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Li J, Li Z, Duan Y, Liu C, Yan M. Secondary Metabolites of Fomitopsis betulina: Chemical Structures, Biological Activity and Application Prospects. J Fungi (Basel) 2024; 10:616. [PMID: 39330376 PMCID: PMC11432923 DOI: 10.3390/jof10090616] [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: 07/19/2024] [Revised: 08/24/2024] [Accepted: 08/27/2024] [Indexed: 09/28/2024] Open
Abstract
Fomitopsis betulina, as a macrofungus with both medicinal and dietary applications, is renowned for its rich content of bioactive substances. The recent advancements in research have significantly enhanced our understanding of its polysaccharides, cellulose-degrading enzymes, and wide range of secondary metabolites. This paper provides a comprehensive review of the artificial cultivation techniques and the chemical profiling of over 100 secondary metabolites identified in F. betulina, including terpenoids, phenols, and various other classes. These compounds exhibit notable pharmacological activities, such as anti-cancer, anti-inflammatory, antimicrobial, antiviral, and anti-malarial effects. Moreover, this review delves into the genomic analysis of F. betulina, focusing on the prediction and classification of terpene synthases, which play a crucial role in the biosynthesis of these bioactive compounds. This insight is instrumental for potentially facilitating future biochemical studies and pharmaceutical applications. Through this review, we aim to solidify the foundation for future in-depth studies and the development of new drugs derived from this promising natural resource.
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Affiliation(s)
- Jianghao Li
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China; (J.L.); (Z.L.); (Y.D.)
| | - Ziheng Li
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China; (J.L.); (Z.L.); (Y.D.)
| | - Yingce Duan
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China; (J.L.); (Z.L.); (Y.D.)
| | - Chengwei Liu
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China; (J.L.); (Z.L.); (Y.D.)
| | - Meixia Yan
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
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Xie X, Zhao L, Song Y, Qiao Y, Wang ZX, Qi J. Genome-wide characterization and metabolite profiling of Cyathus olla: insights into the biosynthesis of medicinal compounds. BMC Genomics 2024; 25:618. [PMID: 38890562 PMCID: PMC11186289 DOI: 10.1186/s12864-024-10528-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024] Open
Abstract
Cyathus olla, belonging to the genus Cyathus within the order Agaricales, is renowned for its bird's nest-like fruiting bodies and has been utilized in folk medicine. However, its genome remains poorly understood. To investigate genomic diversity within the genus Cyathus and elucidate biosynthetic pathways for medicinal compounds, we generated a high-quality genome assembly of C. olla with fourteen chromosomes. The comparative genome analysis revealed variations in both genomes and specific functional genes within the genus Cyathus. Phylogenomic and gene family variation analyses provided insights into evolutionary divergence, as well as genome expansion and contraction in individual Cyathus species and 36 typical Basidiomycota. Furthermore, analysis of LTR-RT and Ka/Ks revealed apparent whole-genome duplication (WGD) events its genome. Through genome mining and metabolite profiling, we identified the biosynthetic gene cluster (BGC) for cyathane diterpenes from C. olla. Furthermore, we predicted 32 BGCs, containing 41 core genes, involved in other bioactive metabolites. These findings represent a valuable genomic resource that will enhance our understanding of Cyathus species genetic diversity. The genome analysis of C. olla provides insights into the biosynthesis of medicinal compounds and establishes a fundamental basis for future investigations into the genetic basis of chemodiversity in this significant medicinal fungus.
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Affiliation(s)
- Xiuchao Xie
- Shaanxi Province Key Laboratory of Bio-resources, Qinba State Key Laboratory of Biological Resources and Ecological Environment (Incubation), School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, 723000, China
| | - Ling Zhao
- Department of Pharmacy, School of Medicine, Xi'an International University, Xi'an 710077, China
| | - Yu Song
- Shaanxi Province Key Laboratory of Bio-resources, Qinba State Key Laboratory of Biological Resources and Ecological Environment (Incubation), School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, 723000, China
| | - Yanming Qiao
- Shaanxi Province Key Laboratory of Bio-resources, Qinba State Key Laboratory of Biological Resources and Ecological Environment (Incubation), School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, 723000, China
| | - Zhen-Xin Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, China
| | - Jianzhao Qi
- Shaanxi Province Key Laboratory of Bio-resources, Qinba State Key Laboratory of Biological Resources and Ecological Environment (Incubation), School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, 723000, China.
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, China.
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Ding M, Yang Y, Zhang Z, Liu H, Dai Y, Wang Z, Ma S, Liu Y, Wang Q. Structural characterization of the polysaccharide from the black crystal region of Inonotus obliquus and its effect on AsPC-1 and SW1990 pancreatic cancer cell apoptosis. Int J Biol Macromol 2024; 268:131891. [PMID: 38677687 DOI: 10.1016/j.ijbiomac.2024.131891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 04/09/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
In this study, one water soluble polysaccharide (IOP1-1) with a weight average molecular weight of 6886 Da was obtained from the black crystal region of Inonotus obliquus by hot water extraction, DEAE-52 cellulose extraction and Sephadex-100 column chromatography purification. Structural analysis indicated that IOP1-1 was a glucan with a main chain composed of α-Glcp-(1 → 4)-α-Glcp-(1 → 4)-β-Glcp-(1 → 4)-β-Glcp-(1 → 4)-α-Glcp-(1 → 6)-β-Glcp-(1 → 4)-α-Glcp-(1 → 3)-β-Glcp-(1→. The CCK-8 assay results showed that IOP1-1 inhibited AsPC-1 and SW1990 pancreatic cancer cell proliferation in a concentration-dependent manner. Flow cytometric analysis revealed that IOP1-1 induced cell cycle arrest in AsPC-1 and SW1990 cells. Hoechst 33342 staining and Annexin V-FITC/PI double staining analysis showed that IOP1-1 could induce apoptosis in AsPC-1 and SW1990 cells. Furthermore, western blot analysis confirmed that IOP1-1 could induce apoptosis in AsPC-1 and SW1990 pancreatic cancer cells through three pathways: the mitochondrial pathway, the death receptor pathway, and endoplasmic reticulum stress. According to these research data, IOP1-1 may be utilized as an adjuvant treatment to anticancer medications, opening up new application prospects and opportunities.
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Affiliation(s)
- Miao Ding
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China; College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Yu Yang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China; College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Ziyang Zhang
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Hongxiang Liu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China; College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Yingdi Dai
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China; College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Zixuan Wang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China; College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Sijia Ma
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China; College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Yang Liu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China; College of Plant Protection, Jilin Agricultural University, Changchun 130118, China.
| | - Qi Wang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China; College of Plant Protection, Jilin Agricultural University, Changchun 130118, China.
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Qi J, Kang SJ, Zhao L, Gao JM, Liu C. Natural and engineered xylosyl products from microbial source. NATURAL PRODUCTS AND BIOPROSPECTING 2024; 14:13. [PMID: 38296905 PMCID: PMC10830979 DOI: 10.1007/s13659-024-00435-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 01/18/2024] [Indexed: 02/02/2024]
Abstract
Glycosylation is a prevalent post-modification found in natural products and has a significant impact on the structural diversity and activity variation of natural products. Glucosylation is the most common type of glycosylation, whereas xylosylation is relatively rare. Despite their unique chemical structures and beneficial activities, xylosylated natural products from microorganisms have received little attention. This review provides, for the first time, a comprehensive summary of 126 microbial-derived xylosylated natural products, including xylosyl-cyathane diterpenes, xylosylated triterpenes, xylosyl aromatic compounds, and others. Among these compounds, xylosyl-cyathane diterpenes represent the highest number of derivatives, followed by xylosylated triterpenes. Xylosyl compounds from bacterial sources have less defined structural profiles compared to those from fungi. The characterization of xylosyltransferase EriJ from Basidiomycota extended the structural diversity of xylosyl cyathane diterpenes. This work provides a valuable reference for the research and use of xylosyltransferase for drug discovery and synthetic chemistry. Further work is needed to explore the potential applications of microbial derived xylosyl compounds and to develop novel xylosyl transferases. With the deepening of genomic sequencing of medicinal fungi, more biosynthesis of bioactive xylosyl compounds is expected to be elucidated in the future.
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Affiliation(s)
- Jianzhao Qi
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, China.
- Department of Pharmacy, School of Medicine, Xi'an International University, Xi'an, 710077, China.
- Key Laboratory for Enzyme and Enzyme‑Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin, 150040, China.
| | - Shi-Jie Kang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, China
| | - Ling Zhao
- Department of Pharmacy, School of Medicine, Xi'an International University, Xi'an, 710077, China
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, China
| | - Chengwei Liu
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, China.
- Key Laboratory for Enzyme and Enzyme‑Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin, 150040, China.
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Jin C, Ma JX, Wang H, Tang LX, Ye YF, Li X, Si J. First genome assembly and annotation of Sanghuangporus weigelae uncovers its medicinal functions, metabolic pathways, and evolution. Front Cell Infect Microbiol 2024; 13:1325418. [PMID: 38264724 PMCID: PMC10803629 DOI: 10.3389/fcimb.2023.1325418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024] Open
Abstract
Sanghuangporus, also known as "Sanghuang" in China, is a well-known genus of traditional Chinese medicinal macrofungi. To make more effective use of Sanghuangporus resources, we completed the first genome assembly and annotation of a monokaryon strain of S. weigelae in the present study. A 33.96-Mb genome sequence was assembled as 13 contigs, leading to prediction of 9377 protein-coding genes. Phylogenetic and average nucleotide identity analyses indicated that the S. weigelae genome is closely related to those of other Sanghuangporus species in evolutionary tree, which clustered in one clade. Collinearity analysis revealed a high level of collinearity of S. weigelae with S. baumii, S. vaninii, and S. sanghuang. Biosynthesis pathways potentially involved in medicinal properties, including terpenoid and polysaccharide synthesis, were identified in S. weigelae, while polysaccharides were identified as the main medicinal metabolites in S. weigelae, with flavonoids more important in Sanghuangporus than other medicinal mushroom groups. Genes encoding 332 carbohydrate-active enzymes were identified in the S. weigelae genome, including major glycoside hydrolases and glycosyltransferases predicted, revealing the robust lignocellulose degradation capacity of S. weigelae. Further, 130 genes, clustered in seven classes were annotated to encode cytochromes P450 in the S. weigelae genome. Overall, our results reveal the remarkably medicinal capacity of S. weigelae and provide new insights that will inform the study of evolution and medicinal application of S. weigelae. The data are a reference resource for the formulation of scientific and rational ecological protection policies for Sanghuangporus species.
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Affiliation(s)
| | | | | | | | | | | | - Jing Si
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
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Qi JS, Duan Y, Li ZC, Gao JM, Qi J, Liu C. The alkynyl-containing compounds from mushrooms and their biological activities. NATURAL PRODUCTS AND BIOPROSPECTING 2023; 13:50. [PMID: 37946001 PMCID: PMC10636002 DOI: 10.1007/s13659-023-00416-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
Mushrooms have been utilized by humans for thousands of years due to their medicinal and nutritional properties. They are a crucial natural source of bioactive secondary metabolites, and recent advancements have led to the isolation of several alkynyl-containing compounds with potential medicinal uses. Despite their relatively low abundance, naturally occurring alkynyl compounds have attracted considerable attention due to their high reactivity. Bioactivity studies have shown that alkynyl compounds exhibit significant biological and pharmacological activities, including antitumor, antibacterial, antifungal, insecticidal, phototoxic, HIV-inhibitory, and immunosuppressive properties. This review systematically compiles 213 alkynyl-containing bioactive compounds isolated from mushrooms since 1947 and summarizes their diverse biological activities, focusing mainly on cytotoxicity and anticancer effects. This review serves as a detailed and comprehensive reference for the chemical structures and bioactivity of alkynyl-containing secondary metabolites from mushrooms. Moreover, it provides theoretical support for the development of chemical constituents containing alkynyl compounds in mushrooms based on academic research and theory.
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Affiliation(s)
- Ji-Shuang Qi
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Yingce Duan
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Zhao-Chen Li
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, China
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, China
| | - Jianzhao Qi
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin, 150040, China.
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, China.
| | - Chengwei Liu
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin, 150040, China.
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Wei J, Liu L, Yuan X, Wang D, Wang X, Bi W, Yang Y, Wang Y. Transcriptome Analysis Reveals the Putative Polyketide Synthase Gene Involved in Hispidin Biosynthesis in Sanghuangporus sanghuang. MYCOBIOLOGY 2023; 51:360-371. [PMID: 37929012 PMCID: PMC10621269 DOI: 10.1080/12298093.2023.2257999] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/30/2023] [Indexed: 11/07/2023]
Abstract
Hispidin is an important styrylpyrone produced by Sanghuangporus sanghuang. To analyze hispidin biosynthesis in S. sanghuang, the transcriptomes of hispidin-producing and non-producing S. sanghuang were determined by Illumina sequencing. Five PKSs were identified using genome annotation. Comparative analysis with the reference transcriptome showed that two PKSs (ShPKS3 and ShPKS4) had low expression levels in four types of media. The gene expression pattern of only ShPKS1 was consistent with the yield variation of hispidin. The combined analyses of gene expression with qPCR and hispidin detection by liquid chromatography-mass spectrometry coupled with ion-trap and time-of-flight technologies (LCMS-IT-TOF) showed that ShPKS1 was involved in hispidin biosynthesis in S. sanghuang. ShPKS1 is a partially reducing PKS gene with extra AMP and ACP domains before the KS domain. The domain architecture of ShPKS1 was AMP-ACP-KS-AT-DH-KR-ACP-ACP. Phylogenetic analysis shows that ShPKS1 and other PKS genes from Hymenochaetaceae form a unique monophyletic clade closely related to the clade containing Agaricales hispidin synthase. Taken together, our data indicate that ShPKS1 is a novel PKS of S. sanghuang involved in hispidin biosynthesis.
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Affiliation(s)
- Jiansheng Wei
- Haba Snow Mountain Provincial Nature Reserve Management and Protection Bureau, Diqing, P.R. China
- Laboratory of Forest Plant Cultivation and Utilization, Yunnan Academy of Forestry & Grassland, Kunming, Yunnan, P.R. China
| | - Liangyan Liu
- College of Agronomy and Biotechnology, Yunnan Agriculture University, Kunming, Yunnan, P.R. China
| | - Xiaolong Yuan
- Laboratory of Forest Plant Cultivation and Utilization, Yunnan Academy of Forestry & Grassland, Kunming, Yunnan, P.R. China
| | - Dong Wang
- Laboratory of Forest Plant Cultivation and Utilization, Yunnan Academy of Forestry & Grassland, Kunming, Yunnan, P.R. China
| | - Xinyue Wang
- Laboratory of Forest Plant Cultivation and Utilization, Yunnan Academy of Forestry & Grassland, Kunming, Yunnan, P.R. China
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, P.R. China
| | - Wei Bi
- Laboratory of Forest Plant Cultivation and Utilization, Yunnan Academy of Forestry & Grassland, Kunming, Yunnan, P.R. China
| | - Yan Yang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, P.R. China
| | - Yi Wang
- Laboratory of Forest Plant Cultivation and Utilization, Yunnan Academy of Forestry & Grassland, Kunming, Yunnan, P.R. China
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Hao J, Wang X, Shi Y, Li L, Chu J, Li J, Lin W, Yu T, Hou D. Integrated omic profiling of the medicinal mushroom Inonotus obliquus under submerged conditions. BMC Genomics 2023; 24:554. [PMID: 37726686 PMCID: PMC10507853 DOI: 10.1186/s12864-023-09656-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 09/06/2023] [Indexed: 09/21/2023] Open
Abstract
BACKGROUND The Inonotus obliquus mushroom, a wondrous fungus boasting edible and medicinal qualities, has been widely used as a folk medicine and shown to have many potential pharmacological secondary metabolites. The purpose of this study was to supply a global landscape of genome-based integrated omic analysis of the fungus under lab-growth conditions. RESULTS This study presented a genome with high accuracy and completeness using the Pacbio Sequel II third-generation sequencing method. The de novo assembled fungal genome was 36.13 Mb, and contained 8352 predicted protein-coding genes, of which 365 carbohydrate-active enzyme (CAZyme)-coding genes and 19 biosynthetic gene clusters (BCGs) for secondary metabolites were identified. Comparative transcriptomic and proteomic analysis revealed a global view of differential metabolic change between seed and fermentation culture, and demonstrated positive correlations between transcription and expression levels of 157 differentially expressed genes involved in the metabolism of amino acids, fatty acids, secondary metabolites, antioxidant and immune responses. Facilitated by the widely targeted metabolomic approach, a total of 307 secondary substances were identified and quantified, with a significant increase in the production of antioxidant polyphenols. CONCLUSION This study provided the comprehensive analysis of the fungus Inonotus obliquus, and supplied fundamental information for further screening of promising target metabolites and exploring the link between the genome and metabolites.
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Affiliation(s)
- Jinghua Hao
- School of Bioscience and Technology, Weifang Medical University, Weifang, 261053, China
| | - Xiaoli Wang
- School of Bioscience and Technology, Weifang Medical University, Weifang, 261053, China
| | - Yanhua Shi
- School of Bioscience and Technology, Weifang Medical University, Weifang, 261053, China
| | - Lingjun Li
- School of Modern Agriculture and Environment, Weifang Institute of Technology, Weifang, 261053, China
| | - Jinxin Chu
- School of Bioscience and Technology, Weifang Medical University, Weifang, 261053, China
| | - Junjie Li
- School of Bioscience and Technology, Weifang Medical University, Weifang, 261053, China
| | - Weiping Lin
- School of Bioscience and Technology, Weifang Medical University, Weifang, 261053, China.
| | - Tao Yu
- School of Bioscience and Technology, Weifang Medical University, Weifang, 261053, China.
| | - Dianhai Hou
- School of Bioscience and Technology, Weifang Medical University, Weifang, 261053, China.
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Li ZC, Xie TC, Feng XL, Wang ZX, Lin C, Li GM, Li XZ, Qi J. The First Five Mitochondrial Genomes for the Family Nidulariaceae Reveal Novel Gene Rearrangements, Intron Dynamics, and Phylogeny of Agaricales. Int J Mol Sci 2023; 24:12599. [PMID: 37628782 PMCID: PMC10454537 DOI: 10.3390/ijms241612599] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
The family Nidulariaceae, consisting of five genera including Cyathus, is a unique group of mushrooms commonly referred to as bird's nest fungi due to their striking resemblance to bird's nests. These mushrooms are considered medicinal mushrooms in Chinese medicine and have received attention in recent years for their anti-neurodegenerative properties. However, despite the interest in these mushrooms, very little is known about their mitochondrial genomes (mitogenomes). This study is the first comprehensive investigation of the mitogenomes of five Nidulariaceae species with circular genome structures ranging in size from 114,236 bp to 129,263 bp. Comparative analyses based on gene content, gene length, tRNA, and codon usage indicate convergence within the family Nidulariaceae and heterogeneity within the order Agaricales. Phylogenetic analysis based on a combined mitochondrial conserved protein dataset provides a well-supported phylogenetic tree for the Basidiomycetes, which clearly demonstrates the evolutionary relationships between Nidulariaceae and other members of Agaricales. Furthermore, phylogenetic inferences based on four different gene sets reveal the stability and proximity of evolutionary relationships within Agaricales. These results reveal the uniqueness of the family Nidulariaceae and its similarity to other members of Agaricales; provide valuable insights into the origin, evolution, and genetics of Nidulariaceae species; and enrich the fungal mitogenome resource. This study will help to expand the knowledge and understanding of the mitogenomes in mushrooms.
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Affiliation(s)
- Zhao-chen Li
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Tian-chen Xie
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Xi-long Feng
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Zhen-xin Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Chao Lin
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Guo-ming Li
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Xiu-Zhang Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Sciences, Qinghai University, Xining 810016, China
| | - Jianzhao Qi
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
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Zhao H, Dai YC, Wu F, Liu XY, Maurice S, Krutovsky KV, Pavlov IN, Lindner DL, Martin FM, Yuan Y. Insights into the Ecological Diversification of the Hymenochaetales based on Comparative Genomics and Phylogenomics With an Emphasis on Coltricia. Genome Biol Evol 2023; 15:evad136. [PMID: 37498334 PMCID: PMC10410303 DOI: 10.1093/gbe/evad136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/01/2023] [Accepted: 07/16/2023] [Indexed: 07/28/2023] Open
Abstract
To elucidate the genomic traits of ecological diversification in the Hymenochaetales, we sequenced 15 new genomes, with attention to ectomycorrhizal (EcM) Coltricia species. Together with published data, 32 genomes, including 31 Hymenochaetales and one outgroup, were comparatively analyzed in total. Compared with those of parasitic and saprophytic members, EcM species have significantly reduced number of plant cell wall degrading enzyme genes, and expanded transposable elements, genome sizes, small secreted proteins, and secreted proteases. EcM species still retain some of secreted carbohydrate-active enzymes (CAZymes) and have lost the key secreted CAZymes to degrade lignin and cellulose, while possess a strong capacity to degrade a microbial cell wall containing chitin and peptidoglycan. There were no significant differences in secreted CAZymes between fungi growing on gymnosperms and angiosperms, suggesting that the secreted CAZymes in the Hymenochaetales evolved before differentiation of host trees into gymnosperms and angiosperms. Nevertheless, parasitic and saprophytic species of the Hymenochaetales are very similar in many genome features, which reflect their close phylogenetic relationships both being white rot fungi. Phylogenomic and molecular clock analyses showed that the EcM genus Coltricia formed a clade located at the base of the Hymenochaetaceae and divergence time later than saprophytic species. And Coltricia remains one to two genes of AA2 family. These indicate that the ancestors of Coltricia appear to have originated from saprophytic ancestor with the ability to cause a white rot. This study provides new genomic data for EcM species and insights into the ecological diversification within the Hymenochaetales based on comparative genomics and phylogenomics analyses.
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Affiliation(s)
- Heng Zhao
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yu-Cheng Dai
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Fang Wu
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Xiao-Yong Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Sundy Maurice
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Konstantin V Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Göttingen, Germany
- Center for Integrated Breeding Research, George-August University of Göttingen, Göttingen, Germany
- Laboratory of Population Genetics, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Laboratory of Forest Genomics, Department of Genomics and Bioinformatics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
- Scientific and Methodological Center, G. F. Morozov Voronezh State University of Forestry and Technologies, Voronezh, Russia
| | - Igor N Pavlov
- Mycology and Plant Pathology, V.N. Sukachev Institute of Forest SB RAS, Krasnoyarsk, Russia
- Department of Chemical Technology of Wood and Biotechnology, Reshetnev Siberian State University of Science and Technology, Krasnoyarsk, Russia
| | | | - Francis M Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE-GrandEst-Nancy, Champenoux, France
| | - Yuan Yuan
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
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11
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Wang Q, Bao H, Li Z. Genomic comparison between two Inonotus hispidus strains isolated from growing in different tree species. Front Genet 2023; 14:1221491. [PMID: 37519891 PMCID: PMC10372432 DOI: 10.3389/fgene.2023.1221491] [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: 05/12/2023] [Accepted: 07/03/2023] [Indexed: 08/01/2023] Open
Abstract
Inonotus hispidus mainly growing in broad-leaved trees, including Morus alba, Fraxinus mandshurica, and Ulmus macrocarpa etc. The fruiting body of I. hispidus growing in M. alba (hereafter as MA) is used as a traditional Chinese medicine "Sanghuang". However, differences between the genetic material basis of I. hispidus growing in other tree species have not been reported. Therefore, in this paper, the genomic comparison between MA and I. hispidus growing in F. mandshurica (hereafter as FM) were studied. The whole genome of MA monokaryon was sequenced by Illumina combined with Pac Bio platform. Next, genome assembly, genome component prediction and genome functional annotation were performed. Comparative genomics analysis was performed between FM monokaryon and MA monokaryon, using MA as the reference. The results showed that, MA had 24 contigs with a N50 length of 2.6 Mb. Specifically, 5,342, 6,564, 1,595, 383 and 123 genes were annotated from GO, KEGG, KOG, CAZymes and CYP450, respectively. Moreover, comparative genomics showed that, the coding genes and total number of genes annotated in different databases of FM were higher than that of MA. This study provides a foundation for the medicinal application of FM as MA from the perspective of genetic composition.
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Affiliation(s)
- Qingchun Wang
- Key Laboratory for Development and Utilization of Fungi Traditional Chinese Medicine Resources, Jilin Agricultural University, Changchun, Jilin, China
- Key Laboratory of Edible Fungal Resources and Utilization (North), Ministry of Agriculture and Rural Affairs, Jilin Agricultural University, Changchun, Jilin, China
| | - Haiying Bao
- Key Laboratory for Development and Utilization of Fungi Traditional Chinese Medicine Resources, Jilin Agricultural University, Changchun, Jilin, China
- Key Laboratory of Edible Fungal Resources and Utilization (North), Ministry of Agriculture and Rural Affairs, Jilin Agricultural University, Changchun, Jilin, China
| | - Zhijun Li
- Key Laboratory for Development and Utilization of Fungi Traditional Chinese Medicine Resources, Jilin Agricultural University, Changchun, Jilin, China
- Key Laboratory of Edible Fungal Resources and Utilization (North), Ministry of Agriculture and Rural Affairs, Jilin Agricultural University, Changchun, Jilin, China
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12
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Shen ZQ, Jiang JH, Li CT, Li Y, Zhou LW. Genome Re-Annotation and Transcriptome Analyses of Sanghuangporus sanghuang. J Fungi (Basel) 2023; 9:jof9050505. [PMID: 37233216 DOI: 10.3390/jof9050505] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/17/2023] [Accepted: 04/22/2023] [Indexed: 05/27/2023] Open
Abstract
Sanghuangporus sanghuang, the generic type of Sanghuangporus belonging to Hymenochaetaceae, is a precious medicinal wood-inhabiting macrofungus with high commercial potential. To facilitate the medicinal utilization of this fungal resource, transcriptome sequences are newly generated from S. sanghuang strain MS2. In association with the previously generated genome sequences from the same strain by our lab and all available fungal homologous protein sequences in the UniProtKB/Swiss-Prot Protein Sequence Database, a new methodology was employed for genome assembly and annotation. A total of 13,531 protein-coding genes were identified from the new version of the genome of S. sanghuang strain MS2 with a complete BUSCOs of 92.8%, which indicates a remarkable improvement in the accuracy and completeness of the genome assembly. In general, more genes involved in medicinal functions were annotated compared with the original version of the genome annotation, and most of these genes were also found in the transcriptome data of the currently sampled growth period. Given the above, the current genomic and transcriptomic data provides valuable insights into the evolution and metabolites analysis of S. sanghuang.
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Affiliation(s)
- Zi-Qi Shen
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Ministry of Science and Technology, Changchun 130118, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji-Hang Jiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chang-Tian Li
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Ministry of Science and Technology, Changchun 130118, China
| | - Yu Li
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Ministry of Science and Technology, Changchun 130118, China
| | - Li-Wei Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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13
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Zhao C, Feng XL, Wang ZX, Qi J. The First Whole Genome Sequencing of Agaricus bitorquis and Its Metabolite Profiling. J Fungi (Basel) 2023; 9:jof9040485. [PMID: 37108939 PMCID: PMC10142948 DOI: 10.3390/jof9040485] [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: 03/25/2023] [Revised: 04/16/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Agaricus bitorquis, an emerging wild mushroom with remarkable biological activities and a distinctive oversized mushroom shape, has gained increasing attention in recent years. Despite its status as an important resource of wild edible fungi, knowledge about this mushroom is still limited. In this study, we used the Illumina NovaSeq and Nanopore PromethION platforms to sequence, de novo assemble, and annotate the whole genome and mitochondrial genome (mitogenome) of the A. bitorquis strain BH01 isolated from Bosten Lake, Xinjiang Province, China. Using the genome-based biological information, we identified candidate genes associated with mating type and carbohydrate-active enzymes in A. bitorquis. Cluster analysis based on P450 of basidiomycetes revealed the types of P450 members of A. bitorquis. Comparative genomic, mitogenomic, and phylogenetic analyses were also performed, revealing interspecific differences and evolutionary features of A. bitorquis and A. bisporus. In addition, the molecular network of metabolites was investigated, highlighting differences in the chemical composition and content of the fruiting bodies of A. bitorquis and A. bisporus. The genome sequencing provides a comprehensive understanding and knowledge of A. bitorquis and the genus Agaricus mushrooms. This work provides valuable insights into the potential for artificial cultivation and molecular breeding of A. bitorquis, which will facilitate the development of A. bitorquis in the field of edible mushrooms and functional food manufacture.
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Affiliation(s)
- Chunhua Zhao
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xi-Long Feng
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Zhen-Xin Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Jianzhao Qi
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
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14
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Novel Insights into the Mechanism Underlying High Polysaccharide Yield in Submerged Culture of Ganoderma lucidum Revealed by Transcriptome and Proteome Analyses. Microorganisms 2023; 11:microorganisms11030772. [PMID: 36985345 PMCID: PMC10055881 DOI: 10.3390/microorganisms11030772] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/16/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Polysaccharides are crucial dietary supplements and traditional pharmacological components of Ganoderma lucidum; however, the mechanisms responsible for high polysaccharide yields in G. lucidum remain unclear. Therefore, we investigated the mechanisms underlying the high yield of polysaccharides in submerged cultures of G. lucidum using transcriptomic and proteomic analyses. Several glycoside hydrolase (GH) genes and proteins, which are associated with the degradation of fungal cell walls, were significantly upregulated under high polysaccharide yield conditions. They mainly belonged to the GH3, GH5, GH16, GH17, GH18, GH55, GH79, GH128, GH152, and GH154 families. Additionally, the results suggested that the cell wall polysaccharide could be degraded by GHs, which is beneficial for extracting more intracellular polysaccharides from cultured mycelia. Furthermore, some of the degraded polysaccharides were released into the culture broth, which is beneficial for obtaining more extracellular polysaccharides. Our findings provide new insights into the mechanisms underlying the roles that GH family genes play to regulate high polysaccharide yields in G. lucidum.
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15
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Zhu L, Gao X, Zhang M, Hu C, Yang W, Guo L, Yang S, Yu H, Yu H. Whole Genome Sequence of an Edible Mushroom Oudemansiella raphanipes (Changgengu). J Fungi (Basel) 2023; 9:jof9020266. [PMID: 36836380 PMCID: PMC9961838 DOI: 10.3390/jof9020266] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
Oudemansiella raphanipes, considered as a well-known culinary edible mushroom with a high content of natural bioactive substances, is widely cultivated in China with the commercial name Changgengu. However, due to the lack of genomic data, molecular and genetic study on O. raphanipes is rare. To obtain a comprehensive overview of genetic characteristics and enhance the value of O. raphanipes, two mating-compatible monokaryons isolated from the dikaryon were applied for de novo genome sequencing and assembly using Nanopore and /or Illumina sequencing platforms. One of the monokaryons, O. raphanipes CGG-A-s1, was annotated with 21,308 protein-coding genes, of which 56 were predicted to be involved in the biosynthesis of secondary metabolites such as terpene, type I PKS, NRPS, and siderophore. Phylogenetic and comparative analysis of multiple fungi genomes revealed a close evolutionary relationship between O. raphanipes and Mucidula mucid based on single-copy orthologous protein genes. Significant collinearity was detected between O. raphanipes and Flammulina velutipes on the synteny of inter-species genomes. 664 CAZyme genes in CGG-A-s1 were identified with GHs and AAs families significantly elevated when compared with the other 25 sequenced fungi, indicating a strong wood degradation ability. Furthermore, the mating type locus analysis revealed that CGG-A-s1 and CGG-A-s2 were conserved in the gene organization of the mating A locus but various in that of the mating B locus. The genome resource of O. raphanipes will provide new insights into its development of genetic studies and commercial production of high-quality varieties.
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Affiliation(s)
- Liping Zhu
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao 266109, China
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai 201403, China
| | - Xia Gao
- Shandong Agricultural Technology Extending Station, Jinan 250100, China
| | - Meihua Zhang
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao 266109, China
| | - Chunhui Hu
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao 266109, China
| | - Wujie Yang
- Shandong Agricultural Technology Extending Station, Jinan 250100, China
| | - Lizhong Guo
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao 266109, China
| | - Song Yang
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao 266109, China
| | - Hailong Yu
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai 201403, China
- Correspondence: (H.Y.); or (H.Y.); Tel.: +86-532-58957640 (Hailong Yu)
| | - Hao Yu
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao 266109, China
- Correspondence: (H.Y.); or (H.Y.); Tel.: +86-532-58957640 (Hailong Yu)
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16
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Zhang RQ, Feng XL, Wang ZX, Xie TC, Duan Y, Liu C, Gao JM, Qi J. Genomic and Metabolomic Analyses of the Medicinal Fungus Inonotus hispidus for Its Metabolite's Biosynthesis and Medicinal Application. J Fungi (Basel) 2022; 8:1245. [PMID: 36547578 PMCID: PMC9787987 DOI: 10.3390/jof8121245] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/11/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
Inonotus hispidus mushroom is a traditional medicinal fungus with anti-cancer, antioxidation, and immunomodulatory activities, and it is used in folk medicine as a treatment for indigestion, cancer, diabetes, and gastric illnesses. Although I. hispidus is recognized as a rare edible medicinal macrofungi, its genomic sequence and biosynthesis potential of secondary metabolites have not been investigated. In this study, using Illumina NovaSeq combined with the PacBio platform, we sequenced and de novo assembled the whole genome of NPCB_001, a wild I. hispidus isolate from the Aksu area of Xinjiang Province, China. Comparative genomic and phylogenomic analyses reveal interspecific differences and evolutionary traits in the genus Inonotus. Bioinformatics analysis identified candidate genes associated with mating type, polysaccharide synthesis, carbohydrate-active enzymes, and secondary metabolite biosynthesis. Additionally, molecular networks of metabolites exhibit differences in chemical composition and content between fruiting bodies and mycelium, as well as association clusters of related compounds. The deciphering of the genome of I. hispidus will deepen the understanding of the biosynthesis of bioactive components, open the path for future biosynthesis research, and promote the application of Inonotus in the fields of drug research and functional food manufacturing.
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Affiliation(s)
- Rui-Qi Zhang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Xi-Long Feng
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Zhen-Xin Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Tian-Chen Xie
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yingce Duan
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Chengwei Liu
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Jianzhao Qi
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
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17
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Dong WG, Wang ZX, Feng XL, Zhang RQ, Shen DY, Du S, Gao JM, Qi J. Chromosome-Level Genome Sequences, Comparative Genomic Analyses, and Secondary-Metabolite Biosynthesis Evaluation of the Medicinal Edible Mushroom Laetiporus sulphureus. Microbiol Spectr 2022; 10:e0243922. [PMID: 36200896 PMCID: PMC9602373 DOI: 10.1128/spectrum.02439-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/09/2022] [Indexed: 01/04/2023] Open
Abstract
Laetiporus sulphureus mushroom is a complementary and alternative medicine that has anticancer, antioxidation, and analgesic effects and immunomodulatory activity; it is used as a treatment for cough and rheumatism and is a functional food that can improve physical fitness. Even though L. sulphureus has garnered considerable biotechnological and pharmacological interest due to its excellent cellulose-degrading ability and diverse biological activities, its biosynthetic potential regarding polysaccharides and secondary metabolites has not been thoroughly examined. In this study, we sequenced and assembled the whole genome of a wild L. sulphureus isolate, NWAFU-1, from the Qinling Mountains in China. Comparative genomes analysis revealed genomic differences between subspecies, and phylogenomic analysis revealed evolutionary divergence as well as genome expansion and contraction of individual Polyporaceae family species. Bioinformatics investigation identified candidate genes associated with mating type, polysaccharide synthesis, carbohydrate-active enzymes, and secondary-metabolite biosynthesis, which included multiple terpenoids, nonribosomal peptides, and polyketides. The locations of biosynthetic core genes were mapped and displayed on chromosomes and contigs. Totals of 143 proteins from 126 coding genes were identified and divided into 14 cytochrome P450 families. Furthermore, the biosynthetic network of tetracyclic triterpenoid active components was postulated by genome mining of related genes combined with the molecular network of metabolites. The genome analysis of L. sulphureus in this study improves the understanding of the biosynthesis of active compounds, which will lay a theoretical foundation for subsequent research on active-compound biosynthesis and promote the application of Laetiporus in the field of drug research and functional-food creation. IMPORTANCE L. sulphureus is a parasitic basidiomycete fungus that causes brown rot. The fruiting bodies of L. sulphureus are used as ancient medicines in China and Europe to cure cancer, analgesia, cough, and rheumatism and are considered a functional food that regulates the body and improves health. L. sulphureus was inferred to be a tetrapolar system based on a high-quality genome, which will aid molecular breeding and artificial farming. Screening polysaccharide synthesis candidate genes and comparing carbohydrate-associated genes in brown-rot basidiomycetes help understand their growth. Identifying core genes for secondary-metabolite biosynthesis, gene cluster family analysis, and comparative cluster analysis will guide heterologous-biosynthesis investigations of these genes and help elucidate the biosynthetic pathways for L. sulphureus bioactive natural components. The biosynthesis network of tetracyclic triterpenes was mapped using metabolite profiling and genome scanning. This work explores the biosynthetic capacity of L. sulphureus-derived natural products and lays the foundation for biosynthetic studies of them.
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Affiliation(s)
- Wei-ge Dong
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhen-xin Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi, China
| | - Xi-long Feng
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi, China
| | - Rui-qi Zhang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi, China
| | - Dao-yin Shen
- Yangling Zhijun Fungi Biotechnology Engineering Co., Ltd., Yangling, Shaanxi, China
| | - Shuangtian Du
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi, China
| | - Jin-ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi, China
| | - Jianzhao Qi
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi, China
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18
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Beltrame G, Mattsson I, Damlin P, Han Z, Kvarnström C, Leino R, Yang B. Study of the sterile conk of Inonotus obliquus using 13C CPMAS NMR and FTIR spectroscopies coupled with multivariate analysis. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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19
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Wu J, Yang X, Duan Y, Wang P, Qi J, Gao JM, Liu C. Biosynthesis of Sesquiterpenes in Basidiomycetes: A Review. J Fungi (Basel) 2022; 8:913. [PMID: 36135638 PMCID: PMC9501842 DOI: 10.3390/jof8090913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/10/2022] [Accepted: 08/26/2022] [Indexed: 11/19/2022] Open
Abstract
Sesquiterpenes are common small-molecule natural products with a wide range of promising applications and are biosynthesized by sesquiterpene synthase (STS). Basidiomycetes are valuable and important biological resources. To date, hundreds of related sesquiterpenoids have been discovered in basidiomycetes, and the biosynthetic pathways of some of these compounds have been elucidated. This review summarizes 122 STSs and 2 fusion enzymes STSs identified from 26 species of basidiomycetes over the past 20 years. The biological functions of enzymes and compound structures are described, and related research is discussed.
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Affiliation(s)
- Jiajun Wu
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Xiaoran Yang
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yingce Duan
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Pengchao Wang
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Jianzhao Qi
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China
| | - Chengwei Liu
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
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20
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Diverse Metabolites and Pharmacological Effects from the Basidiomycetes Inonotus hispidus. Antibiotics (Basel) 2022; 11:antibiotics11081097. [PMID: 36009965 PMCID: PMC9405263 DOI: 10.3390/antibiotics11081097] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/11/2022] [Accepted: 08/11/2022] [Indexed: 11/18/2022] Open
Abstract
Inonotus hispidus mushroom is a popular edible and medicinal mushroom with a long history of use. It is well known as a medicinal fungus with various health benefits for its significant anticancer and immunomodulatory activities. Over the last 60 years, secondary metabolites derived from I. hispidus and their biological activities have been discovered and investigated. Structurally, these compounds are mainly polyphenols and triterpenoids, which have anticancer, anti-inflammatory, antioxidant, antimicrobial, and enzyme inhibitor activities. Here, the secondary metabolites derived from I. hispidus and their activities were systematically and comprehensively classified and summarized, and the biosynthetic pathway of stylylpyrones was deduced and analyzed further. This review contributes to our understanding of I. hispidus and will help with research into natural product chemistry, pharmacology, and the biosynthesis of I. hispidus metabolites. According to this review, I. hispidus could be a promising source of bioactive compounds for health promotion and the development of functional foods.
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