI: 10.3390/microorganisms11061535] [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: 05/09/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Siderophores secreted by microorganisms can promote ecological efficiency and could be used to regulate the unbalanced microbial community structure. The influence of the siderophore activity of Trichoderma yunnanense strain 2-14F2 and Beauveria pseudobassiana strain (2-8F2) on the physiological/biochemical functions and community structure of soil microbes affected by tobacco bacterial wilt (TBW) was studied. DNS Colorimetry and Biolog-eco plates were used to quantify the impacts of strain siderophores on soil enzyme activities and microbial metabolism. Based on Illumina MiSeq high-throughput sequencing, the soil 16S rDNA and ITS sequences were amplified to dissect the response characteristics of alpha/beta diversity and the structure/composition of a soil microbial community toward siderophores. The KEGG database was used to perform the PICRUSt functional prediction of the microbial community. We found that siderophores of 2-14F2 and 2-8F2, at certain concentrations, significantly increased the activities of sucrase (S-SC) and urease (S-UE) in the TBW soil and enhanced the average well color development (AWCD, carbon source utilization capacity) of the microbial community. The metabolic capacity of the diseased soil to amino acids, carbohydrates, polymers, aromatics, and carboxylic acids also increased significantly. The response of the bacterial community to siderophore active metabolites was more significant in alpha diversity, while the beta diversity of the fungal community responded more positively to siderophores. The relative abundance of Actinobacteria, Chloroflexi, and Acidobacteria increased and was accompanied by reductions in Proteobacteria and Firmicutes. LEfSe analysis showed that Pseudonocardiaceae, Gemmatimonas, Castellaniella, Chloridiumand and Acrophialophora altered the most under different concentrations of siderophore active metabolites. The PICRUSt functional prediction results showed that siderophore increased the abundance of the redox-related enzymes of the microbial community in TBW soil. The BugBase phenotypic prediction results showed that the siderophore activity could decrease the abundance of pathogenic bacteria. The study concludes that siderophore activity could decrease the abundance of pathogenic bacteria and regulate the composition of the microbial community in TBW soil. The activities of sucrase (S-SC) and urease (S-UE) in TBW soil were significantly increased. Overall, the siderophore regulation of community structures is a sustainable management strategy for soil ecosystems.
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Affiliation(s)
- Yunxin Shen
- College of Plant Protection, Yunnan Agricultural University, Kunming 655508, China
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming 650204, China
| | - Jiangyuan Zhao
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650106, China
| | - Xuefeng Zou
- College of Plant Protection, Yunnan Agricultural University, Kunming 655508, China
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming 650204, China
| | - Zhufeng Shi
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming 650204, China
| | - Yongqin Liao
- College of Plant Protection, Yunnan Agricultural University, Kunming 655508, China
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming 650204, China
| | - Yonghong He
- College of Plant Protection, Yunnan Agricultural University, Kunming 655508, China
| | - Hang Wang
- National Plateau Wetlands Research Center, Wetlands College, Southwest Forestry University, Kunming 650233, China
| | - Qibin Chen
- College of Plant Protection, Yunnan Agricultural University, Kunming 655508, China
| | - Peiweng Yang
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming 650204, China
| | - Minggang Li
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650106, China
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Jenner M, Hai Y, Nguyen HH, Passmore M, Skyrud W, Kim J, Garg NK, Zhang W, Ogorzalek Loo RR, Tang Y. Elucidating the molecular programming of a nonlinear non-ribosomal peptide synthetase responsible for fungal siderophore biosynthesis. Nat Commun 2023; 14:2832. [PMID: 37198174 PMCID: PMC10192304 DOI: 10.1038/s41467-023-38484-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 04/25/2023] [Indexed: 05/19/2023] Open
Abstract
Siderophores belonging to the ferrichrome family are essential for the viability of fungal species and play a key role for virulence of numerous pathogenic fungi. Despite their biological significance, our understanding of how these iron-chelating cyclic hexapeptides are assembled by non-ribosomal peptide synthetase (NRPS) enzymes remains poorly understood, primarily due to the nonlinearity exhibited by the domain architecture. Herein, we report the biochemical characterization of the SidC NRPS, responsible for construction of the intracellular siderophore ferricrocin. In vitro reconstitution of purified SidC reveals its ability to produce ferricrocin and its structural variant, ferrichrome. Application of intact protein mass spectrometry uncovers several non-canonical events during peptidyl siderophore biosynthesis, including inter-modular loading of amino acid substrates and an adenylation domain capable of poly-amide bond formation. This work expands the scope of NRPS programming, allows biosynthetic assignment of ferrichrome NRPSs, and sets the stage for reprogramming towards novel hydroxamate scaffolds.
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Affiliation(s)
- Matthew Jenner
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
- Warwick Integrative Synthetic Biology Centre (WISB), University of Warwick, Coventry, CV4 7AL, UK.
| | - Yang Hai
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, USA.
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, USA.
| | - Hong H Nguyen
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
- Transmed Co., Ltd., Ho Chi Minh City, Vietnam
| | - Munro Passmore
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Will Skyrud
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, USA
- Arzeda, 3421 Thorndyke Ave W, Seattle, WA 98119, USA
| | - Junyong Kim
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Neil K Garg
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, USA
| | | | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, USA
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Narh Mensah DL, Wingfield BD, Coetzee MPA. Nonribosomal peptide synthetase gene clusters and characteristics of predicted NRPS-dependent siderophore synthetases in Armillaria and other species in the Physalacriaceae. Curr Genet 2023; 69:7-24. [PMID: 36369495 DOI: 10.1007/s00294-022-01256-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/13/2022]
Abstract
Fungal secondary metabolites are often pathogenicity or virulence factors synthesized by genes contained in secondary metabolite gene clusters (SMGCs). Nonribosomal polypeptide synthetase (NRPS) clusters are SMGCs which produce peptides such as siderophores, the high affinity ferric iron chelating compounds required for iron uptake under aerobic conditions. Armillaria spp. are mostly facultative necrotrophs of woody plants. NRPS-dependent siderophore synthetase (NDSS) clusters of Armillaria spp. and selected Physalacriaceae were investigated using a comparative genomics approach. Siderophore biosynthesis by strains of selected Armillaria spp. was evaluated using CAS and split-CAS assays. At least one NRPS cluster and other clusters were detected in the genomes studied. No correlation was observed between the number and types of SMGCs and reported pathogenicity of the species studied. The genomes contained one NDSS cluster each. All NDSSs were multi-modular with the domain architecture (ATC)3(TC)2. NDSS clusters of the Armillaria spp. showed a high degree of microsynteny. In the genomes of Desarmillaria spp. and Guyanagaster necrorhizus, NDSS clusters were more syntenic with NDSS clusters of Armillaria spp. than to those of the other Physalacriaceae species studied. Three A-domain orthologous groups were identified in the NDSSs, and atypical Stachelhaus codes were predicted for the A3 orthologous group. In vitro biosynthesis of mainly hydroxamate and some catecholate siderophores was observed. Hence, Armillaria spp. generally contain one highly conserved, NDSS cluster although some interspecific variations in the products of these clusters is expected. Results from this study lays the groundwork for future studies to elucidate the molecular biology of fungal phyto-pathogenicity.
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Affiliation(s)
- Deborah L Narh Mensah
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.,Council for Scientific and Industrial Research-Food Research Institute (CSIR-FRI), P. O. Box M20, Accra, Ghana
| | - Brenda D Wingfield
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Martin P A Coetzee
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.
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Dörner S, Rogge K, Fricke J, Schäfer T, Wurlitzer JM, Gressler M, Pham DNK, Manke DR, Chadeayne AR, Hoffmeister D. Genetic Survey of Psilocybe Natural Products. Chembiochem 2022; 23:e202200249. [PMID: 35583969 PMCID: PMC9400892 DOI: 10.1002/cbic.202200249] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/17/2022] [Indexed: 11/07/2022]
Abstract
Psilocybe magic mushrooms are best known for their main natural product, psilocybin, and its dephosphorylated congener, the psychedelic metabolite psilocin. Beyond tryptamines, the secondary metabolome of these fungi is poorly understood. The genomes of five species (P. azurescens, P. cubensis, P. cyanescens, P. mexicana, and P. serbica) were browsed to understand more profoundly common and species-specific metabolic capacities. The genomic analyses revealed a much greater and yet unexplored metabolic diversity than evident from parallel chemical analyses. P. cyanescens and P. mexicana were identified as aeruginascin producers. Lumichrome and verpacamide A were also detected as Psilocybe metabolites. The observations concerning the potential secondary metabolome of this fungal genus support pharmacological and toxicological efforts to find a rational basis for yet elusive phenomena, such as paralytic effects, attributed to consumption of some magic mushrooms.
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Affiliation(s)
- Sebastian Dörner
- Department Pharmaceutical Microbiology at the Hans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
| | - Kai Rogge
- Department Pharmaceutical Microbiology at the Hans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
| | - Janis Fricke
- Department Pharmaceutical Microbiology at the Hans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
| | - Tim Schäfer
- Department Pharmaceutical Microbiology at the Hans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
| | - Jacob M. Wurlitzer
- Department Pharmaceutical Microbiology at the Hans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
| | - Markus Gressler
- Department Pharmaceutical Microbiology at the Hans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
| | - Duyen N. K. Pham
- Department of Chemistry & BiochemistryUniversity of Massachusetts285 Old Westport RoadDartmouthMA02747USA
| | - David R. Manke
- Department of Chemistry & BiochemistryUniversity of Massachusetts285 Old Westport RoadDartmouthMA02747USA
| | | | - Dirk Hoffmeister
- Department Pharmaceutical Microbiology at the Hans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
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Tomé LMR, da Silva FF, Fonseca PLC, Mendes-Pereira T, Azevedo VADC, Brenig B, Badotti F, Góes-Neto A. Hybrid Assembly Improves Genome Quality and Completeness of Trametes villosa CCMB561 and Reveals a Huge Potential for Lignocellulose Breakdown. J Fungi (Basel) 2022; 8:jof8020142. [PMID: 35205897 PMCID: PMC8876698 DOI: 10.3390/jof8020142] [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: 12/17/2021] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 02/06/2023] Open
Abstract
Trametes villosa is a wood-decaying fungus with great potential to be used in the bioconversion of agro-industrial residues and to obtain high-value-added products, such as biofuels. Nonetheless, the lack of high-quality genomic data hampers studies investigating genetic mechanisms and metabolic pathways in T. villosa, hindering its application in industry. Herein, applying a hybrid assembly pipeline using short reads (Illumina HiSeq) and long reads (Oxford Nanopore MinION), we obtained a high-quality genome for the T. villosa CCMB561 and investigated its genetic potential for lignocellulose breakdown. The new genome possesses 143 contigs, N50 of 1,009,271 bp, a total length of 46,748,415 bp, 14,540 protein-coding genes, 22 secondary metabolite gene clusters, and 426 genes encoding Carbohydrate-Active enzymes. Our CAZome annotation and comparative genomic analyses of nine Trametes spp. genomes revealed T. villosa CCMB561 as the species with the highest number of genes encoding lignin-modifying enzymes and a wide array of genes encoding proteins for the breakdown of cellulose, hemicellulose, and pectin. These results bring to light the potential of this isolate to be applied in the bioconversion of lignocellulose and will support future studies on the expression, regulation, and evolution of genes, proteins, and metabolic pathways regarding the bioconversion of lignocellulosic residues.
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Affiliation(s)
- Luiz Marcelo Ribeiro Tomé
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.M.R.T.); (F.F.d.S.); (T.M.-P.)
| | - Felipe Ferreira da Silva
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.M.R.T.); (F.F.d.S.); (T.M.-P.)
| | - Paula Luize Camargos Fonseca
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil;
| | - Thairine Mendes-Pereira
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.M.R.T.); (F.F.d.S.); (T.M.-P.)
| | - Vasco Ariston de Carvalho Azevedo
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil;
| | - Bertram Brenig
- Institute of Veterinary Medicine, Burckhardtweg, University of Göttingen, 37073 Göttingen, Germany;
| | - Fernanda Badotti
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte 30421-169, MG, Brazil;
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.M.R.T.); (F.F.d.S.); (T.M.-P.)
- Correspondence: ; Tel.: +55-31-994130996
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9
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Comparative Genomic and Metabolomic Analysis of Termitomyces Species Provides Insights into the Terpenome of the Fungal Cultivar and the Characteristic Odor of the Fungus Garden of Macrotermes natalensis Termites. mSystems 2022; 7:e0121421. [PMID: 35014870 PMCID: PMC8751386 DOI: 10.1128/msystems.01214-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Macrotermitinae termites have domesticated fungi of the genus Termitomyces as food for their colony, analogously to human farmers growing crops. Termites propagate the fungus by continuously blending foraged and predigested plant material with fungal mycelium and spores (fungus comb) within designated subterranean chambers. To test the hypothesis that the obligate fungal symbiont emits specific volatiles (odor) to orchestrate its life cycle and symbiotic relations, we determined the typical volatile emission of fungus comb biomass and Termitomyces nodules, revealing α-pinene, camphene, and d-limonene as the most abundant terpenes. Genome mining of Termitomyces followed by gene expression studies and phylogenetic analysis of putative enzymes related to secondary metabolite production encoded by the genomes uncovered a conserved and specific biosynthetic repertoire across strains. Finally, we proved by heterologous expression and in vitro enzymatic assays that a highly expressed gene sequence encodes a rare bifunctional mono-/sesquiterpene cyclase able to produce the abundant comb volatiles camphene and d-limonene. IMPORTANCE The symbiosis between macrotermitinae termites and Termitomyces is obligate for both partners and is one of the most important contributors to biomass conversion in the Old World tropic’s ecosystems. To date, research efforts have dominantly focused on acquiring a better understanding of the degradative capabilities of Termitomyces to sustain the obligate nutritional symbiosis, but our knowledge of the small-molecule repertoire of the fungal cultivar mediating interspecies and interkingdom interactions has remained fragmented. Our omics-driven chemical, genomic, and phylogenetic study provides new insights into the volatilome and biosynthetic capabilities of the evolutionarily conserved fungal genus Termitomyces, which allows matching metabolites to genes and enzymes and, thus, opens a new source of unique and rare enzymatic transformations.
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10
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Shokrollahi N, Ho CL, Zainudin NAIM, Wahab MABA, Wong MY. Identification of non-ribosomal peptide synthetase in Ganoderma boninense Pat. that was expressed during the interaction with oil palm. Sci Rep 2021; 11:16330. [PMID: 34381084 PMCID: PMC8358039 DOI: 10.1038/s41598-021-95549-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 07/16/2021] [Indexed: 02/07/2023] Open
Abstract
Basal stem rot (BSR) of oil palm is a disastrous disease caused by a white-rot fungus Ganoderma boninense Pat. Non-ribosomal peptides (NRPs) synthesized by non-ribosomal peptide synthetases (NRPSs) are a group of secondary metabolites that act as fungal virulent factors during pathogenesis in the host. In this study, we aimed to isolate NRPS gene of G. boninense strain UPMGB001 and investigate the role of this gene during G. boninense-oil palm interaction. The isolated NRPS DNA fragment of 8322 bp was used to predict the putative peptide sequence of different domains and showed similarity with G. sinense (85%) at conserved motifs of three main NRPS domains. Phylogenetic analysis of NRPS peptide sequences demonstrated that NRPS of G. boninense belongs to the type VI siderophore family. The roots of 6-month-old oil palm seedlings were artificially inoculated for studying NRPS gene expression and disease severity in the greenhouse. The correlation between high disease severity (50%) and high expression (67-fold) of G. boninense NRPS gene at 4 months after inoculation and above indicated that this gene played a significant role in the advancement of BSR disease. Overall, these findings increase our knowledge on the gene structure of NRPS in G. boninense and its involvement in BSR pathogenesis as an effector gene.
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Affiliation(s)
- Neda Shokrollahi
- grid.11142.370000 0001 2231 800XDepartment of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Chai-Ling Ho
- grid.11142.370000 0001 2231 800XDepartment of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Nur Ain Izzati Mohd Zainudin
- grid.11142.370000 0001 2231 800XDepartment of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Mohd As’wad Bin Abul Wahab
- grid.11142.370000 0001 2231 800XDepartment of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Mui-Yun Wong
- grid.11142.370000 0001 2231 800XDepartment of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia ,grid.11142.370000 0001 2231 800XInstitute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
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11
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Kim MS, Ro HS. Generation of Iron-Independent Siderophore-Producing Agaricus bisporus through the Constitutive Expression of hapX. Genes (Basel) 2021; 12:genes12050724. [PMID: 34067973 PMCID: PMC8152254 DOI: 10.3390/genes12050724] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 11/16/2022] Open
Abstract
Agaricus bisporus secretes siderophore to uptake environmental iron. Siderophore secretion in A. bisporus was enabled only in the iron-free minimal medium due to iron repression of hapX, a transcriptional activator of siderophore biosynthetic genes. Aiming to produce siderophore using conventional iron-containing complex media, we constructed a recombinant strain of A. bisporus that escapes hapX gene repression. For this, the A. bisporushapX gene was inserted next to the glyceraldehyde 3-phosphate dehydrogenase promoter (pGPD) in a binary vector, pBGgHg, for the constitutive expression of hapX. Transformants of A. bisporus were generated using the binary vector through Agrobacterium tumefaciens-mediated transformation. PCR and Northern blot analyses of the chromosomal DNA of the transformants confirmed the successful integration of pGPD-hapX at different locations with different copy numbers. The stable integration of pGPD-hapX was supported by PCR analysis of chromosomal DNA obtained from the 20 passages of the transformant. The transformants constitutively over-expressed hapX by 3- to 5-fold and sidD, a key gene in the siderophore biosynthetic pathway, by 1.5- to 4-fold in mRNA levels compared to the wild-type strain (without Fe3+), regardless of the presence of iron. Lastly, HPLC analysis of the culture supernatants grown in minimal medium with or without Fe3+ ions presented a peak corresponding to iron-chelating siderophore at a retention time of 5.12 min. The siderophore concentrations of the transformant T2 in the culture supernatant were 9.3-fold (−Fe3+) and 8-fold (+Fe3+) higher than that of the wild-type A. bisporus grown without Fe3+ ions, while no siderophore was detected in the wild-type supernatant grown with Fe3+. The results described here demonstrate the iron-independent production of siderophore by a recombinant strain of A. bisporus, suggesting a new application for mushrooms through molecular biological manipulation.
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12
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Witte TE, Villeneuve N, Boddy CN, Overy DP. Accessory Chromosome-Acquired Secondary Metabolism in Plant Pathogenic Fungi: The Evolution of Biotrophs Into Host-Specific Pathogens. Front Microbiol 2021; 12:664276. [PMID: 33968000 PMCID: PMC8102738 DOI: 10.3389/fmicb.2021.664276] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/09/2021] [Indexed: 11/25/2022] Open
Abstract
Accessory chromosomes are strain- or pathotype-specific chromosomes that exist in addition to the core chromosomes of a species and are generally not considered essential to the survival of the organism. Among pathogenic fungal species, accessory chromosomes harbor pathogenicity or virulence factor genes, several of which are known to encode for secondary metabolites that are involved in plant tissue invasion. Accessory chromosomes are of particular interest due to their capacity for horizontal transfer between strains and their dynamic "crosstalk" with core chromosomes. This review focuses exclusively on secondary metabolism (including mycotoxin biosynthesis) associated with accessory chromosomes in filamentous fungi and the role accessory chromosomes play in the evolution of secondary metabolite gene clusters. Untargeted metabolomics profiling in conjunction with genome sequencing provides an effective means of linking secondary metabolite products with their respective biosynthetic gene clusters that reside on accessory chromosomes. While the majority of literature describing accessory chromosome-associated toxin biosynthesis comes from studies of Alternaria pathotypes, the recent discovery of accessory chromosome-associated biosynthetic genes in Fusarium species offer fresh insights into the evolution of biosynthetic enzymes such as non-ribosomal peptide synthetases (NRPSs), polyketide synthases (PKSs) and regulatory mechanisms governing their expression.
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Affiliation(s)
- Thomas E. Witte
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Nicolas Villeneuve
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Christopher N. Boddy
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - David P. Overy
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
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13
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Gressler M, Löhr NA, Schäfer T, Lawrinowitz S, Seibold PS, Hoffmeister D. Mind the mushroom: natural product biosynthetic genes and enzymes of Basidiomycota. Nat Prod Rep 2021; 38:702-722. [PMID: 33404035 DOI: 10.1039/d0np00077a] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covering: up to September 2020 Mushroom-forming fungi of the division Basidiomycota have traditionally been recognised as prolific producers of structurally diverse and often bioactive secondary metabolites, using the methods of chemistry for research. Over the past decade, -omics technologies were applied on these fungi, and sophisticated heterologous gene expression platforms emerged, which have boosted research into the genetic and biochemical basis of the biosyntheses. This review provides an overview on experimentally confirmed natural product biosyntheses of basidiomycete polyketides, amino acid-derived products, terpenoids, and volatiles. We also present challenges and solutions particular to natural product research with these fungi. 222 references are cited.
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Affiliation(s)
- Markus Gressler
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany.
| | - Nikolai A Löhr
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany.
| | - Tim Schäfer
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany.
| | - Stefanie Lawrinowitz
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany.
| | - Paula Sophie Seibold
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany.
| | - Dirk Hoffmeister
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany.
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14
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Genomics-directed activation of cryptic natural product pathways deciphers codes for biosynthesis and molecular function. J Nat Med 2020; 75:261-274. [PMID: 33274411 PMCID: PMC7902601 DOI: 10.1007/s11418-020-01466-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 11/06/2020] [Indexed: 12/22/2022]
Abstract
Natural products, which can be isolated from living organisms worldwide, have played a pivotal role in drug discovery since ancient times. However, it has become more challenging to identify a structurally novel molecule with promising biological activity for pharmaceutical development, mainly due to the limited methodologies for their acquisition. In this review, we summarize our recent studies that activate the biosynthetic potential of filamentous fungi by genetic engineering to harness the metabolic flow for the efficient production of unprecedented natural products. The recent revolution in genome sequencing technology enables the accumulation of vast amounts of information on biosynthetic genes, the blueprint of the molecular construction. Utilizing the established heterologous expression system, activation of the pathway-specific transcription factor coupled with a knockout strategy, and manipulating the global regulatory gene, the biosynthetic genes were exploited to activate biosynthetic pathways and decipher the encoded enzyme functions. We show that this methodology was beneficial for acquiring fungal treasures for drug discovery. These studies also enabled the investigation of the molecular function of natural products in fungal development.
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15
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Misslinger M, Hortschansky P, Brakhage AA, Haas H. Fungal iron homeostasis with a focus on Aspergillus fumigatus. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118885. [PMID: 33045305 DOI: 10.1016/j.bbamcr.2020.118885] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/15/2020] [Accepted: 10/01/2020] [Indexed: 02/08/2023]
Abstract
To maintain iron homeostasis, fungi have to balance iron acquisition, storage, and utilization to ensure sufficient supply and to avoid toxic excess of this essential trace element. As pathogens usually encounter iron limitation in the host niche, this metal plays a particular role during virulence. Siderophores are iron-chelators synthesized by most, but not all fungal species to sequester iron extra- and intracellularly. In recent years, the facultative human pathogen Aspergillus fumigatus has become a model for fungal iron homeostasis of siderophore-producing fungal species. This article summarizes the knowledge on fungal iron homeostasis and its links to virulence with a focus on A. fumigatus. It covers mechanisms for iron acquisition, storage, and detoxification, as well as the modes of transcriptional iron regulation and iron sensing in A. fumigatus in comparison to other fungal species. Moreover, potential translational applications of the peculiarities of fungal iron metabolism for treatment and diagnosis of fungal infections is addressed.
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Affiliation(s)
- Matthias Misslinger
- Institute of Molecular Biology - Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Peter Hortschansky
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany; Department Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Hubertus Haas
- Institute of Molecular Biology - Biocenter, Medical University of Innsbruck, Innsbruck, Austria.
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16
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Hai Y, Jenner M, Tang Y. Fungal siderophore biosynthesis catalysed by an iterative nonribosomal peptide synthetase. Chem Sci 2020; 11:11525-11530. [PMID: 34094397 PMCID: PMC8162485 DOI: 10.1039/d0sc03627g] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Siderophores play a vital role in the viability of fungi and are essential for the virulence of many pathogenic fungal species. Despite their importance in fungal physiology and pathogenesis, the programming rule of siderophore assembly by fungal nonribosomal peptide synthetases (NRPSs) remains unresolved. Here, we report the characterization of the bimodular fungal NRPS, SidD, responsible for construction of the extracellular siderophore fusarinine C. The use of intact protein mass spectrometry, together with in vitro biochemical assays of native and dissected enzymes, provided snapshots of individual biosynthetic steps during NPRS catalysis. The adenylation and condensation domain of SidD can iteratively load and condense the amino acid building block cis-AMHO, respectively, to synthesize fusarinine C. Our study showcases the iterative programming features of fungal siderophore-producing NRPSs.
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Affiliation(s)
- Yang Hai
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles California 90095 USA
| | - Matthew Jenner
- Department of Chemistry, Warwick Integrative Synthetic Biology Center, University of Warwick Coventry UK
- Warwick Integrative Synthetic Biology (WISB) Centre, University of Warwick Coventry UK
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles California 90095 USA
- Department of Chemistry and Biochemistry, University of California Los Angeles California 90095 USA
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17
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Oghenekaro AO, Kovalchuk A, Raffaello T, Camarero S, Gressler M, Henrissat B, Lee J, Liu M, Martínez AT, Miettinen O, Mihaltcheva S, Pangilinan J, Ren F, Riley R, Ruiz-Dueñas FJ, Serrano A, Thon MR, Wen Z, Zeng Z, Barry K, Grigoriev IV, Martin F, Asiegbu FO. Genome sequencing of Rigidoporus microporus provides insights on genes important for wood decay, latex tolerance and interspecific fungal interactions. Sci Rep 2020; 10:5250. [PMID: 32251355 PMCID: PMC7089950 DOI: 10.1038/s41598-020-62150-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/10/2020] [Indexed: 11/27/2022] Open
Abstract
Fungal plant pathogens remain a serious threat to the sustainable agriculture and forestry, despite the extensive efforts undertaken to control their spread. White root rot disease is threatening rubber tree (Hevea brasiliensis) plantations throughout South and Southeast Asia and Western Africa, causing tree mortality and severe yield losses. Here, we report the complete genome sequence of the basidiomycete fungus Rigidoporus microporus, a causative agent of the disease. Our phylogenetic analysis confirmed the position of R. microporus among the members of Hymenochaetales, an understudied group of basidiomycetes. Our analysis further identified pathogen's genes with a predicted role in the decay of plant cell wall polymers, in the utilization of latex components and in interspecific interactions between the pathogen and other fungi. We also detected putative horizontal gene transfer events in the genome of R. microporus. The reported first genome sequence of a tropical rubber tree pathogen R. microporus should contribute to the better understanding of how the fungus is able to facilitate wood decay and nutrient cycling as well as tolerate latex and utilize resinous extractives.
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Affiliation(s)
- Abbot O Oghenekaro
- Faculty of Life Sciences, Department of Plant Biology and Biotechnology, University of Benin, P.M.B 1154, Benin City, Nigeria
- Faculty of Agriculture and Forestry, Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland
- Department of Plant Science, University of Manitoba, MB R3T 2N2, Winnipeg, Canada
| | - Andriy Kovalchuk
- Faculty of Agriculture and Forestry, Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland
| | - Tommaso Raffaello
- Faculty of Agriculture and Forestry, Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland
| | - Susana Camarero
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, E28040, Madrid, Spain
| | - Markus Gressler
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich Schiller University, Jena, Germany
| | - Bernard Henrissat
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, CNRS, UMR 7257, 13288, Marseille, cedex 9, France
- USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, 23218, Jeddah, Saudi Arabia
| | - Juna Lee
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Mengxia Liu
- Faculty of Agriculture and Forestry, Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland
| | - Angel T Martínez
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, E28040, Madrid, Spain
| | - Otto Miettinen
- Mycology Unit, Botanical Museum, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, Helsinki, Finland
| | - Sirma Mihaltcheva
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Fei Ren
- Faculty of Agriculture and Forestry, Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland
- Forestry experiment center of north China, Chinese Academy of Forestry, 102300, Beijing, China
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Francisco Javier Ruiz-Dueñas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, E28040, Madrid, Spain
| | - Ana Serrano
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, E28040, Madrid, Spain
| | - Michael R Thon
- Universidad de Salamanca, Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Villamayor, Spain
| | - Zilan Wen
- Faculty of Agriculture and Forestry, Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland
| | - Zhen Zeng
- Faculty of Agriculture and Forestry, Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Francis Martin
- Institut National de la Recherche Agronomique (INRA), Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), UMR 1136, Champenoux, France
- University of Lorraine, Laboratory of Excellence ARBRE, UMR 1136, Champenoux, France
| | - Fred O Asiegbu
- Faculty of Agriculture and Forestry, Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland.
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18
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Genome and secretome analysis of jute endophyte Grammothele lineata strain SDL-CO-2015-1: Insights into its lignocellulolytic structure and secondary metabolite profile. Genomics 2020; 112:2794-2803. [PMID: 32217134 DOI: 10.1016/j.ygeno.2020.03.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 03/02/2020] [Accepted: 03/22/2020] [Indexed: 12/30/2022]
Abstract
Grammothele lineata strain SDL-CO-2015-1, jute (Corchorus olitorius) endophyte has been reported to produce anti-cancer drug paclitaxel in culture condition. Here we investigated the genome using different bioinformatic tools to find its association with the production of commercially important compounds including taxol. Carbohydrate-active enzymes, proteases, and secretory proteins were annotated revealing a complex endophytic relationship with its plant host. The presences of a diverse range of CAZymes including numerous lignocellulolytic enzymes support its potentiality in biomass degradation. Genome annotation led to the identification of 28 clusters for secondary metabolite biosynthesis. Several biosynthesis gene clusters were identified for terpene biosynthesis from antiSMASH analysis but none could be specifically pinned to taxol synthesis. This study will direct us to understand the genomic organization of endophytic basidiomycetes with a potential for producing numerous commercially important enzymes and secondary metabolites taking G. lineata as a model.
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19
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Heterologous expression of intact biosynthetic gene clusters in Fusarium graminearum. Fungal Genet Biol 2019; 132:103248. [DOI: 10.1016/j.fgb.2019.103248] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/27/2019] [Accepted: 06/27/2019] [Indexed: 11/18/2022]
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20
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Vassaux A, Meunier L, Vandenbol M, Baurain D, Fickers P, Jacques P, Leclère V. Nonribosomal peptides in fungal cell factories: from genome mining to optimized heterologous production. Biotechnol Adv 2019; 37:107449. [PMID: 31518630 DOI: 10.1016/j.biotechadv.2019.107449] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 12/15/2022]
Abstract
Fungi are notoriously prolific producers of secondary metabolites including nonribosomal peptides (NRPs). The structural complexity of NRPs grants them interesting activities such as antibiotic, anti-cancer, and anti-inflammatory properties. The discovery of these compounds with attractive activities can be achieved by using two approaches: either by screening samples originating from various environments for their biological activities, or by identifying the related clusters in genomic sequences thanks to bioinformatics tools. This genome mining approach has grown tremendously due to recent advances in genome sequencing, which have provided an incredible amount of genomic data from hundreds of microbial species. Regarding fungal organisms, the genomic data have revealed the presence of an unexpected number of putative NRP-related gene clusters. This highlights fungi as a goldmine for the discovery of putative novel bioactive compounds. Recent development of NRP dedicated bioinformatics tools have increased the capacity to identify these gene clusters and to deduce NRPs structures, speeding-up the screening process for novel metabolites discovery. Unfortunately, the newly identified compound is frequently not or poorly produced by native producers due to a lack of expression of the related genes cluster. A frequently employed strategy to increase production rates consists in transferring the related biosynthetic pathway in heterologous hosts. This review aims to provide a comprehensive overview about the topic of NRPs discovery, from gene cluster identification by genome mining to the heterologous production in fungal hosts. The main computational tools and methods for genome mining are herein presented with an emphasis on the particularities of the fungal systems. The different steps of the reconstitution of NRP biosynthetic pathway in heterologous fungal cell factories will be discussed, as well as the key factors to consider for maximizing productivity. Several examples will be developed to illustrate the potential of heterologous production to both discover uncharacterized novel compounds predicted in silico by genome mining, and to enhance the productivity of interesting bio-active natural products.
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Affiliation(s)
- Antoine Vassaux
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium; Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, F-59000 Lille, France
| | - Loïc Meunier
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium; InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liege, Boulevard du Rectorat 27, B-4000 Liège, Belgium
| | - Micheline Vandenbol
- TERRA Teaching and Research Centre, Microbiologie et Génomique, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Denis Baurain
- InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liege, Boulevard du Rectorat 27, B-4000 Liège, Belgium
| | - Patrick Fickers
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Philippe Jacques
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Valérie Leclère
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, F-59000 Lille, France.
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21
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Tsunematsu Y, Takanishi J, Asai S, Masuya T, Nakazawa T, Watanabe K. Genomic Mushroom Hunting Decrypts Coprinoferrin, A Siderophore Secondary Metabolite Vital to Fungal Cell Development. Org Lett 2019; 21:7582-7586. [PMID: 31496254 DOI: 10.1021/acs.orglett.9b02861] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
LaeA is a positive global regulator of secondary metabolism in Ascomycetes, but its role in Basidiomycetes, including medicinal mushrooms, remains uncharacterized. Here, knockout of laeA in the model mushroom Coprinopsis cinerea unexpectedly upregulated the biosynthesis of a novel siderophore, coprinoferrin. Furthermore, knockout of the nonribosomal peptide synthetase-encoding cpf1 responsible for coprinoferrin biosynthesis resulted in growth defect and loss of fruiting body formation, indicating the complex role that this natural product plays in fungal cell development.
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Affiliation(s)
- Yuta Tsunematsu
- Department of Pharmaceutical Sciences , University of Shizuoka , Shizuoka 422-8526 , Japan
| | - Jun Takanishi
- Department of Pharmaceutical Sciences , University of Shizuoka , Shizuoka 422-8526 , Japan
| | - Shihori Asai
- Department of Pharmaceutical Sciences , University of Shizuoka , Shizuoka 422-8526 , Japan
| | - Takahiro Masuya
- Department of Pharmaceutical Sciences , University of Shizuoka , Shizuoka 422-8526 , Japan
| | - Takehito Nakazawa
- Graduate School of Agriculture , Kyoto University , Kyoto 606-8502 , Japan
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences , University of Shizuoka , Shizuoka 422-8526 , Japan
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22
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Dörfer M, Heine D, König S, Gore S, Werz O, Hertweck C, Gressler M, Hoffmeister D. Melleolides impact fungal translation via elongation factor 2. Org Biomol Chem 2019; 17:4906-4916. [PMID: 31042251 DOI: 10.1039/c9ob00562e] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Melleolides from the honey mushroom Armillaria mellea represent a structurally diverse group of polyketide-sesquiterpene hybrids. Among various bioactivites, melleolides show antifungal effects against Aspergillus and other fungi. This bioactivity depends on a Δ2,4-double bond present in dihydroarmillylorsellinate (DAO) or arnamial, for example. Yet, the mode of action of Δ2,4-unsaturated, antifungal melleolides has been unknown. Here, we report on the molecular target of DAO in the fungus Aspergillus nidulans. Using a combination of synthetic chemistry to create a DAO-labelled probe, protein pulldown assays, MALDI-TOF-based peptide analysis and western blotting, we identify the eukaryotic translation elongation factor 2 (eEF2) as a binding partner of DAO. We confirm the inhibition of protein biosynthesis in vivo with an engineered A. nidulans strain producing the red fluorescent protein mCherry. Our work suggests a binding site dissimilar from that of the protein biosynthesis inhibitor sordarin, and highlights translational elongation as a valid antifungal drug target.
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Affiliation(s)
- Maximilian Dörfer
- Department Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University, Beutenbergstrasse 11a, 07745 Jena, Germany.
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Biological and chemical diversity go hand in hand: Basidiomycota as source of new pharmaceuticals and agrochemicals. Biotechnol Adv 2019; 37:107344. [PMID: 30738916 DOI: 10.1016/j.biotechadv.2019.01.011] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 12/20/2022]
Abstract
The Basidiomycota constitutes the second largest higher taxonomic group of the Fungi after the Ascomycota and comprises over 30.000 species. Mycelial cultures of Basidiomycota have already been studied since the 1950s for production of antibiotics and other beneficial secondary metabolites. Despite the fact that unique and selective compounds like pleuromutilin were obtained early on, it took several decades more until they were subjected to a systematic screening for antimicrobial and anticancer activities. These efforts led to the discovery of the strobilurins and several hundreds of further compounds that mainly constitute terpenoids. In parallel the traditional medicinal mushrooms of Asia were also studied intensively for metabolite production, aimed at finding new therapeutic agents for treatment of various diseases including metabolic disorders and the central nervous system. While the evaluation of this organism group has in general been more tedious as compared to the Ascomycota, the chances to discover new metabolites and to develop them further to candidates for drugs, agrochemicals and other products for the Life Science industry have substantially increased over the past decade. This is owing to the revolutionary developments in -OMICS techniques, bioinformatics, analytical chemistry and biotechnological process technology, which are steadily being developed further. On the other hand, the new developments in polythetic fungal taxonomy now also allow a more concise selection of previously untapped organisms. The current review is dedicated to summarize the state of the art and to give an outlook to further developments.
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Strategies for Engineering Natural Product Biosynthesis in Fungi. Trends Biotechnol 2018; 37:416-427. [PMID: 30316556 DOI: 10.1016/j.tibtech.2018.09.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 09/02/2018] [Accepted: 09/12/2018] [Indexed: 01/22/2023]
Abstract
Fungi are a prolific source of bioactive compounds, some of which have been developed as essential medicines and life-enhancing drugs. Genome sequencing has revealed that fungi have the potential to produce considerably more natural products (NPs) than are typically observed in the laboratory. Recently, there have been significant advances in the identification, understanding, and engineering of fungal biosynthetic gene clusters (BGCs). This review briefly describes examples of the engineering of fungal NP biosynthesis at the global, pathway, and enzyme level using in vivo and in vitro approaches and refers to the range and scale of heterologous expression systems available, developments in combinatorial biosynthesis, progress in understanding how fungal BGCs are regulated, and the applications of these novel biosynthetic enzymes as biocatalysts.
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Geib E, Brock M. ATNT: an enhanced system for expression of polycistronic secondary metabolite gene clusters in Aspergillus niger. Fungal Biol Biotechnol 2017; 4:13. [PMID: 29270299 PMCID: PMC5735947 DOI: 10.1186/s40694-017-0042-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 12/12/2017] [Indexed: 11/16/2022] Open
Abstract
Background Fungi are treasure chests for yet unexplored natural products. However, exploitation of their real potential remains difficult as a significant proportion of biosynthetic gene clusters appears silent under standard laboratory conditions. Therefore, elucidation of novel products requires gene activation or heterologous expression. For heterologous gene expression, we previously developed an expression platform in Aspergillus niger that is based on the transcriptional regulator TerR and its target promoter PterA. Results In this study, we extended this system by regulating expression of terR by the doxycycline inducible Tet-on system. Reporter genes cloned under the control of the target promoter PterA remained silent in the absence of doxycycline, but were strongly expressed when doxycycline was added. Reporter quantification revealed that the coupled system results in about five times higher expression rates compared to gene expression under direct control of the Tet-on system. As production of secondary metabolites generally requires the expression of several biosynthetic genes, the suitability of the self-cleaving viral peptide sequence P2A was tested in this optimised expression system. P2A allowed polycistronic expression of genes required for Asp-melanin formation in combination with the gene coding for the red fluorescent protein tdTomato. Gene expression and Asp-melanin formation was prevented in the absence of doxycycline and strongly induced by addition of doxycycline. Fluorescence studies confirmed the correct subcellular localisation of the respective enzymes. Conclusion This tightly regulated but strongly inducible expression system enables high level production of secondary metabolites most likely even those with toxic potential. Furthermore, this system is compatible with polycistronic gene expression and, thus, suitable for the discovery of novel natural products. Electronic supplementary material The online version of this article (10.1186/s40694-017-0042-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elena Geib
- Fungal Genetics and Biology, School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Matthias Brock
- Fungal Genetics and Biology, School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
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