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Noushahi HA, Khan AH, Khan HA, Kiedrzyński M, Akbar A, Shahzad R, Koerniati S, Alrefaei AF, Shu S. Optimizing liquid fermentation for Wolfiporia cocos: gene expression and biosynthesis of pachymic acid and mycelial biomass. Lett Appl Microbiol 2024; 77:ovae054. [PMID: 38866707 DOI: 10.1093/lambio/ovae054] [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: 10/30/2023] [Revised: 05/29/2024] [Accepted: 06/11/2024] [Indexed: 06/14/2024]
Abstract
Wolfiporia cocos, a versatile fungus acclaimed for its nutritional and therapeutic benefits in Traditional Chinese Medicine, holds immense potential for pharmaceutical and industrial applications. In this study, we aimed to optimize liquid fermentation techniques and culture medium composition to maximize mycelial biomass (MB) yield, pachymic acid (PA) concentration, and overall PA production. Additionally, we investigated the molecular basis of our findings by quantifying the expression levels of genes associated with PA and MB biosynthesis using quantitative real-time polymerase chain reaction. Under the optimized fermentation conditions, significant results were achieved, with maximum MB reaching 6.68 g l-1, PA content peaking at 1.25 mg g-1, and a total PA yield of 4.76 g l-1. Notably, among the four examined genes, squalene monooxygenase, exhibited enhanced expression at 0.06 ratio under the optimized conditions. Furthermore, within the realm of carbohydrate-active enzymes, the glycoside hydrolases 16 family displayed elevated expression levels at 21 ratios, particularly during MB production. This study enhances understanding of genetic mechanism governing MB and PA production in W. cocos, highlighting the roles of squalene monooxygenase and glycoside hydrolases 16 carbohydrate-active enzymes.
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Affiliation(s)
- Hamza Armghan Noushahi
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Plant Breeding and Phenomic Centre, Faculty of Agricultural Sciences, University of Talca, Talca 3460000, Chile
| | - Aamir Hamid Khan
- Department of Biogeography, Paleoecology and Nature Conservation, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 1/3, 90-237 Lodz, Poland
| | - Hamza Ali Khan
- Plant Breeding and Phenomic Centre, Faculty of Agricultural Sciences, University of Talca, Talca 3460000, Chile
| | - Marcin Kiedrzyński
- Department of Biogeography, Paleoecology and Nature Conservation, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 1/3, 90-237 Lodz, Poland
| | - Adnan Akbar
- Department of Biogeography, Paleoecology and Nature Conservation, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 1/3, 90-237 Lodz, Poland
| | - Raheel Shahzad
- Research Center for Genetics Engineering, National Research and Innovation Agency (BRIN), KST-Cibinong, JI Raya Bogor KM46, Cibinong 16911, Indonesia
| | - Sri Koerniati
- Research Center for Genetics Engineering, National Research and Innovation Agency (BRIN), KST-Cibinong, JI Raya Bogor KM46, Cibinong 16911, Indonesia
| | - Abdulwahed Fahad Alrefaei
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Shaohua Shu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Liu H, Jing N, Li F, Wang K, Tang J, Zhao Q, Zhang Y, Noushahi HA, Xu R, Wang X, Zhu W, Feng S, Shu S, Mei Z. An omics-based characterization of Wolfiporia cocos reveals three CYP450 members involved in the biosynthetic pathway of pachymic acid. Commun Biol 2024; 7:666. [PMID: 38816492 PMCID: PMC11139888 DOI: 10.1038/s42003-024-06323-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/13/2024] [Indexed: 06/01/2024] Open
Abstract
Wolfiporia cocos is a medicinal mushroom used in China. It biosynthesizes pachymic acid (PA), a main therapeutic triterpene associated with therapies. Nowadays, the unknown PA biosynthesis leads to difficulties in increasing its content in W. cocos. Herein, we report sequencing, assembling, and characterization of the genome and several transcriptomes of W. cocos. Sequence mining determined candidate genes that encode lanosterol synthase, sterol O-acyltransferase, and sterol C-24 methyltransferase likely involved in the steps from lanosterol to PA. Gene cluster analysis identified four CYP450 cDNAs likely involved in the biosynthesis of PA, namely WcCYP64-1, WcCYP64-2, WcCYP52, and WcCYP_FUM15, which were subjected to both overexpression and silencing in mycelia. The overexpression of each of WcCYP64-1, WcCYP52 and WcCYP_FUM15 increased the content of PA, 16α-hydroxytrametenolic acid, eburicoic acid, and tumulosic acid, while the silencing of each gene either significantly or slightly decreased the contents of these four compounds, indicating their involvement in the PA biosynthesis. In addition, different temperatures affected the expression of these genes and the formation of PA. By contrast, the overexpression and silencing of WcCYP64-2 did not alter the formation of these compounds. Taken together, these findings determine more potential steps in the biosynthetic pathway of PA for metabolic engineering.
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Affiliation(s)
- Heping Liu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Naliang Jing
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Fengfeng Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Keyue Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Jing Tang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Qin Zhao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Yipeng Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Hamza Armghan Noushahi
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Ran Xu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei Province, China
| | | | - Wenjun Zhu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei Province, China.
| | - Shengqiu Feng
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China.
| | - Shaohua Shu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China.
| | - Zhinan Mei
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
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Guo M, Lv H, Chen H, Dong S, Zhang J, Liu W, He L, Ma Y, Yu H, Chen S, Luo H. Strategies on biosynthesis and production of bioactive compounds in medicinal plants. CHINESE HERBAL MEDICINES 2024; 16:13-26. [PMID: 38375043 PMCID: PMC10874775 DOI: 10.1016/j.chmed.2023.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/05/2023] [Accepted: 01/26/2023] [Indexed: 02/21/2024] Open
Abstract
Medicinal plants are a valuable source of essential medicines and herbal products for healthcare and disease therapy. Compared with chemical synthesis and extraction, the biosynthesis of natural products is a very promising alternative for the successful conservation of medicinal plants, and its rapid development will greatly facilitate the conservation and sustainable utilization of medicinal plants. Here, we summarize the advances in strategies and methods concerning the biosynthesis and production of natural products of medicinal plants. The strategies and methods mainly include genetic engineering, plant cell culture engineering, metabolic engineering, and synthetic biology based on multiple "OMICS" technologies, with paradigms for the biosynthesis of terpenoids and alkaloids. We also highlight the biosynthetic approaches and discuss progress in the production of some valuable natural products, exemplifying compounds such as vindoline (alkaloid), artemisinin and paclitaxel (terpenoids), to illustrate the power of biotechnology in medicinal plants.
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Affiliation(s)
- Miaoxian Guo
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Haizhou Lv
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Hongyu Chen
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Shuting Dong
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Jianhong Zhang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Wanjing Liu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Liu He
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Yimian Ma
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Hua Yu
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Shilin Chen
- Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Hongmei Luo
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
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Zhang C, Chen L, Chen M, Xu Z. First report on the regulation and function of carbon metabolism during large sclerotia formation in medicinal fungus Wolfiporia cocos. Fungal Genet Biol 2023; 166:103793. [PMID: 37120905 DOI: 10.1016/j.fgb.2023.103793] [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: 01/18/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023]
Abstract
The medicinal fungus Wolfiporia cocos colonizes and then grows on the wood of Pinus species, and utilizes a variety of Carbohydrate Active Enzymes (CAZymes) to degrades wood for the development of large sclerotia that is mostly built up of beta-glucans. Some differentially expressed CAZymes were revealed by comparisons between the mycelia cultured on potato dextrose agar (PDA) and sclerotia formed on pine logs in previous studies. Here, different profile of expressed CAZymes were revealed by comparisons between the mycelia colonization on pine logs (Myc.) and sclerotia (Scl.b). To further explore the regulation and function of carbon metabolism in the conversion of carbohydrates from Pine species by W. cocos, the transcript profile of core carbon metabolism was firstly analyzed, and it was characterized by the up-regulated expression of genes in the glycolysis pathway (EMP) and pentose phosphate pathway (PPP) in Scl.b, as well as high expression of genes in the tricarboxylic acid cycle (TCA) in both Myc. and Scl.b stages. The conversion between glucose and glycogen and between glucose and β-glucan was firstly identified as the main carbon flow in the differentiation process of W. cocos sclerotia, with a gradual increase in the content of β-glucan, trehalose and polysaccharide during this process. Additionally, gene functional analysis revealed that the two key genes (PGM and UGP1) may mediate the formation and development of W. cocos sclerotia possibly by regulating β-glucan synthesis and hyphal branching. This study has shed light on the regulation and function of carbon metabolism during large W. cocos sclerotium formation and may facilitate its commercial production.
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Affiliation(s)
- Cong Zhang
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Lianfu Chen
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Mengting Chen
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Zhangyi Xu
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
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Zhang Y, Shen T, Zuo Z, Wang Y. ResNet and MaxEnt modeling for quality assessment of Wolfiporia cocos based on FT-NIR fingerprints. FRONTIERS IN PLANT SCIENCE 2022; 13:996069. [PMID: 36407623 PMCID: PMC9666765 DOI: 10.3389/fpls.2022.996069] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
As a fungus with both medicinal and edible value, Wolfiporia cocos (F. A. Wolf) Ryvarden & Gilb. has drawn more public attention. Chemical components' content fluctuates in wild and cultivated W. cocos, whereas the accumulation ability of chemical components in different parts is different. In order to perform a quality assessment of W. cocos, we proposed a comprehensive method which was mainly realized by Fourier transform near-infrared (FT-NIR) spectroscopy and ultra-fast liquid chromatography (UFLC). A qualitative analysis means was built a residual convolutional neural network (ResNet) to recognize synchronous two-dimensional correlation spectroscopy (2DCOS) images. It can rapidly identify samples from wild and cultivated W. cocos in different parts. As a quantitative analysis method, UFLC was used to determine the contents of three triterpene acids in 547 samples. The results showed that a simultaneous qualitative and quantitative strategy could accurately evaluate the quality of W. cocos. The accuracy of ResNet models combined synchronous FT-NIR 2DCOS in identifying wild and cultivated W. cocos in different parts was as high as 100%. The contents of three triterpene acids in Poriae Cutis were higher than that in Poria, and the one with wild Poriae Cutis was the highest. In addition, the suitable habitat plays a crucial role in the quality of W. cocos. The maximum entropy (MaxEnt) model is a common method to predict the suitable habitat area for W. cocos under the current climate. Through the results, we found that suitable habitats were mostly situated in Yunnan Province of China, which accounted for approximately 49% of the total suitable habitat area of China. The research results not only pave the way for the rational planting in Yunnan Province of China and resource utilization of W. cocos, but also provide a basis for quality assessment of medicinal fungi.
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Affiliation(s)
- YanYing Zhang
- Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Tao Shen
- College of Chemistry, Biology and Environment, Yuxi Normal University, Yuxi, China
| | - ZhiTian Zuo
- Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - YuanZhong Wang
- Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, China
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Genome Resequencing and Transcriptome Analysis Reveal the Genetic Diversity of Wolfiporia cocos Germplasm and Genes Related to High Yield. Curr Microbiol 2022; 79:312. [DOI: 10.1007/s00284-022-03011-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 08/26/2022] [Indexed: 11/03/2022]
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Homokaryotic High-Quality Genome Assembly of Medicinal Fungi Wolfiporia hoelen Reveals Auto-Regulation and High-Temperature Adaption of Probable Two-Speed Genome. Int J Mol Sci 2022; 23:ijms231810484. [PMID: 36142397 PMCID: PMC9503964 DOI: 10.3390/ijms231810484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
Sclerotia of Wolfiporia hoelen are one of the most important traditional Chinese medicines and are commonly used in China, Japan, Korea, and other Asian countries. In the present study, we presented the first high-quality homokaryotic genome of W. hoelen with 14 chromosomes which was evaluated with assembly index, telomere position detection, and whole-genome collinearity. A 64.44 Mb genome was assembled with a Contig N50 length of 3.76 Mb. The imbalanced distribution of transposons and chromosome characters revealed the probable two-speed genome of W. hoelen. High consistency between methylation and transposon conserved the genome stability. The expansion of the gene family about signal transduction and nutritional transport has intimate relationships with sclerotial formation. Up-regulation of expression for distinctive decomposition enzymes, ROS clearance genes, biosynthesis of unsaturated fatty acids, and change of the cell wall components maintained high-speed growth of mycelia that may be the high-temperature adaption strategy of W. hoelen. Further, the analysis of mating-control genes demonstrated that HD3 probably had no function on mating recognition, with the HD protein in a distant genetic with known species. Overall, the high-quality genome of W. hoelen provided crucial information for genome structure and stability, high-temperature adaption, and sexual and asexual process.
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Xie Z, Zhong C, Liu X, Wang Z, Zhou R, Xie J, Zhang S, Jin J. Genome editing in the edible fungus Poria cocos using CRISPR-Cas9 system integrating genome-wide off-target prediction and detection. Front Microbiol 2022; 13:966231. [PMID: 36071963 PMCID: PMC9441760 DOI: 10.3389/fmicb.2022.966231] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 07/14/2022] [Indexed: 11/13/2022] Open
Abstract
Poria cocos is an important edible and medicinal fungus with a long history. However, the lack of adequate genetic tools has hindered molecular genetic research and the genetic modification of this species. In this study, the endogenous U6 promoters were identified by mining data from the P. cocos genome, and the promoter sequence was used to construct a sgRNA expression vector pFC332-PcU6. Then, the protoplast isolation protocol was developed, and the sgRNA-Cas9 vector was successfully transformed into the cells of P. cocos via PEG/CaCl2-mediated transformation approach. Off-target sites were genome-widely predicted and detected. As a result, the target marker gene ura3 was successfully disrupted by the CRISPR-Cas9 system. This is the first report of genome editing in P. cocos using CRISPR-Cas9 system integrating genome-wide off-target prediction and detection. These data will open up new avenues for the investigation of genetic breeding and commercial production of edible and medicinal fungus.
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Affiliation(s)
- Zhenni Xie
- Graduate School, Hunan University of Chinese Medicine, Changsha, China
| | - Can Zhong
- Institute of Chinese Materia Medica, Hunan Academy of Chinese Medicine, Changsha, China
| | - Xiaoliu Liu
- Graduate School, Hunan University of Chinese Medicine, Changsha, China
| | - Ziling Wang
- Graduate School, Hunan University of Chinese Medicine, Changsha, China
| | - Rongrong Zhou
- Institute of Chinese Materia Medica, Hunan Academy of Chinese Medicine, Changsha, China
| | - Jing Xie
- Institute of Chinese Materia Medica, Hunan Academy of Chinese Medicine, Changsha, China
| | - Shuihan Zhang
- Institute of Chinese Materia Medica, Hunan Academy of Chinese Medicine, Changsha, China
| | - Jian Jin
- Graduate School, Hunan University of Chinese Medicine, Changsha, China
- Institute of Chinese Materia Medica, Hunan Academy of Chinese Medicine, Changsha, China
- *Correspondence: Jian Jin,
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Papp V, Dai YC. What is the correct scientific name for “Fuling” medicinal mushroom? Mycology 2022; 13:207-211. [PMID: 35938080 PMCID: PMC9354628 DOI: 10.1080/21501203.2022.2089755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In recent years, the scientific names of many cultivated and well-known medicinal fungal species have been changed. However, the results of taxonomic and nomenclature works on these economically important fungi are often overlooked or ignored in applied researches. The incorrect use of scientific names may cause uncertainty in research and in the global medicinal mushroom market. In this paper, we briefly review the current taxonomy and nomenclature of “Fuling” medicinal mushroom and make a proposal for biochemists, pharmacists and businessmen on the correct use of scientific names related to this species. Based on the recent taxonomic results and nomenclatural proposals, the use of the names Wolfiporia extensa, W. cocos and especially Poria cocos for the “Fuling” mushroom are incorrect and misleading; therefore, the acceptance of the names Pachyma hoelen or Wolfiporia hoelen is recommended.
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Affiliation(s)
- Viktor Papp
- Department of Botany, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| | - Yu-Cheng Dai
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
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Duan Y, Han H, Qi J, Gao JM, Xu Z, Wang P, Zhang J, Liu C. Genome sequencing of Inonotus obliquus reveals insights into candidate genes involved in secondary metabolite biosynthesis. BMC Genomics 2022; 23:314. [PMID: 35443619 PMCID: PMC9020118 DOI: 10.1186/s12864-022-08511-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 03/27/2022] [Indexed: 11/10/2022] Open
Abstract
Background Inonotus obliquus is an important edible and medicinal mushroom that was shown to have many pharmacological activities in preclinical trials, including anti-inflammatory, antitumor, immunomodulatory, and antioxidant effects. However, the biosynthesis of these pharmacological components has rarely been reported. The lack of genomic information has hindered further molecular characterization of this mushroom. Results In this study, we report the genome of I. obliquus using a combined high-throughput Illumina NovaSeq with Oxford Nanopore PromethION sequencing platform. The de novo assembled 38.18 Mb I. obliquus genome was determined to harbor 12,525 predicted protein-coding genes, with 81.83% of them having detectable sequence similarities to others available in public databases. Phylogenetic analysis revealed the close evolutionary relationship of I. obliquus with Fomitiporia mediterranea and Sanghuangporus baumii in the Hymenochaetales clade. According to the distribution of reproduction-related genes, we predict that this mushroom possesses a tetrapolar heterothallic reproductive system. The I. obliquus genome was found to encode a repertoire of enzymes involved in carbohydrate metabolism, along with 135 cytochrome P450 proteins. The genome annotation revealed genes encoding key enzymes responsible for secondary metabolite biosynthesis, such as polysaccharides, polyketides, and terpenoids. Among them, we found four polyketide synthases and 20 sesquiterpenoid synthases belonging to four more types of cyclization mechanism, as well as 13 putative biosynthesis gene clusters involved in terpenoid synthesis in I. obliquus. Conclusions To the best of our knowledge, this is the first reported genome of I. obliquus; we discussed its genome characteristics and functional annotations in detail and predicted secondary metabolic biosynthesis-related genes, which provides genomic information for future studies on its associated molecular mechanism. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08511-x.
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Affiliation(s)
- Yingce Duan
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Haiyan Han
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Jianzhao Qi
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhichao Xu
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Pengchao Wang
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Jie Zhang
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Chengwei Liu
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, China.
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Improved Foods Using Enzymes from Basidiomycetes. Processes (Basel) 2022. [DOI: 10.3390/pr10040726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022] Open
Abstract
Within the kingdom of fungi, the division Basidiomycota represents more than 30,000 species, some with huge genomes indicating great metabolic potential. The fruiting bodies of many basidiomycetes are appreciated as food (“mushrooms”). Solid-state and submerged cultivation processes have been established for many species. Specifically, xylophilic fungi secrete numerous enzymes but also form smaller metabolites along unique pathways; both groups of compounds may be of interest to the food processing industry. To stimulate further research and not aim at comprehensiveness in the broad field, this review describes some recent progress in fermentation processes and the knowledge of fungal genetics. Processes with potential for food applications based on lipases, esterases, glycosidases, peptidases and oxidoreductases are presented. The formation and degradation of colourants, the degradation of harmful food components, the formation of food ingredients and particularly of volatile and non-volatile flavours serve as examples. In summary, edible basidiomycetes are foods—and catalysts—for food applications and rich donors of genes to construct heterologous cell factories for fermentation processes. Options arise to support the worldwide trend toward greener, more eco-friendly and sustainable processes.
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Kim B, Min B, Han JG, Park H, Baek S, Jeong S, Choi IG. Draft Genome Sequence of the Reference Strain of the Korean Medicinal Mushroom Wolfiporia cocos KMCC03342. MYCOBIOLOGY 2022; 50:254-257. [PMID: 36158046 PMCID: PMC9467534 DOI: 10.1080/12298093.2022.2109874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Wolfiporia cocos is a wood-decay brown rot fungus belonging to the family Polyporaceae. While the fungus grows, the sclerotium body of the strain, dubbed Bokryeong in Korean, is formed around the roots of conifer trees. The dried sclerotium has been widely used as a key component of many medicinal recipes in East Asia. Wolfiporia cocos strain KMCC03342 is the reference strain registered and maintained by the Korea Seed and Variety Service for commercial uses. Here, we present the first draft genome sequence of W. cocos KMCC03342 using a hybrid assembly technique combining both short- and long-read sequences. The genome has a total length of 55.5 Mb comprised of 343 contigs with N50 of 332 kb and 95.8% BUSCO completeness. The GC ratio was 52.2%. We predicted 14,296 protein-coding gene models based on ab initio gene prediction and evidence-based annotation procedure using RNAseq data. The annotated genome was predicted to have 19 terpene biosynthesis gene clusters, which was the same number as the previously sequenced W. cocos strain MD-104 genome but higher than Chinese W. cocos strains. The genome sequence and the predicted gene clusters allow us to study biosynthetic pathways for the active ingredients of W. cocos.
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Affiliation(s)
- Bogun Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Byoungnam Min
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Jae-Gu Han
- Mushroom Research Division, National Institute of Horticultural and Herbal Science, RDA, Eumseong, Chungbuk, Republic of Korea
| | - Hongjae Park
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Seungwoo Baek
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Subin Jeong
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - In-Geol Choi
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
- CONTACT In-Geol Choi
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Functional Analysis of Sterol O-Acyltransferase Involved in the Biosynthetic Pathway of Pachymic Acid in Wolfiporia cocos. MOLECULES (BASEL, SWITZERLAND) 2021; 27:molecules27010143. [PMID: 35011377 PMCID: PMC8746942 DOI: 10.3390/molecules27010143] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/18/2021] [Accepted: 12/24/2021] [Indexed: 11/19/2022]
Abstract
Pachymic acid from Wolfiporia cocos possesses important medicinal values including anti-bacterial, anti-inflammatory, anti-viral, invigorating, anti-rejection, anti-tumor, and antioxidant activities. However, little is known about the biosynthetic pathway from lanostane to pachymic acid. In particular, the associated genes in the biosynthetic pathway have not been characterized, which limits the high-efficiency obtaining and application of pachymic acid. To characterize the synthetic pathway and genes involved in pachymic acid synthesis, in this study, we identified 11 triterpenoids in W. cocos using liquid chromatography tandem mass spectrometry (LC-MS/MS), and inferred the putative biosynthetic pathway from lanostane to pachymic acid based on analyzing the chemical structure of triterpenoids and the transcriptome data. In addition, we identified a key gene in the biosynthetic pathway encoding W. cocos sterol O-acyltransferase (WcSOAT), which catalyzes tumolusic acid to pachymic acid. The results show that silence of WcSOAT gene in W. cocos strain led to reduction of pachymic acid production, whereas overexpression of this gene increased pachymic acid production, indicating that WcSOAT is involved in pachymic acid synthesis in W. cocos and the biosynthesis of W. cocos pachymic acid is closely dependent on the expression of WcSOAT gene. In summary, the biosynthetic pathway of pachymic acid and the associated genes complement our knowledge on the biosynthesis of W. cocos pachymic acid and other triterpenoids, and also provides a reference for target genes modification for exploring high-efficiency obtaining of active components.
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