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Im JH, Park CH, Shin JH, Oh YL, Oh M, Paek NC, Park YJ. Effects of Light on the Fruiting Body Color and Differentially Expressed Genes in Flammulina velutipes. J Fungi (Basel) 2024; 10:372. [PMID: 38921359 PMCID: PMC11204606 DOI: 10.3390/jof10060372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024] Open
Abstract
Light plays vital roles in fungal growth, development, reproduction, and pigmentation. In Flammulina velutipes, the color of the fruiting body exhibits distinct changes in response to light; however, the underlying molecular mechanisms remain unknown. Therefore, in this study, we aimed to analyze the F. velutipes transcriptome under red, green, and blue light-emitting diode (LED) lights to identify the key genes affecting the light response and fruiting body color in this fungus. Additionally, we conducted protein-protein interaction (PPI) network analysis of the previously reported fruiting body color-related gene, Fvpal1, to identify the hub genes. Phenotypic analysis revealed that fruiting bodies exposed to green and blue lights were darker than those untreated or exposed to red light, with the color intensifying more after 48 h of exposure to blue light compared to that after 24 h of exposure. Differentially expressed gene (DEG) analyses of all light treatments for 24 h revealed that the numbers of DEGs were 17, 74, and 257 under red, green, and blue lights, respectively. Subsequently, functional enrichment analysis was conducted of the DEGs identified under green and blue lights, which influenced the color of F. velutipes. In total, 103 of 168 downregulated DEGs under blue and green lights were included in the enrichment analysis. Among the DEGs enriched under both green and blue light treatments, four genes were related to monooxygenases, with three genes annotated as cytochrome P450s that are crucial for various metabolic processes in fungi. PPI network analysis of Fvpal1 revealed associations with 11 genes, among which the expression of one gene, pyridoxal-dependent decarboxylase, was upregulated in F. velutipes exposed to blue light. These findings contribute to our understanding of the molecular mechanisms involved in the fruiting body color changes in response to light and offer potential molecular markers for further exploration of light-mediated regulatory pathways.
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Affiliation(s)
- Ji-Hoon Im
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea;
- Mushroom Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong-gun 27709, Republic of Korea; (Y.-L.O.); (M.O.)
| | - Che-Hwon Park
- Department of Medicinal Biosciences, Research Institute for Biomedicinal & Health Science, College of Biomedicinal and Health Science, Konkuk University, Chungju 27478, Republic of Korea; (C.-H.P.); (J.-H.S.)
| | - Ju-Hyeon Shin
- Department of Medicinal Biosciences, Research Institute for Biomedicinal & Health Science, College of Biomedicinal and Health Science, Konkuk University, Chungju 27478, Republic of Korea; (C.-H.P.); (J.-H.S.)
| | - Youn-Lee Oh
- Mushroom Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong-gun 27709, Republic of Korea; (Y.-L.O.); (M.O.)
| | - Minji Oh
- Mushroom Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong-gun 27709, Republic of Korea; (Y.-L.O.); (M.O.)
| | - Nam-Chon Paek
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea;
| | - Young-Jin Park
- Department of Medicinal Biosciences, Research Institute for Biomedicinal & Health Science, College of Biomedicinal and Health Science, Konkuk University, Chungju 27478, Republic of Korea; (C.-H.P.); (J.-H.S.)
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Sun X, Liu D, Zhao X. Transcription factors: switches for regulating growth and development in macrofungi. Appl Microbiol Biotechnol 2023; 107:6179-6191. [PMID: 37624406 DOI: 10.1007/s00253-023-12726-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/31/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023]
Abstract
Macrofungi (or mushrooms) act as an extraordinarily important part to human health due to their nutritional and/or medicinal value, but the detailed researches in growth and development mechanisms have yet to be explored further. Transcription factors (TFs) play indispensable roles in signal transduction and affect growth, development, and metabolism of macrofungi. In recent years, increasing research effort has been employed to probe the relationship between the development of macrofungi and TFs. Herein, the present review comprehensively summarized the functional TFs researched in macrofungi, including modulating mycelial growth, fructification, sclerotial formation, sexual reproduction, spore formation, and secondary metabolism. Meanwhile, the possible effect mechanisms of TFs on the growth and development of some macrofungi were also revealed. Specific examples of functional characterizations of TFs in macrofungi (such as Schizophyllum commune and Coprinopsis cinerea) were described to a better comprehension of regulatory effect. Future research prospects in the field of TFs of macrofungi are discussed. We illustrated the functional versatility of the TFs in macrofungi based on specific examples. A systematical realization of the interaction and possible mechanisms between TFs and macrofungi can supply possible solutions to regulate genetic characteristics, which supply novel insights into the regulation of growth, development and metabolism of macrofungi. KEY POINTS: • The functional TFs researched in macrofungi were summarized. • The possible effect mechanisms of TFs in macrofungal were described. • The multiple physiological functions of TFs in macrofungi were discussed.
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Affiliation(s)
- Xueyan Sun
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemistry Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Dongmei Liu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Xihong Zhao
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemistry Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China.
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Raethong N, Thananusak R, Cheawchanlertfa P, Prabhakaran P, Rattanaporn K, Laoteng K, Koffas M, Vongsangnak W. Functional genomics and systems biology of Cordyceps species for biotechnological applications. Curr Opin Biotechnol 2023; 81:102939. [PMID: 37075529 DOI: 10.1016/j.copbio.2023.102939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 04/21/2023]
Abstract
The use of Cordyceps species for the manufacture of natural products has been established; however, the tremendous advances observed in recent years in genetic engineering and molecular biology have revolutionized the optimization of Cordyceps as cell factories and drastically expanded the biotechnological potential of these fungi. Here, we present a review of systems and synthetic biology studies of Cordyceps and their implications for fungal biology and industrial applications. We summarize the current status of synthetic biology for enhancing targeted metabolites in Cordyceps species, such as cordycepin, adenosine, polysaccharide, and pentostatin. Progress in the systems and synthetic biology of Cordyceps provides a strategy for comprehensively comprehensive controlling efficient cell factories of natural bioproducts and novel synthetic biology toolbox for targeted engineering.
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Affiliation(s)
- Nachon Raethong
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Institute of Nutrition, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Roypim Thananusak
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Pattsarun Cheawchanlertfa
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Pranesha Prabhakaran
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Kittipong Rattanaporn
- Fermentation Technology Research Center (FTRC), Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand
| | - Kobkul Laoteng
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology BIOTEC, National Science and Technology Development Agency NSTDA, Pathum Thani 12120, Thailand
| | - Mattheos Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand.
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Mechanism Underlying Light Intensity-Induced Melanin Synthesis of Auricularia heimuer Revealed by Transcriptome Analysis. Cells 2022; 12:cells12010056. [PMID: 36611851 PMCID: PMC9818193 DOI: 10.3390/cells12010056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Auricularia heimuer is a traditional edible and medicinal mushroom, which is widely used in biochemical research and is regarded as a good dietary supplement. The color of the ear-like fruiting body is an important indicator of its commercial quality. However, the mechanism by which light intensity influences the melanin synthesis of A. heimuer remains unclear. Here, we show that fruiting body color is significantly affected by light intensity. Transcriptional profiles of the fruiting bodies of A. heimuer grown in different light intensities were further analyzed. More differentially expressed genes (DEGs) were identified with a greater light intensity difference. A total of 1388 DEGs were identified from six comparisons, including 503 up-regulated genes and 885 down-regulated genes. The up-regulated genes were mainly associated with light sensing via photoreceptors, signal transduction via the mitogen-activated protein kinase (MAPK) signaling pathway, and melanin synthesis via the tyrosine metabolic pathway. Therefore, the genes involved in these processes may participate in regulating melanin synthesis under high light intensity. This insight into the transcriptional regulation of A. heimuer to light intensity should help to further comprehensively elucidate the underlying mechanism of light-induced melanin synthesis.
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Cmcrf1, a Putative Zn2Cys6 Fungal Transcription Factor, Is Involved in Conidiation, Carotenoid Production, and Fruiting Body Development in Cordyceps militaris. BIOLOGY 2022; 11:biology11101535. [PMID: 36290438 PMCID: PMC9598893 DOI: 10.3390/biology11101535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/03/2022] [Accepted: 10/16/2022] [Indexed: 11/06/2022]
Abstract
Cordyceps militaris is a high-value medicinal and edible fungus that produces many bioactive compounds, including carotenoid, and thus, improving the carotenoid productivity of C. militaris will increase its commercial value. However, little is known about the genetic regulatory mechanism of carotenoid biosynthesis in C. militaris. To further understanding the regulatory mechanism of carotenoid biosynthesis, we performed a large-scale screen of T-DNA insertional mutant library and identified a defective mutant, denoted T111, whose colonies did not change color from white to yellow upon exposure to light. Mutation analysis confirmed that a single T-DNA insertion occurred in the gene encoding a 695-amino-acid putative fungal-specific transcription factor with a predicted Zn2Cys6 binuclear cluster DNA-binding domain found uniquely in fungi. Targeted deletion of this gene, denoted C. militaris carotenogenesis regulatory factor 1 (Cmcrf1), generated the ΔCmcrf1 mutant that exhibited drastically reduced carotenoid biosynthesis and failed to generate fruiting bodies. In addition, the ΔCmcrf1 mutant showed significantly increased conidiation and increased hypersensitivity to cell-wall-perturbing agents compared with the wild-type strain. However, the Cmcrf1 gene did not have an impact on the mycelia growth of C. militaris. These results show that Cmcrf1 is involved in carotenoid biosynthesis and is required for conidiation and fruiting body formation in C. militaris.
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