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Song B, Wang W, Jia C, Han Z, Yang J, Yang J, Wu Z, Xu H, Qiao M. Identification and Characterization of a Predominant Hydrophobin in the Edible Mushroom Grifola frondosa. J Fungi (Basel) 2023; 10:25. [PMID: 38248935 PMCID: PMC10820438 DOI: 10.3390/jof10010025] [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: 11/25/2023] [Revised: 12/27/2023] [Accepted: 12/27/2023] [Indexed: 01/23/2024] Open
Abstract
Hydrophobins (HFBs) are a group of small, secreted amphipathic proteins of fungi with multiple physiological functions and potential commercial applications. In this study, HFB genes of the edible mushroom, Grifola frondosa, were systematically identified and characterized, and their transcriptional profiles during fungal development were determined. In total, 19 typical class I HFB genes were discovered and bioinformatically analyzed. Gene expression profile examination showed that Gf.hyd9954 was particularly highly upregulated during primordia formation, suggesting its major role as the predominant HFB in the lifecycle of G. frondosa. The wettability alteration profile and the surface modification ability of recombinant rGf.hyd9954 were greater than for the Grifola HFB HGFII-his. rGf.hyd9954 was also demonstrated to form the typical class I HFB characteristic-rodlet bundles. In addition, rGf.hyd9954 was shown to possess nanoparticle characteristics and emulsification activities. This research sheds light on the regulation of fungal development and its association with the expression of HFB genes.
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Affiliation(s)
- Bo Song
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300110, China; (B.S.)
| | - Wenjun Wang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300110, China; (B.S.)
| | - Chunhui Jia
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300110, China; (B.S.)
| | - Zhiqiang Han
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300110, China; (B.S.)
| | - Jiyuan Yang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300110, China; (B.S.)
| | - Jiuxia Yang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300110, China; (B.S.)
| | - Zhenzhou Wu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300110, China; (B.S.)
| | - Haijin Xu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300110, China; (B.S.)
| | - Mingqiang Qiao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300110, China; (B.S.)
- School of Life Science, Shanxi University, Taiyuan 030000, China
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Yan K, Guo L, Zhang B, Chang M, Meng J, Deng B, Liu J, Hou L. MAC Family Transcription Factors Enhance the Tolerance of Mycelia to Heat Stress and Promote the Primordial Formation Rate of Pleurotus ostreatus. J Fungi (Basel) 2023; 10:13. [PMID: 38248923 PMCID: PMC10816978 DOI: 10.3390/jof10010013] [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: 10/31/2023] [Revised: 12/05/2023] [Accepted: 12/10/2023] [Indexed: 01/23/2024] Open
Abstract
Pleurotus ostreatus is a typical tetrapolar heterologous edible mushroom, and its growth and development regulatory mechanism has become a research hotspot in recent years. The MAC1 protein is a transcription factor that perceives copper and can regulate the expression of multiple genes, thereby affecting the growth and development of organisms. However, its function in edible mushrooms is still unknown. In this study, two transcription factor genes, PoMCA1a and PoMAC1b, were identified. Afterwards, PoMAC1 overexpression (OE) and RNA interference (RNAi) strains were constructed to further explore gene function. The results showed that the PoMAC1 mutation had no significant effect on the growth rate of mycelia. Further research has shown that OE-PoMAC1a strains and RNAi-PoMAC1b strains exhibit strong tolerance under 32 °C heat stress. However, under 40 °C heat stress, the OE of PoMAC1a and PoMAC1b promoted the recovery of mycelial growth after heat stress. Second, the OE of PoMAC1a can promote the rapid formation of primordia and shorten the cultivation cycle. In summary, this study indicated that there are functional differences between PoMAC1a and PoMAC1b under different heat stresses during the vegetative growth stage, and PoMAC1a has a positive regulatory effect on the formation of primordia during the reproductive growth stage.
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Affiliation(s)
- Kexing Yan
- College of Food Science and Engineering, Shanxi Agricultural University, Jinzhong 030801, China; (K.Y.); (L.G.); (B.Z.); (M.C.); (J.M.); (B.D.)
| | - Lifeng Guo
- College of Food Science and Engineering, Shanxi Agricultural University, Jinzhong 030801, China; (K.Y.); (L.G.); (B.Z.); (M.C.); (J.M.); (B.D.)
| | - Benfeng Zhang
- College of Food Science and Engineering, Shanxi Agricultural University, Jinzhong 030801, China; (K.Y.); (L.G.); (B.Z.); (M.C.); (J.M.); (B.D.)
| | - Mingchang Chang
- College of Food Science and Engineering, Shanxi Agricultural University, Jinzhong 030801, China; (K.Y.); (L.G.); (B.Z.); (M.C.); (J.M.); (B.D.)
- Shanxi Research Center for Engineering Technology of Edible Fungi, Jinzhong 030801, China
| | - Junlong Meng
- College of Food Science and Engineering, Shanxi Agricultural University, Jinzhong 030801, China; (K.Y.); (L.G.); (B.Z.); (M.C.); (J.M.); (B.D.)
- Shanxi Research Center for Engineering Technology of Edible Fungi, Jinzhong 030801, China
| | - Bing Deng
- College of Food Science and Engineering, Shanxi Agricultural University, Jinzhong 030801, China; (K.Y.); (L.G.); (B.Z.); (M.C.); (J.M.); (B.D.)
- Shanxi Key Laboratory of Edible Fungi for Loess Plateau, Jinzhong 030801, China
| | - Jingyu Liu
- College of Food Science and Engineering, Shanxi Agricultural University, Jinzhong 030801, China; (K.Y.); (L.G.); (B.Z.); (M.C.); (J.M.); (B.D.)
- Shanxi Key Laboratory of Edible Fungi for Loess Plateau, Jinzhong 030801, China
| | - Ludan Hou
- College of Food Science and Engineering, Shanxi Agricultural University, Jinzhong 030801, China; (K.Y.); (L.G.); (B.Z.); (M.C.); (J.M.); (B.D.)
- Shanxi Key Laboratory of Edible Fungi for Loess Plateau, Jinzhong 030801, China
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3
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Ke S, Ding L, Niu X, Shan H, Song L, Xi Y, Feng J, Wei S, Liang Q. Comparative transcriptome analysis on candidate genes associated with fruiting body growth and development in Lyophyllum decastes. PeerJ 2023; 11:e16288. [PMID: 37904843 PMCID: PMC10613438 DOI: 10.7717/peerj.16288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/22/2023] [Indexed: 11/01/2023] Open
Abstract
Lyophyllum decastes is a mushroom that is highly regarded for its culinary and medicinal properties. Its delectable taste and texture make it a popular choice for consumption. To gain a deeper understanding of the molecular mechanisms involved in the development of the fruiting body of L. decastes, we used RNA sequencing to conduct a comparative transcriptome analysis. The analysis encompassed various developmental stages, including the vegetative mycelium, primordial initiation, young fruiting body, medium-size fruiting body, and mature fruiting body stages. A range of 40.1 to 60.6 million clean reads were obtained, and de novo assembly generated 15,451 unigenes with an average length of 1,462.68 bp. Functional annotation of transcriptomes matched 76.84% of the unigenes to known proteins available in at least one database. The gene expression analysis revealed a significant number of differentially expressed genes (DEGs) between each stage. These genes were annotated and subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. Highly differentially expressed unigenes were also identified, including those that encode extracellular enzymes, transcription factors, and signaling pathways. The accuracy of the RNA-Seq and DEG analyses was validated using quantitative PCR. Enzyme activity analysis experiments demonstrated that the extracellular enzymes exhibited significant differences across different developmental stages. This study provides valuable insights into the molecular mechanisms that underlie the development of the fruiting body in L. decastes.
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Affiliation(s)
- Shanwen Ke
- Gansu Engineering Laboratory of Applied Mycology, Hexi University, Zhangye, Gansu, China
- Gansu Key Laboratory of Genetics and Breeding of Edible Fungi, Hexi University, Zhangye, Gansu, China
| | - LingQiang Ding
- Gansu Engineering Laboratory of Applied Mycology, Hexi University, Zhangye, Gansu, China
- Gansu Key Laboratory of Genetics and Breeding of Edible Fungi, Hexi University, Zhangye, Gansu, China
| | - Xin Niu
- Gansu Engineering Laboratory of Applied Mycology, Hexi University, Zhangye, Gansu, China
- Gansu Key Laboratory of Genetics and Breeding of Edible Fungi, Hexi University, Zhangye, Gansu, China
| | - Huajia Shan
- Gansu Engineering Laboratory of Applied Mycology, Hexi University, Zhangye, Gansu, China
- Gansu Key Laboratory of Genetics and Breeding of Edible Fungi, Hexi University, Zhangye, Gansu, China
| | - Liru Song
- Gansu Engineering Laboratory of Applied Mycology, Hexi University, Zhangye, Gansu, China
- Gansu Key Laboratory of Genetics and Breeding of Edible Fungi, Hexi University, Zhangye, Gansu, China
| | - Yali Xi
- Gansu Engineering Laboratory of Applied Mycology, Hexi University, Zhangye, Gansu, China
- Gansu Key Laboratory of Genetics and Breeding of Edible Fungi, Hexi University, Zhangye, Gansu, China
| | - Jiuhai Feng
- Gansu Engineering Laboratory of Applied Mycology, Hexi University, Zhangye, Gansu, China
- Gansu Key Laboratory of Genetics and Breeding of Edible Fungi, Hexi University, Zhangye, Gansu, China
| | - Shenglong Wei
- Gansu Engineering Laboratory of Applied Mycology, Hexi University, Zhangye, Gansu, China
- Gansu Key Laboratory of Genetics and Breeding of Edible Fungi, Hexi University, Zhangye, Gansu, China
| | - Qianqian Liang
- Gansu Engineering Laboratory of Applied Mycology, Hexi University, Zhangye, Gansu, China
- Gansu Key Laboratory of Genetics and Breeding of Edible Fungi, Hexi University, Zhangye, Gansu, China
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4
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Yu H, Jiang N, Yan M, Cheng X, Zhang L, Zhai D, Liu J, Zhang M, Song C, Yu H, Li Q. Comparative analysis of proteomes and transcriptomes revealed the molecular mechanism of development and nutrition of Pleurotus giganteus at different fruiting body development stages. Front Nutr 2023; 10:1197983. [PMID: 37545588 PMCID: PMC10402744 DOI: 10.3389/fnut.2023.1197983] [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: 03/31/2023] [Accepted: 06/23/2023] [Indexed: 08/08/2023] Open
Abstract
Pleurotus giganteus is a commercially cultivated high-temperature mushroom. Investigating the molecular mechanism of fruiting body development will help us to better understand the regulation of substrates and energy in this process. However, little information has been reported on the development and nutrients of the P. giganteus fruiting body. In the present study, P. giganteus is cultivated in a climate chamber, and comparative transcriptome, proteome, and nutritional analysis of P. giganteus fruiting bodies were performed. Our results revealed that Cytochrome P450 monooxygenases and hydrophobin proteins play important roles during the differentiation in the elongation stage. Later, carbon metabolism dominate the fruiting body metabolism and genes related to the carbohydrate metabolic process, glycolytic process, and gluconeogenesis were up-regulated in the mature fruiting bodies. The up-regulation of carbohydrate substrates utilization CAZymes genes and inconsistent protein expression in pileus indicated a reverse transportation of mRNA from the fruiting body to vegetative mycelia. In addition, protein concentration in the pileus is higher than that in the stem, while the stem is the major nitrogen metabolic and amino acid synthetic location. The integrated transcriptomic, proteomic, and nutritional analysis indicated a two-way transportation of substrates and mRNAs in P. giganteus. Stem synthesizes amino acids and transported them to pileus with reducing sugars, while pileus induces the expression of substrate degradation mRNA according to the needs of growth and development and transports them in the other direction.
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Affiliation(s)
- Hailong Yu
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Ning Jiang
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Miaomiao Yan
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, Jilin, China
| | - Xuan Cheng
- Agricultural Specialty Industry Development Center, Qujiang, Zhejiang, China
| | - Lujun Zhang
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Dandan Zhai
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, Jilin, China
| | - Jianyu Liu
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Meiyan Zhang
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Chunyan Song
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Hao Yu
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Qiaozhen Li
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
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5
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Xu L, Liu H, Zhu S, Meng Y, Wang Y, Li J, Zhang F, Huang L. VmPacC-mediated pH regulation of Valsa mali confers to host acidification identified by comparative proteomics analysis. STRESS BIOLOGY 2023; 3:18. [PMID: 37676527 PMCID: PMC10441875 DOI: 10.1007/s44154-023-00097-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 05/24/2023] [Indexed: 09/06/2023]
Abstract
Apple valsa canker caused by the Ascomycete fungus Valsa mali is one of the most serious diseases of apple, resulting in huge economic losses in the apple-growing area of China. Previous study found that the pathogen could acidify the infected tissues to make lower ambient pH (from 6.0 to 3.5) for their successfully colonization. The pH signaling transcription factor VmPacC is required for acidification of its environment and for full virulence in V. mali. It is known that the functional cooperation of proteins secreted by V. mali plays pivotal role in its successful colonization of host plants. In this study, we used tandem mass tag (TMT) labeling coupled with LC-MS/MS-based quantitative proteomics to analyze the VmPacC-mediated pH regulation in V. mali, focusing on differentially expressed proteins (DEPs). We identified 222 DEPs specific to VmPacC deletion, and 921 DEPs specific to different pH conditions (pH 6.0 and 3.4). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that these DEPs were mainly involved in pathways associated with carbon metabolism, biosynthesis of antibiotics, citrate cycle (TCA cycle), glycolysis/gluconeogenesis, glutathione metabolism, ribosomes, and pentose phosphate pathways. Additionally, we identified 119 DEPs that were shared among the VmPacC deletion mutant and different pH conditions, which were mainly related to energy metabolism pathways, providing the energy required for the hyphal growth and responses to environmental stresses. A protein-protein interaction (PPI) network analysis indicated that most of the shared proteins were mapped to an interaction network with a medium confidence score of 0.4. Notably, one uncharacterized protein (KUI69106.1), and two known proteins (heat shock protein 60 (KUI73579.1), aspartate aminotransferase (KUI73864.1)) located in the core of the network were highly connected (with ≥ 38 directed edges) with the other shared DEPs. Our results suggest that VmPacC participates in the pathogen's regulation to ambient pH through the regulation of energy metabolism pathways such as the glycolysis/gluconeogenesis pathway and TCA cycle. Finally, we proposed a sophisticated molecular regulatory network to explain pH decrease in V. mali. Our study, by providing insights into V. mali regulating pH, helps to elucidate the mechanisms of host acidification during pathogen infection.
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Affiliation(s)
- Liangsheng Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Hailong Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shan Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yangguang Meng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yinghao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jianyu Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Feiran Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Shu L, Wang M, Xu H, Qiu Z, Li T. De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia. Sci Rep 2022; 12:11075. [PMID: 35773379 PMCID: PMC9247108 DOI: 10.1038/s41598-022-15382-5] [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] [Received: 04/04/2022] [Accepted: 06/23/2022] [Indexed: 11/11/2022] Open
Abstract
The genes associated with fruiting body formation of Sparasis latifolia are valuable for improving mushroom breeding. To investigate this process, 4.8 × 108 RNA-Seq reads were acquired from three stages: hyphal knot (SM), primordium (SP), and primordium differentiation (SPD). The de novo assembly generated a total of 48,549 unigenes, of which 71.53% (34,728) unigenes could be annotated by at least one of the KEGG (Kyoto Encyclopedia of Genes and Genomes), GO (Gene Ontology), and KOG (Eukaryotic Orthologous Group) databases. KEGG and KOG analyses respectively mapped 32,765 unigenes to 202 pathways and 19,408 unigenes to 25 categories. KEGG pathway enrichment analysis of DEGs (differentially expressed genes) indicated primordium initiation was significantly related to 66 pathways, such as “Ribosome”, “metabolism of xenobiotics by cytochrome P450”, and “glutathione metabolism” (among others). The MAPK and mTOR signal transduction pathways underwent significant adjustments during the SM to SP transition. Further, our research revealed the PI3K-Akt signaling pathway related to cell proliferation could play crucial functions during the development of SP and SPD. These findings provide crucial candidate genes and pathways related to primordium differentiation and development in S. latifolia, and advances our knowledge about mushroom morphogenesis.
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Affiliation(s)
- Lili Shu
- School of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Miaoyue Wang
- School of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Hui Xu
- School of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhiheng Qiu
- School of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Tianlai Li
- School of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China.
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Cultivating Lentinula edodes on Substrate Containing Composted Sawdust Affects the Expression of Carbohydrate and Aromatic Amino Acid Metabolism-Related Genes. mSystems 2022; 7:e0082721. [PMID: 35191774 PMCID: PMC8862593 DOI: 10.1128/msystems.00827-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In mushroom cultivation, composting the substrate can make the nutrients more easily absorbed by hyphae due to the degradation of lignin, cellulose, and other organic matter. However, the effects of cultivating Lentinula edodes on composted substrate and the related molecular mechanisms have not been studied systemically. We applied transcriptomics, qRT-PCR, and proteomics to study L. edodes cultivated on substrates with fresh (CK) and composted (ND) sawdust, focusing on the brown film formation stage. The time of brown film formation was shorter and the mycelium growth rate and crude polysaccharide content of the brown film were higher in ND than in CK. The faster growth rate in ND may have been due to the higher nitrogen content in ND than in CK. Among the 9,455 genes annotated using transcriptomics, 96 were upregulated and 139 downregulated in ND compared with CK. Among the 2,509 proteins identified using proteomics sequencing, 74 were upregulated and 113 downregulated. In the KEGG pathway analyses, both differentially expressed genes and proteins were detected in cyanoamino acid metabolism, inositol phosphate metabolism, pentose and glucuronate interconversions, phosphatidylinositol signaling system, RNA polymerase, starch and sucrose metabolism, and tyrosine metabolism pathways. A large number of differentially expressed genes (DEGs) related to aromatic amino acid metabolic and biosynthetic process were upregulated in ND. Most of the DEGs annotated to carbohydrate active enzymes were downregulated in L. edodes growing on composted sawdust containing substrate, possibly due to the lower hemicellulose and cellulose contents in the composted sawdust. The results suggested that using composted substrate may decrease the cultivation time and improve the quality of L. edodes and revealed the underlying molecular mechanisms. IMPORTANCE Composted substrates are not commonly used in the cultivation of Lentinula edodes, thus the effects of cultivating L. edodes on composted substrate and the related molecular mechanisms have not been studied systemically. We studied L. edodes cultivated on substrates with fresh (CK) and composted (ND) sawdust, focusing on the brown film formation stage, and determined the composting related differences in the substrate and in the growth and gene expression of L. edodes. Cultivation on composted substrate was beneficial and showed potential for decreasing the cultivation time and improving the quality of L. edodes. Analyzing the expression levels of genes and proteins in brown film revealed gene and metabolism pathway level changes that accompanied the cultivation on composted substrate.
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8
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Wang W, Wang Y, Gong Z, Yang S, Jia F. Comparison of the Nutritional Properties and Transcriptome Profiling Between the Two Different Harvesting Periods of Auricularia polytricha. Front Nutr 2021; 8:771757. [PMID: 34765633 PMCID: PMC8576271 DOI: 10.3389/fnut.2021.771757] [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: 09/07/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
Auricularia polytricha (A. polytricha), regarded as an edible and medical mushroom, has attracted toward the research interests because of the high nutrition and bioactivity. The nutritional and medical properties of A. polytricha have been well-studied; however, research about the difference of the nutritional properties and transcriptome profiling between the two different harvesting periods of A. polytricha was limited. In this study, the nutritional properties and transcriptome profiling were compared between the two different harvesting periods of A. polytricha: AP_S1 (the stage for the first harvesting period) and AP_S2 (the stage for the third harvesting period). This study showed that AP_S1 had the more growth advantages than AP_S2 including biomass, auricle area and thickness, protein and calcium contents, and most species of the amino acid contents, which contributed to the higher sensory evaluation and acceptability of AP_S1. Transcriptome profiling showed that a total of 30,298 unigenes were successfully annotated in the two different harvesting periods of A. polytricha. At a threshold of two-fold change, 1,415 and 3,213 unigenes were up- and downregulated, respectively. All the differentially expressed genes (DEGs) analysis showed that the some synthesis and metabolic processes were strengthened in AP_S1, especially the synthesis and metabolism of the amino acids and protein. The enhanced energy metabolism pathways could provide more energy for AP_S1 to synthesize the nutritional substance. Moreover, the expressions of 10 selected DEGs involved in the amino acid and protein synthesis pathways and energy metabolism pathways were higher in AP_S1 compared to AP_S2, consistent with Illumina analysis. To the best of our knowledge, this is the first study that compares the nutritional properties and transcriptome profiling between the two different harvesting periods of A. polytricha and the results can present insights into the growth and genetic characteristics of A. polytricha.
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Affiliation(s)
- Wenliang Wang
- Shandong Academy of Agricultural Science, Jinan, China.,Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan, China.,Key Laboratory of Agro-Products Processing Technology of Shandong Province, Jinan, China.,Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Yansheng Wang
- Shandong Academy of Agricultural Science, Jinan, China.,Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan, China.,Key Laboratory of Agro-Products Processing Technology of Shandong Province, Jinan, China.,Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Zhiqing Gong
- Shandong Academy of Agricultural Science, Jinan, China.,Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan, China.,Key Laboratory of Agro-Products Processing Technology of Shandong Province, Jinan, China.,Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Shifa Yang
- Shandong Academy of Agricultural Science, Jinan, China
| | - Fengjuan Jia
- Shandong Academy of Agricultural Science, Jinan, China.,Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan, China.,Key Laboratory of Agro-Products Processing Technology of Shandong Province, Jinan, China.,Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs, Jinan, China
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9
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Wan JN, Li Y, Guo T, Ji GY, Luo SZ, Ji KP, Cao Y, Tan Q, Bao DP, Yang RH. Whole-Genome and Transcriptome Sequencing of Phlebopus portentosus Reveals Its Associated Ectomycorrhizal Niche and Conserved Pathways Involved in Fruiting Body Development. Front Microbiol 2021; 12:732458. [PMID: 34659161 PMCID: PMC8511702 DOI: 10.3389/fmicb.2021.732458] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/03/2021] [Indexed: 02/03/2023] Open
Abstract
Phlebopus portentosus (Berk. and Broome) Boedijin, a widely consumed mushroom in China and Thailand, is the first species in the order Boletaceae to have been industrially cultivated on a large scale. However, to date, the lignocellulose degradation system and molecular basis of fruiting body development in P. portentosus have remained cryptic. In the present study, genome and transcriptome sequencing of P. portentosus was performed during the mycelium (S), primordium (P), and fruiting body (F) stages. A genome of 32.74 Mb with a 48.92% GC content across 62 scaffolds was obtained. A total of 9,464 putative genes were predicted from the genome, of which the number of genes related to plant cell wall-degrading enzymes was much lower than that of some saprophytic mushrooms with specific ectomycorrhizal niches. Principal component analysis of RNA-Seq data revealed that the gene expression profiles at all three stages were different. The low expression of plant cell wall-degrading genes also confirmed the limited ability to degrade lignocellulose. The expression profiles also revealed that some conserved and specific pathways were enriched in the different developmental stages of P. portentosus. Starch and sucrose metabolic pathways were enriched in the mycelium stage, while DNA replication, the proteasome and MAPK signaling pathways may be associated with maturation. These results provide a new perspective for understanding the key pathways and hub genes involved in P. portentosus development.
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Affiliation(s)
- Jia-Ning Wan
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yan Li
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ting Guo
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Guang-Yan Ji
- Hongzhen Agricultural Science and Technology Co. Ltd., Jinghong, China
| | - Shun-Zhen Luo
- Hongzhen Agricultural Science and Technology Co. Ltd., Jinghong, China
| | - Kai-Ping Ji
- Hongzhen Agricultural Science and Technology Co. Ltd., Jinghong, China
| | - Yang Cao
- Hongzhen Agricultural Science and Technology Co. Ltd., Jinghong, China
| | - Qi Tan
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Da-Peng Bao
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Rui-Heng Yang
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
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10
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Krah F, Hess J, Hennicke F, Kar R, Bässler C. Transcriptional response of mushrooms to artificial sun exposure. Ecol Evol 2021; 11:10538-10546. [PMID: 34367595 PMCID: PMC8328440 DOI: 10.1002/ece3.7862] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 05/18/2021] [Accepted: 06/17/2021] [Indexed: 01/08/2023] Open
Abstract
Climate change causes increased tree mortality leading to canopy loss and thus sun-exposed forest floors. Sun exposure creates extreme temperatures and radiation, with potentially more drastic effects on forest organisms than the current increase in mean temperature. Such conditions might potentially negatively affect the maturation of mushrooms of forest fungi. A failure of reaching maturation would mean no sexual spore release and, thus, entail a loss of genetic diversity. However, we currently have a limited understanding of the quality and quantity of mushroom-specific molecular responses caused by sun exposure. Thus, to understand the short-term responses toward enhanced sun exposure, we exposed mushrooms of the wood-inhabiting forest species Lentinula edodes, while still attached to their mycelium and substrate, to artificial solar light (ca. 30°C and 100,000 lux) for 5, 30, and 60 min. We found significant differentially expressed genes at 30 and 60 min. Eukaryotic Orthologous Groups (KOG) class enrichment pointed to defense mechanisms. The 20 most significant differentially expressed genes showed the expression of heat-shock proteins, an important family of proteins under heat stress. Although preliminary, our results suggest mushroom-specific molecular responses to tolerate enhanced sun exposure as expected under climate change. Whether mushroom-specific molecular responses are able to maintain fungal fitness under opening forest canopies remains to be tested.
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Affiliation(s)
- Franz‐Sebastian Krah
- Conservation BiologyInstitute for Ecology, Evolution and DiversityFaculty of Biological SciencesGoethe University FrankfurtFrankfurt am MainGermany
| | - Jaqueline Hess
- Department of Soil EcologyUFZ Helmholtz Centre for Environmental ResearchHalle (Saale)Germany
| | - Florian Hennicke
- Conservation BiologyInstitute for Ecology, Evolution and DiversityFaculty of Biological SciencesGoethe University FrankfurtFrankfurt am MainGermany
- Project Group Genetics and Genomics of FungiChair Evolution of Plants and FungiRuhr‐University Bochum (RUB)BochumGermany
| | - Ritwika Kar
- Centre for Plant Molecular Biology, Developmental GeneticsUniversity of TübingenTübingenGermany
| | - Claus Bässler
- Conservation BiologyInstitute for Ecology, Evolution and DiversityFaculty of Biological SciencesGoethe University FrankfurtFrankfurt am MainGermany
- Bavarian Forest National ParkGrafenauGermany
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11
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Lü BB, Wu GG, Sun Y, Zhang LS, Wu X, Jiang W, Li P, Huang YN, Wang JB, Zhao YC, Liu H, Song LL, Mo Q, Pan AH, Yang Y, Long XQ, Cui WD, Zhang C, Wang X, Tang XM. Comparative Transcriptome and Endophytic Bacterial Community Analysis of Morchella conica SH. Front Microbiol 2021; 12:682356. [PMID: 34354681 PMCID: PMC8329594 DOI: 10.3389/fmicb.2021.682356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/10/2021] [Indexed: 12/13/2022] Open
Abstract
The precious rare edible fungus Morchella conica is popular worldwide for its rich nutrition, savory flavor, and varieties of bioactive components. Due to its high commercial, nutritional, and medicinal value, it has always been a hot spot. However, the molecular mechanism and endophytic bacterial communities in M. conica were poorly understood. In this study, we sequenced, assembled, and analyzed the genome of M. conica SH. Transcriptome analysis reveals significant differences between the mycelia and fruiting body. As shown in this study, 1,329 and 2,796 genes were specifically expressed in the mycelia and fruiting body, respectively. The Gene Ontology (GO) enrichment showed that RNA polymerase II transcription activity-related genes were enriched in the mycelium-specific gene cluster, and nucleotide binding-related genes were enriched in the fruiting body-specific gene cluster. Further analysis of differentially expressed genes in different development stages resulted in finding two groups with distinct expression patterns. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment displays that glycan degradation and ABC transporters were enriched in the group 1 with low expressed level in the mycelia, while taurine and hypotaurine metabolismand tyrosine metabolism-related genes were significantly enriched in the group 2 with high expressed level in mycelia. Moreover, a dynamic shift of bacterial communities in the developing fruiting body was detected by 16S rRNA sequencing, and co-expression analysis suggested that bacterial communities might play an important role in regulating gene expression. Taken together, our study provided a better understanding of the molecular biology of M. conica SH and direction for future research on artificial cultivation.
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Affiliation(s)
- Bei B Lü
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Guo G Wu
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yu Sun
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Liang S Zhang
- Institute of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiao Wu
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Wei Jiang
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Peng Li
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yan N Huang
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jin B Wang
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yong C Zhao
- Institute of Edible Fungi, Yunnan Academy of Agricultural Sciences, Yunnan, China
| | - Hua Liu
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Li L Song
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Qin Mo
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ai H Pan
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yan Yang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Xuan Q Long
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Ürümqi, China
| | - Wei D Cui
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Ürümqi, China
| | - Chao Zhang
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xu Wang
- Department of Pathobiology, Auburn University, Auburn, AL, United States.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Xue M Tang
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
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12
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Al-Obaidi JR, Jambari NN, Ahmad-Kamil EI. Mycopharmaceuticals and Nutraceuticals: Promising Agents to Improve Human Well-Being and Life Quality. J Fungi (Basel) 2021; 7:jof7070503. [PMID: 34202552 PMCID: PMC8304235 DOI: 10.3390/jof7070503] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 01/19/2023] Open
Abstract
Fungi, especially edible mushrooms, are considered as high-quality food with nutritive and functional values. They are of considerable interest and have been used in the synthesis of nutraceutical supplements due to their medicinal properties and economic significance. Specific fungal groups, including predominantly filamentous endophytic fungi from Ascomycete phylum and several Basidiomycetes, produce secondary metabolites (SMs) with bioactive properties that are involved in the antimicrobial and antioxidant activities. These beneficial fungi, while high in protein and important fat contents, are also a great source of several minerals and vitamins, in particular B vitamins that play important roles in carbohydrate and fat metabolism and the maintenance of the nervous system. This review article will summarize and discuss the abilities of fungi to produce antioxidant, anticancer, antiobesity, and antidiabetic molecules while also reviewing the evidence from the last decade on the importance of research in fungi related products with direct and indirect impact on human health.
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Affiliation(s)
- Jameel R. Al-Obaidi
- Department of Biology, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, Tanjong Malim 35900, Perak, Malaysia
- Correspondence: (J.R.A.-O.); (N.N.J.)
| | - Nuzul Noorahya Jambari
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Correspondence: (J.R.A.-O.); (N.N.J.)
| | - E. I. Ahmad-Kamil
- Malaysian Nature Society (MNS), JKR 641, Jalan Kelantan, Bukit Persekutuan, Kuala Lumpur 50480, Malaysia;
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13
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Orban A, Weber A, Herzog R, Hennicke F, Rühl M. Transcriptome of different fruiting stages in the cultivated mushroom Cyclocybe aegerita suggests a complex regulation of fruiting and reveals enzymes putatively involved in fungal oxylipin biosynthesis. BMC Genomics 2021; 22:324. [PMID: 33947322 PMCID: PMC8097960 DOI: 10.1186/s12864-021-07648-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/19/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Cyclocybe aegerita (syn. Agrocybe aegerita) is a commercially cultivated mushroom. Its archetypal agaric morphology and its ability to undergo its whole life cycle under laboratory conditions makes this fungus a well-suited model for studying fruiting body (basidiome, basidiocarp) development. To elucidate the so far barely understood biosynthesis of fungal volatiles, alterations in the transcriptome during different developmental stages of C. aegerita were analyzed and combined with changes in the volatile profile during its different fruiting stages. RESULTS A transcriptomic study at seven points in time during fruiting body development of C. aegerita with seven mycelial and five fruiting body stages was conducted. Differential gene expression was observed for genes involved in fungal fruiting body formation showing interesting transcriptional patterns and correlations of these fruiting-related genes with the developmental stages. Combining transcriptome and volatilome data, enzymes putatively involved in the biosynthesis of C8 oxylipins in C. aegerita including lipoxygenases (LOXs), dioxygenases (DOXs), hydroperoxide lyases (HPLs), alcohol dehydrogenases (ADHs) and ene-reductases could be identified. Furthermore, we were able to localize the mycelium as the main source for sesquiterpenes predominant during sporulation in the headspace of C. aegerita cultures. In contrast, changes in the C8 profile detected in late stages of development are probably due to the activity of enzymes located in the fruiting bodies. CONCLUSIONS In this study, the combination of volatilome and transcriptome data of C. aegerita revealed interesting candidates both for functional genetics-based analysis of fruiting-related genes and for prospective enzyme characterization studies to further elucidate the so far barely understood biosynthesis of fungal C8 oxylipins.
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Affiliation(s)
- Axel Orban
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, 35392, Giessen, Hesse, Germany
| | - Annsophie Weber
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, 35392, Giessen, Hesse, Germany
| | - Robert Herzog
- International Institute Zittau, Technical University Dresden, 02763, Zittau, Saxony, Germany
| | - Florian Hennicke
- Project Group Genetics and Genomics of Fungi, Ruhr-University Bochum, Chair Evolution of Plants and Fungi, 44780, Bochum, North Rhine-Westphalia, Germany.
| | - Martin Rühl
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, 35392, Giessen, Hesse, Germany. .,Fraunhofer Institute for Molecular Biology and Applied Ecology IME Branch for Bioresources, 35392, Giessen, Hesse, Germany.
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14
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Ragucci S, Landi N, Russo R, Valletta M, Pedone PV, Chambery A, Di Maro A. Ageritin from Pioppino Mushroom: The Prototype of Ribotoxin-Like Proteins, a Novel Family of Specific Ribonucleases in Edible Mushrooms. Toxins (Basel) 2021; 13:263. [PMID: 33917246 PMCID: PMC8068006 DOI: 10.3390/toxins13040263] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/31/2021] [Accepted: 04/05/2021] [Indexed: 12/15/2022] Open
Abstract
Ageritin is a specific ribonuclease, extracted from the edible mushroom Cyclocybe aegerita (synonym Agrocybe aegerita), which cleaves a single phosphodiester bond located within the universally conserved alpha-sarcin loop (SRL) of 23-28S rRNAs. This cleavage leads to the inhibition of protein biosynthesis, followed by cellular death through apoptosis. The structural and enzymatic properties show that Ageritin is the prototype of a novel specific ribonucleases family named 'ribotoxin-like proteins', recently found in fruiting bodies of other edible basidiomycetes mushrooms (e.g., Ostreatin from Pleurotus ostreatus, Edulitins from Boletus edulis, and Gambositin from Calocybe gambosa). Although the putative role of this toxin, present in high amount in fruiting body (>2.5 mg per 100 g) of C. aegerita, is unknown, its antifungal and insecticidal actions strongly support a role in defense mechanisms. Thus, in this review, we focus on structural, biological, antipathogenic, and enzymatic characteristics of this ribotoxin-like protein. We also highlight its biological relevance and potential biotechnological applications in agriculture as a bio-pesticide and in biomedicine as a therapeutic and diagnostic agent.
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Affiliation(s)
| | | | | | | | | | | | - Antimo Di Maro
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, 81100-Caserta, Italy; (S.R.); (N.L.); (R.R.); (M.V.); (P.V.P.); (A.C.)
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15
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Duan M, Bao H, Bau T. Analyses of transcriptomes and the first complete genome of Leucocalocybe mongolica provide new insights into phylogenetic relationships and conservation. Sci Rep 2021; 11:2930. [PMID: 33536487 PMCID: PMC7858605 DOI: 10.1038/s41598-021-81784-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 01/12/2021] [Indexed: 01/30/2023] Open
Abstract
In this study, we report a de novo assembly of the first high-quality genome for a wild mushroom species Leucocalocybe mongolica (LM). We performed high-throughput transcriptome sequencing to analyze the genetic basis for the life history of LM. Our results show that the genome size of LM is 46.0 Mb, including 26 contigs with a contig N50 size of 3.6 Mb. In total, we predicted 11,599 protein-coding genes, of which 65.7% (7630) could be aligned with high confidence to annotated homologous genes in other species. We performed phylogenetic analyses using genes form 3269 single-copy gene families and showed support for distinguishing LM from the genus Tricholoma (L.) P.Kumm., in which it is sometimes circumscribed. We believe that one reason for limited wild occurrences of LM may be the loss of key metabolic genes, especially carbohydrate-active enzymes (CAZymes), based on comparisons with other closely related species. The results of our transcriptome analyses between vegetative (mycelia) and reproductive (fruiting bodies) organs indicated that changes in gene expression among some key CAZyme genes may help to determine the switch from asexual to sexual reproduction. Taken together, our genomic and transcriptome data for LM comprise a valuable resource for both understanding the evolutionary and life history of this species.
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Affiliation(s)
- Mingzheng Duan
- grid.464353.30000 0000 9888 756XKey Laboratory of Edible Fungi Resources and Utilization (North), Ministry of Agriculture and Rural Affairs, Jilin Agricultural University, Changchun, 130118 Jilin China
| | - Haiying Bao
- grid.464353.30000 0000 9888 756XKey Laboratory of Edible Fungi Resources and Utilization (North), Ministry of Agriculture and Rural Affairs, Jilin Agricultural University, Changchun, 130118 Jilin China
| | - Tolgor Bau
- grid.464353.30000 0000 9888 756XKey Laboratory of Edible Fungi Resources and Utilization (North), Ministry of Agriculture and Rural Affairs, Jilin Agricultural University, Changchun, 130118 Jilin China
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16
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Li J, Li Z, Zhao T, Yan X, Pang Q. Proteomic Analysis of Auricularia auricula-judae Under Freezing Treatment Revealed Proteins and Pathways Associated With Melanin Reduction. Front Microbiol 2021; 11:610173. [PMID: 33519763 PMCID: PMC7844145 DOI: 10.3389/fmicb.2020.610173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/09/2020] [Indexed: 11/13/2022] Open
Abstract
Auricularia auricula-judae is an edible nutrient-rich mushroom, which is a traditional medicinal resource in China. It is known that environment stimuli will affect the production of melanin by A. auricula-judae, but the mechanism of the effects of freezing treatment on melanin accumulation remains unknown. In the present study, the synthesis of melanin in A. auricula-judae was analyzed by physiological assays and a proteomics approach. Our findings showed that a longer freezing treatment causes a lighter color of A. auricula-judae fruiting bodies. The proteomic analysis showed that proteins involved in glycolysis/gluconeogenesis, tyrosine metabolism, ribosome, and arginine biosynthesis might contribute to the color differences in the A. auricula-judae after freezing treatment. This work will be expected to provide valuable information on the physiological and molecular mechanisms of freezing treatment on the color quality of A. auricula-judae.
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Affiliation(s)
- Jiawen Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
| | - Ziwei Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
| | - Tong Zhao
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
| | - Xiufeng Yan
- College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Qiuying Pang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
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17
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Tang X, Ding X, Hou YL. Comparative analysis of transcriptomes revealed the molecular mechanism of development of Tricholoma matsutake at different stages of fruiting bodies. Food Sci Biotechnol 2020; 29:939-951. [PMID: 32582456 DOI: 10.1007/s10068-020-00732-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/17/2019] [Accepted: 01/02/2020] [Indexed: 11/27/2022] Open
Abstract
The purpose of the study is to investigate the molecular mechanisms of development of Tricholoma matsutake fruiting body at the primordial stage (TM-1), the intermediate stage (TM-2) and the mature stage (TM-3) using RNA-Seq sequencing technology. The analysis of gene expression level revealed that the Spn2 and Eef1a1 gene were the key genes in the primordial stage of T. matsutake by regulating cytokinesis, protein synthesis, and cell growth. And the Ubc, Atp6, Cytb, and Pth2 gene were the key genes in the mature stage of T. matsutake by regulating energy metabolism and protein synthesis. Differential expression genes (DEGs) analysis results showed that Cdc28, Rad53, Dun1, Pho85 and Pho81 were the key DEGs regulating cell cycle genes of T. matsutake from primordial stage to intermediate stage. And APC, Cyr1, Cdc45, Spo11 and Rec8 genes were the key DEGs for the meiosis and sporogenesis of T. matsutake from the intermediate stage to the mature stage.
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Affiliation(s)
- Xian Tang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Sciences, China West Normal University, 1# Shida Road, Nanchong, 637009 Sichuan Province China
| | - Xiang Ding
- College of Environmental Science and Engineering, China West Normal University, 1# Shida Road, Nanchong, 637009 Sichuan Province China
| | - Yi-Ling Hou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Sciences, China West Normal University, 1# Shida Road, Nanchong, 637009 Sichuan Province China
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18
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A putative transcription factor LFC1 negatively regulates development and yield of winter mushroom. Appl Microbiol Biotechnol 2020; 104:5827-5844. [PMID: 32356196 DOI: 10.1007/s00253-020-10642-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/08/2020] [Accepted: 04/21/2020] [Indexed: 10/24/2022]
Abstract
Basidioma is the fruiting body of mushroom species. The deep understanding on the mechanism of basidioma development is valuable for mushroom breeding and cultivation. From winter mushroom (Flammulina velutipes), one of the top five industrially cultivated mushrooms, a novel putative Zn(II)2Cys6 transcription factor LFC1 with negative regulatory function in basidioma development was identified. The transcript level of lfc1 was dramatically decreased during basidioma development. Neither overexpression nor knockdown of lfc1 affected hyphal vegetative growth. However, knockdown of lfc1 could promote basidioma development and shorten cultivation time by 2 days, while overexpression of lfc1 delayed the optimal harvest time by 3 days. In the lfc1 knockdown strain, in which the lfc1 expression was reduced by 72%, mushroom yield and biological efficiency could be increased at least by 24%. Knockdown of lfc1 did not affect the shape of caps but significantly increased basidioma length and number, while its overexpression did not affect basidioma length but dramatically reduced basidioma number. In addition, rather than producing basidiomata with round caps as in wild type, the caps of basidiomata in the lfc1 overexpression mutants were significantly larger and the cap edge was wrinkled. RNA-seq analysis revealed that 455 genes had opposite transcriptional responses to lfc1 overexpression and knockdown. Some of them were previously reported as genes involved in basidioma development, including 3 hydrophobin encoding genes, 2 lectin encoding genes, FVFD16, an Eln2 ortholog encoding gene, and 3 genes encoding membrane components. As LFC1 homologs are widely present in mushroom species, lfc1 can be useful in mushroom breeding.Key Points• A novel transcription factor LFC1 negatively regulates fruiting in winter mushroom• LFC1 regulated transcription of more than 400 genes.• Reduction of LFC1 expression could shorten cultivation time and increase yield.• lfc1 could be a potentially useful reference gene for mushroom breeding.
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19
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Lu YP, Liao JH, Guo ZJ, Cai ZX, Chen MY. Genome Survey and Transcriptome Analysis on Mycelia and Primordia of Agaricus blazei. BIOMED RESEARCH INTERNATIONAL 2020; 2020:1824183. [PMID: 32025516 PMCID: PMC6983287 DOI: 10.1155/2020/1824183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/14/2019] [Accepted: 09/26/2019] [Indexed: 12/13/2022]
Abstract
Agaricus blazei, a type of edible straw-rotting mushroom with somewhat sweet taste and fragrance of almonds, has attracted considerable scientific and practical attention. High-throughput Illumina PE150 and PacBio RSII platform were employed to generate a genomic sequence. De novo assembly generated 36 contigs with 38,686,133 bp in size, containing 10,119 putative predicted genes. Additionally, we also studied transcriptional regulation of the mycelia and the primordia for exploration of genes involved in fruiting body formation. Expression profiling analysis revealed that 2,164 genes were upregulated in mycelia and 1,557 in primordia. Functional enrichment showed that differentially expressed genes associated with response to stress, ribosome biogenesis, arginine biosynthesis, and steroid biosynthesis pathway were more active in fruiting body. The genome and transcriptome analysis of A. blazei provide valuable sequence resources and contribute to our understanding of genes related to the biosynthesis pathway of polysaccharide and benzaldehyde, as well as the fruiting body formation.
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Affiliation(s)
- Yuan-Ping Lu
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences, Fuzhou 350014, Fujian Province, China
| | - Jian-Hua Liao
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences, Fuzhou 350014, Fujian Province, China
| | - Zhong-Jie Guo
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences, Fuzhou 350014, Fujian Province, China
| | - Zhi-Xin Cai
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences, Fuzhou 350014, Fujian Province, China
| | - Mei-Yuan Chen
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences, Fuzhou 350014, Fujian Province, China
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Integrated Metabolomics and Transcriptomics Unravel the Metabolic Pathway Variations for Different Sized Beech Mushrooms. Int J Mol Sci 2019; 20:ijms20236007. [PMID: 31795288 PMCID: PMC6928633 DOI: 10.3390/ijms20236007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 11/23/2022] Open
Abstract
Beech mushrooms (Hypsizygus marmoreus) are largely relished for their characteristic earthy flavor, chewy-texture, and gustatory and nutritional properties in East Asian societies. Intriguingly, the aforementioned properties of beech mushroom can be subsumed under its elusive metabolome and subtle transcriptome regulating its various stages of growth and development. Herein, we carried out an integrated metabolomic and transcriptomic profiling for different sized beech mushrooms across spatial components (cap and stipe) to delineate their signature pathways. We observed that metabolite profiles and differentially expressed gene (DEGs) displayed marked synergy for specific signature pathways according to mushroom sizes. Notably, the amino acid, nucleotide, and terpenoid metabolism-related metabolites and genes were more abundant in small-sized mushrooms. On the other hand, the relative levels of carbohydrates and TCA intermediate metabolites as well as corresponding genes were linearly increased with mushroom size. However, the composition of flavor-related metabolites was varying in different sized beech mushrooms. Our study explores the signature pathways associated with growth, development, nutritional, functional and organoleptic properties of different sized beech mushrooms.
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A Single Transcription Factor (PDD1) Determines Development and Yield of Winter Mushroom ( Flammulina velutipes). Appl Environ Microbiol 2019; 85:AEM.01735-19. [PMID: 31604770 DOI: 10.1128/aem.01735-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/09/2019] [Indexed: 11/20/2022] Open
Abstract
Most of the edible mushrooms cannot be cultivated or have low yield under industrial conditions, partially due to the lack of knowledge on how basidioma (fruiting body) development is regulated. From winter mushroom (Flammulina velutipes), one of the most popular industrially cultivated mushrooms, a transcription factor, PDD1, with a high-mobility group (HMG)-box domain was identified based on its increased transcription during basidioma development. pdd1 knockdown by RNA interference affected vegetative growth and dramatically impaired basidioma development. A strain with an 89.9% reduction in the level of pdd1 transcription failed to produce primordia, while overexpression of pdd1 promoted basidioma development. When the transcriptional level of pdd1 was increased to 5 times the base level, the mushroom cultivation time was shortened by 9.8% and the yield was increased by at least 33%. RNA sequencing (RNA-seq) analysis revealed that pdd1 knockdown downregulated 331 genes and upregulated 463 genes. PDD1 positively regulated several genes related to fruiting, including 6 pheromone receptor-encoding genes, 3 jacalin-related lectin-encoding genes, FVFD16, and 2 FVFD16 homolog-encoding genes. PDD1 is a novel transcription factor with regulatory function in basidioma development found in industrially cultivated mushrooms. Since its orthologs are widely present in fungal species of the Basidiomycota phylum, PDD1 might have important application prospects in mushroom breeding.IMPORTANCE Mushrooms are sources of food and medicine and provide abundant nutrients and bioactive compounds. However, most of the edible mushrooms cannot be cultivated commercially due to the limited understanding of basidioma development. From winter mushroom (Flammulina velutipes; also known as Enokitake), one of the most commonly cultivated mushrooms, we identified a novel transcription factor, PDD1, positively regulating basidioma development. PDD1 increases expression during basidioma development. Artificially increasing its expression promoted basidioma formation and dramatically increased mushroom yield, while reducing its expression dramatically impaired its development. In its PDD1 overexpression mutants, mushroom number, height, yield, and biological efficiency were significantly increased. PDD1 regulates the expression of some genes that are important in or related to basidioma development. PDD1 is the first identified transcription factor with defined functions in mushroom development among commercially cultivated mushroom species, and it might be useful in mushroom breeding.
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22
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Novak M, Čepin U, Hodnik V, Narat M, Jamnik M, Kraševec N, Sepčić K, Anderluh G. Functional studies of aegerolysin and MACPF-like proteins in Aspergillus niger. Mol Microbiol 2019; 112:1253-1269. [PMID: 31376198 DOI: 10.1111/mmi.14360] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2019] [Indexed: 12/21/2022]
Abstract
Proteins of the aegerolysin family have a high abundance in Fungi. Due to their specific binding to membrane lipids, and their membrane-permeabilization potential in concert with protein partner(s) belonging to a membrane-attack-complex/perforin (MACPF) superfamily, they were proposed as useful tools in different biotechnological and biomedical applications. In this work, we performed functional studies on expression of the genes encoding aegerolysin and MACPF-like proteins in Aspergillus niger. Our results suggest the sporulation process being crucial for strong induction of the expression of all these genes. However, deletion of either of the aegerolysin genes did not influence the growth, development, sporulation efficiency and phenotype of the mutants, indicating that aegerolysins are not key factors in the sporulation process. In all our expression studies we noticed a strong correlation in the expression of one aegerolysin and MACPF-like gene. Aegerolysins were confirmed to be secreted from the fungus. We also showed the specific interaction of a recombinant A. niger aegerolysin with an invertebrate-specific membrane sphingolipid. Moreover, using this protein labelled with mCherry we successfully stained insect cells membranes containing this particular sphingolipid. Our combined results suggest, that aegerolysins in this species, and probably also in other aspergilli, could be involved in defence against predators.
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Affiliation(s)
- Maruša Novak
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Urška Čepin
- BioSistemika Ltd and National Institute of Biology, Ljubljana, Slovenia
| | - Vesna Hodnik
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Mojca Narat
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Jamnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Nada Kraševec
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Kristina Sepčić
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
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23
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Hao H, Zhang J, Wang H, Wang Q, Chen M, Juan J, Feng Z, Chen H. Comparative transcriptome analysis reveals potential fruiting body formation mechanisms in Morchella importuna. AMB Express 2019; 9:103. [PMID: 31300949 PMCID: PMC6626090 DOI: 10.1186/s13568-019-0831-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 07/04/2019] [Indexed: 01/02/2023] Open
Abstract
Morchella importuna has been artificially cultivated, but stable production remains difficult because its mechanisms of fruiting body formation are unclear. To investigate the fruiting body formation mechanisms, we sequenced the transcriptomes of Morchella importuna at the mycelial and young fruiting body stages. Among the 12,561 differentially expressed genes (DEGs), 9215 were upregulated, and 3346 were downregulated. DEG enrichment analysis showed that these genes were enriched in the "generation of precursor metabolites and energy", "carbohydrate catabolic process", and "oxidoreductase activity" Gene Ontology (GO) functional categories. Enzyme activity assay results indicated that the activity levels of CAZymes (carbohydrate-active enzymes), oxidoreductases (SOD (superoxide dismutase), CAT (catalase)) and mitochondrial complex (complex I, II, III) proteins were significantly increased from the mycelial stage to the young fruiting body stage. In addition, the genes encoding CAZymes, mitochondrial proteins, oxidoreductases and heat shock proteins had higher expression levels in the young fruiting body stage than in the mycelial stage, and the qRT-PCR results showed similar trends to the RNA-Seq results. In summary, these results suggest that carbohydrate catabolism and energy metabolism are significantly enhanced in the young fruiting body stage and that growth environment temperature changes affect the formation of fruiting bodies.
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24
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Transcriptome Changes during Major Developmental Transitions Accompanied with Little Alteration of DNA Methylome in Two Pleurotus Species. Genes (Basel) 2019; 10:genes10060465. [PMID: 31212970 PMCID: PMC6627472 DOI: 10.3390/genes10060465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/08/2019] [Accepted: 06/12/2019] [Indexed: 12/13/2022] Open
Abstract
Pleurotus tuoliensis (Pt) and P. eryngii var. eryngii (Pe) are important edible mushrooms. The epigenetic and gene expression signatures characterizing major developmental transitions in these two mushrooms remain largely unknown. Here, we report global analyses of DNA methylation and gene expression in both mushrooms across three major developmental transitions, from mycelium to primordium and to fruit body, by whole-genome bisulfite sequencing (WGBS) and RNA-seq-based transcriptome profiling. Our results revealed that in both Pt and Pe the landscapes of methylome are largely stable irrespective of genomic features, e.g., in both protein-coding genes and transposable elements (TEs), across the developmental transitions. The repressive impact of DNA methylation on expression of a small subset of genes is likely due to TE-associated effects rather than their own developmental dynamics. Global expression of gene orthologs was also broadly conserved between Pt and Pe, but discernible interspecific differences exist especially at the fruit body formation stage, and which are primarily due to differences in trans-acting factors. The methylome and transcriptome repertories we established for the two mushroom species may facilitate further studies of the epigenetic and transcriptional regulatory mechanisms underpinning gene during development in Pleurotus and related genera.
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25
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Li X, Yan L, Li Q, Tan H, Zhou J, Miao R, Ye L, Peng W, Zhang X, Tan W, Zhang B. Transcriptional profiling of Auricularia cornea in selenium accumulation. Sci Rep 2019; 9:5641. [PMID: 30948778 PMCID: PMC6449350 DOI: 10.1038/s41598-019-42157-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 03/26/2019] [Indexed: 01/26/2023] Open
Abstract
Auricularia cornea is a widely cultivated edible fungus with substantial nutritive value. This study aimed to enrich the multifunctional bionutrient element selenium in A. cornea to improve its quality and explore the accumulation of selenium in the fungus using high-throughput RNA-Seq technology. In general, the treatment group with a 100 µg/g supply of selenium outperformed the other treatment groups in terms of high yield, rich crude polysaccharides and a high total selenium concentration. Additional evidences demonstrated the budding and mature phases were two typical growth stages of A. cornea and were important for the accumulation of selenium. Therefore, the budding and mature phase tissues of A. cornea in the treatment group with a 100 µg/g supply of selenium were used for transcriptome analysis and compared to those of a control group that lacked additional selenium. A total of 2.56 × 105 unigenes from A. cornea transcriptome were assembled and annotated to five frequently used databases including NR, GO, KEGG, eggNOG and SwissProt. GO and KEGG pathway analysis revealed that genes involved in metabolic process and translation were up-expressed at the budding stage in response to selenium supplementation, including amino acid metabolism, lipid metabolism, ribosome. In addition, the differential gene expression patterns of A. cornea suggested that the up-expressed genes were more likely to be detected at the budding stage than at the mature stage. These results provide insights into the transcriptional response of A. cornea to selenium accumulation.
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Affiliation(s)
- Xiaolin Li
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China.
| | - Lijuan Yan
- Chair for Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, D-07743, Germany
| | - Qiang Li
- Research Center of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
- College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Hao Tan
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Jie Zhou
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Renyun Miao
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Lei Ye
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Weihong Peng
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Xiaoping Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Tan
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China.
| | - Bo Zhang
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China.
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26
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Herzog R, Solovyeva I, Bölker M, Lugones LG, Hennicke F. Exploring molecular tools for transformation and gene expression in the cultivated edible mushroom Agrocybe aegerita. Mol Genet Genomics 2019; 294:663-677. [PMID: 30778675 DOI: 10.1007/s00438-018-01528-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/24/2018] [Indexed: 12/22/2022]
Abstract
Agrocybe aegerita is a cultivated edible mushroom in numerous countries, which also serves as a model basidiomycete to study fruiting body formation. Aiming to create an easily expandable customised molecular toolset for transformation and constitutive gene of interest expression, we first created a homologous dominant marker for transformant selection. Progeny monokaryons of the genome-sequenced dikaryon A. aegerita AAE-3 used here were identified as sensitive to the systemic fungicide carboxin. We cloned the wild-type gene encoding the iron-sulphur protein subunit of succinate dehydrogenase AaeSdi1 including its up- and downstream regions, and introduced a single-point mutation (His237 to Leu) to make it confer carboxin resistance. PEG-mediated transformation of protoplasts derived from either oidia or vegetative monokaryotic mycelium with the resulting carboxin resistance marker (CbxR) plasmid pSDI1E3 yielded carboxin-resistant transformants in both cases. Plasmid DNA linearised within the selection marker resulted in transformants with ectopic multiple insertions of plasmid DNA in a head-to-tail repeat-like fashion. When circular plasmid was used, ectopic single integration into the fungal genome was favoured, but also gene conversion at the homologous locus was seen in 1 out of 11 analysed transformants. Employing CbxR as selection marker, two versions of a reporter gene construct were assembled via Golden Gate cloning which allows easy recombination of its modules. These consisted of an eGFP expression cassette controlled by the native promoter PAaeGPDII and the heterologous terminator Tnos, once with and once without an intron in front of the eGFP start codon. After protoplast transformation with either construct as circular plasmid DNA, GFP fluorescence was detected with either transformants, indicating that expression of eGFP is intron-independent in A. aegerita. This paves the way for functional genetics approaches to A. aegerita, e.g., via constitutive expression of fruiting-related genes.
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Affiliation(s)
- Robert Herzog
- Junior Research Group Genetics and Genomics of Fungi, Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Institute of Ecology, Evolution and Diversity, Goethe-University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany.,LOEWE Cluster of Integrative Fungal Research, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Department of Environmental Biotechnology, TU Dresden, Markt 23, 02763, Zittau, Germany
| | - Irina Solovyeva
- Junior Research Group Genetics and Genomics of Fungi, Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,LOEWE Cluster of Integrative Fungal Research, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Michael Bölker
- LOEWE Cluster of Integrative Fungal Research, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Department of Biology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, 35032, Marburg, Germany
| | - Luis G Lugones
- Department of Biology, Microbiology, Utrecht University, Utrecht, The Netherlands
| | - Florian Hennicke
- Junior Research Group Genetics and Genomics of Fungi, Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany. .,Institute of Ecology, Evolution and Diversity, Goethe-University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany. .,LOEWE Cluster of Integrative Fungal Research, Senckenberganlage 25, 60325, Frankfurt am Main, Germany. .,Department of Biology, Microbiology, Utrecht University, Utrecht, The Netherlands.
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27
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Comparative transcriptome analysis reveals relationship of three major domesticated varieties of Auricularia auricula-judae. Sci Rep 2019; 9:78. [PMID: 30635591 PMCID: PMC6329756 DOI: 10.1038/s41598-018-36984-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 09/28/2018] [Indexed: 12/14/2022] Open
Abstract
Auricularia auricula-judae is an edible mushroom and a traditional medicine in China as well as the fourth largest cultivated mushroom species in the world. Here for the first time, we present comparative transcriptome analyses of the fruiting bodies of three morphologically distinguishable A. auricula-judae cultivated varieties (Wujin, smooth; Banjin, partially wrinkled; and Quanjin, fully wrinkled) collected from Jilin Province, China. Biological triplicates were performed to determine the expression levels of 13,937 unigenes. Among them, only 13 unigenes were annotated to A. auricula-judae, highlighting the lack of publicly available reference sequences for this economically important species. Principal component analysis (PCA) determined that the gene expression profile of Quanjin was unique when compared to those of Banjin and Wujin. Such relationships were further supported by analyses of annotated and unannotated unigenes, differentially expressed unigenes, gene ontology functions, and the family of peroxidase genes. Using the KEGG database, significant alternations in biological pathways were detected among the three cultivars. This work contributes a large set of A. auricula-judae sequences to public database, establishes the relationships among major cultivars, and provides molecular guidance for breeding and cultivation.
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28
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Anticancer and other therapeutic relevance of mushroom polysaccharides: A holistic appraisal. Biomed Pharmacother 2018; 105:377-394. [DOI: 10.1016/j.biopha.2018.05.138] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 05/27/2018] [Accepted: 05/28/2018] [Indexed: 11/17/2022] Open
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29
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Song HY, Kim DH, Kim JM. Comparative transcriptome analysis of dikaryotic mycelia and mature fruiting bodies in the edible mushroom Lentinula edodes. Sci Rep 2018; 8:8983. [PMID: 29895888 PMCID: PMC5997629 DOI: 10.1038/s41598-018-27318-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/31/2018] [Indexed: 02/08/2023] Open
Abstract
Lentinula edodes is a popular cultivated edible mushroom with high nutritional and medicinal value. To understand the regulation of gene expression in the dikaryotic mycelium and mature fruiting body in the commercially important Korean L. edodes strain, we first performed comparative transcriptomic analysis, using Illumina HiSeq platform. De novo assembly of these sequences revealed 11,675 representative transcripts in two different stages of L. edodes. A total of 9,092 unigenes were annotated and subjected to Gene Ontology, EuKaryotic Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Gene expression analysis revealed that 2,080 genes were differentially expressed, with 1,503 and 577 upregulated in the mycelium and a mature fruiting body, respectively. Analysis of 18 KEGG categories indicated that fruiting body-specific transcripts were significantly enriched in ‘replication and repair’ and ‘transcription’ pathways, which are important for premeiotic replication, karyogamy, and meiosis during maturation. We also searched for fruiting body-specific proteins such as aspartic protease, gamma-glutamyl transpeptidase, and cyclohexanone monooxygenase, which are involved in fruiting body maturation and isolation of functional substances. These transcriptomes will be useful in elucidating the molecular mechanisms of mature fruiting body development and beneficial properties, and contribute to the characterization of novel genes in L. edodes.
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Affiliation(s)
- Ha-Yeon Song
- Department of Bio-Environmental Chemistry, Institute of Life Science and Natural Resources, Wonkwang University, Iksan, Chonbuk, 54538, Korea
| | - Dae-Hyuk Kim
- Institute for Molecular Biology and Genetics, Center for Fungal Pathogenesis, Chonbuk National University, Jeonju, Chonbuk, 54896, Korea
| | - Jung-Mi Kim
- Department of Bio-Environmental Chemistry, Institute of Life Science and Natural Resources, Wonkwang University, Iksan, Chonbuk, 54538, Korea.
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30
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Gupta DK, Rühl M, Mishra B, Kleofas V, Hofrichter M, Herzog R, Pecyna MJ, Sharma R, Kellner H, Hennicke F, Thines M. The genome sequence of the commercially cultivated mushroom Agrocybe aegerita reveals a conserved repertoire of fruiting-related genes and a versatile suite of biopolymer-degrading enzymes. BMC Genomics 2018; 19:48. [PMID: 29334897 PMCID: PMC5769442 DOI: 10.1186/s12864-017-4430-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 12/29/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Agrocybe aegerita is an agaricomycete fungus with typical mushroom features, which is commercially cultivated for its culinary use. In nature, it is a saprotrophic or facultative pathogenic fungus causing a white-rot of hardwood in forests of warm and mild climate. The ease of cultivation and fructification on solidified media as well as its archetypal mushroom fruit body morphology render A. aegerita a well-suited model for investigating mushroom developmental biology. RESULTS Here, the genome of the species is reported and analysed with respect to carbohydrate active genes and genes known to play a role during fruit body formation. In terms of fruit body development, our analyses revealed a conserved repertoire of fruiting-related genes, which corresponds well to the archetypal fruit body morphology of this mushroom. For some genes involved in fruit body formation, paralogisation was observed, but not all fruit body maturation-associated genes known from other agaricomycetes seem to be conserved in the genome sequence of A. aegerita. In terms of lytic enzymes, our analyses suggest a versatile arsenal of biopolymer-degrading enzymes that likely account for the flexible life style of this species. Regarding the amount of genes encoding CAZymes relevant for lignin degradation, A. aegerita shows more similarity to white-rot fungi than to litter decomposers, including 18 genes coding for unspecific peroxygenases and three dye-decolourising peroxidase genes expanding its lignocellulolytic machinery. CONCLUSIONS The genome resource will be useful for developing strategies towards genetic manipulation of A. aegerita, which will subsequently allow functional genetics approaches to elucidate fundamentals of fruiting and vegetative growth including lignocellulolysis.
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Affiliation(s)
- Deepak K Gupta
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany.,Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany.,LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany
| | - Martin Rühl
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Giessen, Germany.,LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany.,Project Group "Bioresources", Fraunhofer IME, Giessen, Germany
| | - Bagdevi Mishra
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany.,Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany.,LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany
| | - Vanessa Kleofas
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Giessen, Germany.,LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany
| | - Martin Hofrichter
- International Institute (IHI) Zittau, Technische Universität Dresden, Zittau, Germany
| | - Robert Herzog
- Junior Research Group Genetics and Genomics of Fungi, Senckenberg Gesellschaft für Naturforschung, Frankfurt a. M., Germany.,Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany.,LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany
| | - Marek J Pecyna
- University of Applied Sciences Zittau/Görlitz, Zittau, Germany
| | - Rahul Sharma
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany.,Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany.,LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany
| | - Harald Kellner
- International Institute (IHI) Zittau, Technische Universität Dresden, Zittau, Germany
| | - Florian Hennicke
- Junior Research Group Genetics and Genomics of Fungi, Senckenberg Gesellschaft für Naturforschung, Frankfurt a. M., Germany. .,Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany. .,LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany. .,Department of Biology, Microbiology, Utrecht University, Utrecht, The Netherlands.
| | - Marco Thines
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany. .,Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany. .,LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany.
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31
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Comparative Transcriptome Analysis Identified Candidate Genes Related to Bailinggu Mushroom Formation and Genetic Markers for Genetic Analyses and Breeding. Sci Rep 2017; 7:9266. [PMID: 28839254 PMCID: PMC5571210 DOI: 10.1038/s41598-017-08049-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 07/04/2017] [Indexed: 01/12/2023] Open
Abstract
Bailinggu (Pleurotus tuoliensis) is a major, commercially cultivated mushroom and widely used for nutritional, medicinal, and industrial applications. Yet, the mushroom’s genetic architecture and the molecular mechanisms underlying its formation are largely unknown. Here we performed comparative transcriptomic analysis during Bailinggu’s mycelia, primordia, and fruiting body stages to identify genes regulating fruiting body development and develop EST-SSR markers assessing the genetic value of breeding materials. The stage-specific and differentially expressed unigenes (DEGs) involved in morphogenesis, primary carbohydrate metabolism, cold stimulation and blue-light response were identified using GO and KEGG databases. These unigenes might help Bailinggu adapt to genetic and environmental factors that influence fructification. The most pronounced change in gene expression occurred during the vegetative-to-reproductive transition, suggesting that is most active and key for Bailinggu development. We then developed 26 polymorphic and informative EST-SSR markers to assess the genetic diversity in 82 strains of Bailinggu breeding materials. These EST-SSRs exhibited high transferability in closely related species P. eryngii var. ferulae and var. eryngii. Genetic population structure analysis indicated that China’s Bailinggu has low introgression with these two varieties and likely evolved independently. These findings provide new genes, SSR markers, and germplasm to enhance the breeding of commercially cultivated Bailinggu.
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de Freitas Pereira M, Narvaes da Rocha Campos A, Anastacio TC, Morin E, Brommonschenkel SH, Martin F, Kohler A, Costa MD. The transcriptional landscape of basidiosporogenesis in mature Pisolithus microcarpus basidiocarp. BMC Genomics 2017; 18:157. [PMID: 28196466 PMCID: PMC5310086 DOI: 10.1186/s12864-017-3545-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 02/02/2017] [Indexed: 11/17/2022] Open
Abstract
Background Pisolithus microcarpus (Cooke & Massee) G. Cunn is a gasteromycete that produces closed basidiocarps in symbiosis with eucalypts and acacias. The fungus produces a complex basidiocarp composed of peridioles at different developmental stages and an upper layer of basidiospores free of the hyphae and ready for wind dispersal upon the rupture of the basidiocarp pellis. During basidiosporogenesis, a process that takes place inside the basidiocarp peridioles, a conspicuous reserve of fatty acids is present throughout development. While several previous studies have described basidiosporogenesis inside peridioles, very little is known about gene expression changes that may occur during this part of the fungal life cycle. The objective of this work was to analyze gene transcription during peridiole and basidiospore development, while focusing specifically on cell cycle progression and lipid metabolism. Results Throughout different developmental stages of the peridioles we analyzed, 737 genes were regulated between adjacent compartments (>5 fold, FDR-corrected p-value < 0.05) corresponding to 3.49% of the genes present in the P. microcarpus genome. We identified three clusters among the regulated genes which showed differential expression between the peridiole developmental stages and the basidiospores. During peridiole development, transcripts for proteins involved in cellular processes, signaling, and information storage were detected, notably those for coding transcription factors, DNA polymerase subunits, DNA repair proteins, and genes involved in chromatin structure. For both internal embedded basidiospores (hereto referred to as “Internal spores”, IS) and external free basidiospores (hereto referred to as “Free spores”, FS), upregulated transcripts were found to involve primary metabolism, particularly fatty acid metabolism (FA). High expression of transcripts related to β-oxidation and the glyoxylate shunt indicated that fatty acids served as a major carbon source for basidiosporogenesis. Conclusion Our results show that basidiocarp formation in P. microcarpus involves a complex array of genes that are regulated throughout peridiole development. We identified waves of transcripts with coordinated regulation and identified transcription factors which may play a role in this regulation. This is the first work to describe gene expression patterns during basidiocarp formation in an ectomycorrhizal gasteromycete fungus and sheds light on genes that may play important roles in the developmental process. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3545-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maíra de Freitas Pereira
- Department of Microbiology/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil.,INRA, UMR 1136 INRA-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRA-Nancy, 54280, Champenoux, France
| | | | | | - Emmanuelle Morin
- INRA, UMR 1136 INRA-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRA-Nancy, 54280, Champenoux, France
| | | | - Francis Martin
- INRA, UMR 1136 INRA-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRA-Nancy, 54280, Champenoux, France
| | - Annegret Kohler
- INRA, UMR 1136 INRA-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRA-Nancy, 54280, Champenoux, France.
| | - Maurício Dutra Costa
- Department of Microbiology/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
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Dikaryotic fruiting body development in a single dikaryon of Agrocybe aegerita and the spectrum of monokaryotic fruiting types in its monokaryotic progeny. Mycol Prog 2016. [DOI: 10.1007/s11557-016-1221-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Al-Obaidi JR. Proteomics of edible mushrooms: A mini-review. Electrophoresis 2016; 37:1257-63. [PMID: 26891916 DOI: 10.1002/elps.201600031] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 01/22/2016] [Accepted: 02/14/2016] [Indexed: 12/12/2022]
Abstract
Mushrooms are considered an important food for their traditionally famous nutritional and medicinal values, although much information about their potential at the molecular level is unfortunately unknown. Edible mushrooms include fungi that are either collected wild or cultivated. Many important species are difficult to cultivate but attempts have been made with varying degrees of success, with the results showing unsatisfactory economical cultivation methods. Recently, proteomic analysis has been developed as a powerful tool to study the protein content of fungi, particularly basidiomycetes. This mini-review article highlights the contribution of proteomics platforms to the study of edible mushrooms, focusing on the molecular mechanisms involved in developmental stages. This includes extracellular and cytoplasmic effector proteins that have potential or are involved in the synthesis of anticancer, antidiabetic, antioxidant, and antibiotic, in blood pressure control, in the supply of vitamins and minerals, and in other responses to environmental changes. The contribution of different proteomics techniques including classical and more advanced techniques is also highlighted.
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Affiliation(s)
- Jameel R Al-Obaidi
- Agro-biotechnology Institute Malaysia (ABI), c/o MARDI Headquarters, 43400 Serdang, Selangor, Malaysia
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Yap HYY, Chooi YH, Fung SY, Ng ST, Tan CS, Tan NH. Transcriptome Analysis Revealed Highly Expressed Genes Encoding Secondary Metabolite Pathways and Small Cysteine-Rich Proteins in the Sclerotium of Lignosus rhinocerotis. PLoS One 2015; 10:e0143549. [PMID: 26606395 PMCID: PMC4659598 DOI: 10.1371/journal.pone.0143549] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/05/2015] [Indexed: 12/05/2022] Open
Abstract
Lignosus rhinocerotis (Cooke) Ryvarden (tiger milk mushroom) has long been known for its nutritional and medicinal benefits among the local communities in Southeast Asia. However, the molecular and genetic basis of its medicinal and nutraceutical properties at transcriptional level have not been investigated. In this study, the transcriptome of L. rhinocerotis sclerotium, the part with medicinal value, was analyzed using high-throughput Illumina HiSeqTM platform with good sequencing quality and alignment results. A total of 3,673, 117, and 59,649 events of alternative splicing, novel transcripts, and SNP variation were found to enrich its current genome database. A large number of transcripts were expressed and involved in the processing of gene information and carbohydrate metabolism. A few highly expressed genes encoding the cysteine-rich cerato-platanin, hydrophobins, and sugar-binding lectins were identified and their possible roles in L. rhinocerotis were discussed. Genes encoding enzymes involved in the biosynthesis of glucans, six gene clusters encoding four terpene synthases and one each of non-ribosomal peptide synthetase and polyketide synthase, and 109 transcribed cytochrome P450 sequences were also identified in the transcriptome. The data from this study forms a valuable foundation for future research in the exploitation of this mushroom in pharmacological and industrial applications.
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Affiliation(s)
- Hui-Yeng Y. Yap
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail:
| | - Yit-Heng Chooi
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia, Australia
| | - Shin-Yee Fung
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Szu-Ting Ng
- Ligno Biotech Sdn. Bhd., Balakong Jaya, Selangor, Malaysia
| | - Chon-Seng Tan
- Malaysian Agricultural Research and Development Institute (MARDI), Serdang, Selangor, Malaysia
| | - Nget-Hong Tan
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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De novo transcriptome analysis of Inonotus baumii by RNA-seq. J Biosci Bioeng 2015; 121:380-4. [PMID: 26493632 DOI: 10.1016/j.jbiosc.2015.09.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 08/24/2015] [Accepted: 09/05/2015] [Indexed: 01/24/2023]
Abstract
Inonotus baumii, a basidiomycete white rot fungus, has been widely used as traditional herbal medicine in China, Korea, Japan and other Asian countries for many years. Its extract is of great medicinal importance and plays a valuable role in the immune response and disease resistance. However, limited genetic resources for I. baumii have hindered exploration of this species. In order to gain a molecular understanding of this fungus, Illumina high-throughput technology was used to sequence and analyze the transcriptome of I. baumii, and 280,691 contigs, 43,890 scaffolds and 30,051 unigenes were obtained. Additionally, based on similarity search with known proteins, unigenes were annotated with gene descriptions, gene ontology (GO), clusters of orthologous group (COG), and database of protein families (Pfam) terms. According to the annotation of unigenes, a total of 12 candidate genes involved in the triterpenoid biosynthesis pathway and 21 putative FOLymes (fungal oxidative lignin enzymes) and 176 CAZymes (carbohydrate-active enzymes) were obtained using homology-based BlastX. Moreover, for better understanding of the transcripts function, the BlastX algorithm was used to search for homologous sequences against the Yeast genome. This is the first study on transcriptome analyses of I. baumii, which provided a dataset for functional gene mining and laid a basis for further functional genomics studies of I. baumii.
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Zhang J, Ren A, Chen H, Zhao M, Shi L, Chen M, Wang H, Feng Z. Transcriptome analysis and its application in identifying genes associated with fruiting body development in basidiomycete Hypsizygus marmoreus. PLoS One 2015; 10:e0123025. [PMID: 25837428 PMCID: PMC4383556 DOI: 10.1371/journal.pone.0123025] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 01/05/2015] [Indexed: 02/06/2023] Open
Abstract
To elucidate the mechanisms of fruit body development in H. marmoreus, a total of 43609521 high-quality RNA-seq reads were obtained from four developmental stages, including the mycelial knot (H-M), mycelial pigmentation (H-V), primordium (H-P) and fruiting body (H-F) stages. These reads were assembled to obtain 40568 unigenes with an average length of 1074 bp. A total of 26800 (66.06%) unigenes were annotated and analyzed with the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and Eukaryotic Orthologous Group (KOG) databases. Differentially expressed genes (DEGs) from the four transcriptomes were analyzed. The KEGG enrichment analysis revealed that the mycelium pigmentation stage was associated with the MAPK, cAMP, and blue light signal transduction pathways. In addition, expression of the two-component system members changed with the transition from H-M to H-V, suggesting that light affected the expression of genes related to fruit body initiation in H. marmoreus. During the transition from H-V to H-P, stress signals associated with MAPK, cAMP and ROS signals might be the most important inducers. Our data suggested that nitrogen starvation might be one of the most important factors in promoting fruit body maturation, and nitrogen metabolism and mTOR signaling pathway were associated with this process. In addition, 30 genes of interest were analyzed by quantitative real-time PCR to verify their expression profiles at the four developmental stages. This study advances our understanding of the molecular mechanism of fruiting body development in H. marmoreus by identifying a wealth of new genes that may play important roles in mushroom morphogenesis.
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Affiliation(s)
- Jinjing Zhang
- College of Life Science, Nanjing Agricultural University, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing, Jiangsu, China
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, the People’s Republic of China, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ang Ren
- College of Life Science, Nanjing Agricultural University, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing, Jiangsu, China
| | - Hui Chen
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, the People’s Republic of China, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Mingwen Zhao
- College of Life Science, Nanjing Agricultural University, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing, Jiangsu, China
| | - Liang Shi
- College of Life Science, Nanjing Agricultural University, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing, Jiangsu, China
| | - Mingjie Chen
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, the People’s Republic of China, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Hong Wang
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, the People’s Republic of China, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Zhiyong Feng
- College of Life Science, Nanjing Agricultural University, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing, Jiangsu, China
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, the People’s Republic of China, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
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Yu GJ, Yin YL, Yu WH, Liu W, Jin YX, Shrestha A, Yang Q, Ye XD, Sun H. Proteome exploration to provide a resource for the investigation of Ganoderma lucidum. PLoS One 2015; 10:e0119439. [PMID: 25756518 PMCID: PMC4355618 DOI: 10.1371/journal.pone.0119439] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 01/13/2015] [Indexed: 12/16/2022] Open
Abstract
Ganoderma lucidum is a basidiomycete white rot fungus that has been used for medicinal purposes worldwide. Although information concerning its genome and transcriptome has recently been reported, relatively little information is available for G. lucidum at the proteomic level. In this study, protein fractions from G. lucidum at three developmental stages (16-day mycelia, and fruiting bodies at 60 and 90 days) were prepared and subjected to LC-MS/MS analysis. A search against the G. lucidum genome database identified 803 proteins. Among these proteins, 61 lignocellulose degrading proteins were detected, most of which (49 proteins) were found in the 90-day fruiting bodies. Fourteen TCA-cycle related proteins, 17 peptidases, two argonaute-like proteins, and two immunomodulatory proteins were also detected. A majority (470) of the 803 proteins had GO annotations and were classified into 36 GO terms, with "binding", "catalytic activity", and "hydrolase activity" having high percentages. Additionally, 357 out of the 803 proteins were assigned to at least one COG functional category and grouped into 22 COG classifications. Based on the results from the proteomic and sequence alignment analyses, a potentially new immunomodulatory protein (GL18769) was expressed and shown to have high immunomodulatory activity. In this study, proteomic and biochemical analyses of G. lucidum were performed for the first time, revealing that proteins from this fungus can play significant bioactive roles and providing a new foundation for the further functional investigations that this fungus merits.
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Affiliation(s)
- Guo-Jun Yu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Ya-Lin Yin
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wen-Hui Yu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wei Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yan-Xia Jin
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Alok Shrestha
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qing Yang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiang-Dong Ye
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Hui Sun
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan, China
- Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, China
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Cell Factories of Higher Fungi for Useful Metabolite Production. BIOREACTOR ENGINEERING RESEARCH AND INDUSTRIAL APPLICATIONS I 2015; 155:199-235. [DOI: 10.1007/10_2015_335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Laccase production and metabolic diversity among Flammulina velutipes strains. World J Microbiol Biotechnol 2014; 31:121-33. [PMID: 25377764 PMCID: PMC4282699 DOI: 10.1007/s11274-014-1769-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 10/31/2014] [Indexed: 10/26/2022]
Abstract
Twelve Flammulina velutipes strains originating from Poland were identified using internal transcribed spacer (ITS) region sequencing. Based on the sequences obtained, the genomic relationship of the analyzed strains was determined. All F. velutipes strains were also characterized using Biolog FF MicroPlates to obtain data on C-substrate utilization and mitochondrial activity. The ability to decompose various substrates differed among the F. velutipes strains up to five times. The highest catabolic activities were characteristic for only two strains with capabilities to decompose up to 22 carbon sources. The correlation between carbon repression and laccase production by F. velutipes was analyzed based on glucose assimilation by these strains. Moreover, the influence of metal ions (Cu(2+), Cd(2+)), veratric and ferulic acids, and temperature on laccase activities in the analyzed strains was determined. The results obtained proved that all the inducers influenced laccase expression in almost all the analyzed strains. However, the degree of induction depended not only on the strain used but also on the day of the induction.
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Lethal protein in mass consumption edible mushroom Agrocybe aegerita linked to strong hepatic toxicity. Toxicon 2014; 90:273-85. [DOI: 10.1016/j.toxicon.2014.08.066] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 08/10/2014] [Accepted: 08/19/2014] [Indexed: 01/19/2023]
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Nehls U, Dietz S. Fungal aquaporins: cellular functions and ecophysiological perspectives. Appl Microbiol Biotechnol 2014; 98:8835-51. [PMID: 25213914 DOI: 10.1007/s00253-014-6049-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 08/13/2014] [Accepted: 08/15/2014] [Indexed: 12/21/2022]
Abstract
Three aspects have to be taken into consideration when discussing cellular water and solute permeability of fungal cells: cell wall properties, membrane permeability, and transport through proteinaceous pores (the main focus of this review). Yet, characterized major intrinsic proteins (MIPs) can be grouped into three functional categories: (mainly) water transporting aquaporins, aquaglyceroporins that confer preferentially solute permeability (e.g., glycerol and ammonia), and bifunctional aquaglyceroporins that can facilitate efficient water and solute transfer. Two ancestor proteins, a water (orthodox aquaporin) and a solute facilitator (aquaglyceroporin), are supposed to give rise to today's MIPs. Based on primary sequences of fungal MIPs, orthodox aquaporins/X-intrinsic proteins (XIPs) and FPS1-like/Yfl054-like/other aquaglyceroporins are supposed to be respective sister groups. However, at least within the fungal kingdom, no easy functional conclusion can be drawn from the phylogenetic position of a given protein within the MIP pedigree. In consequence, ecophysiological prediction of MIP relevance is not feasible without detailed functional analysis of the respective protein and expression studies. To illuminate the diverse MIP implications in fungal lifestyle, our current knowledge about protein function in two organisms, baker's yeast and the Basidiomycotic Laccaria bicolor, an ectomycorrhizal model fungus, was exemplarily summarized in this review. MIP function has been investigated in such a depth in Saccharomyces cerevisiae that a system-wide view is possible. Yeast lifestyle, however, is special in many circumstances. Therefore, L. bicolor as filamentous Basidiomycete was added and allows insight into a very different way of life. Special emphasis was laid in this review onto ecophysiological interpretation of MIP function.
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Affiliation(s)
- Uwe Nehls
- Botany, University of Bremen, Leobenerstr. 2, 28359, Bremen, Germany,
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Tasaki Y, Sato R, Toyama S, Kasahara K, Ona Y, Sugawara M. Cloning of glyceraldehyde-3-phosphate dehydrogenase genes from the basidiomycete mushroom Pleurotus ostreatus and analysis of their expression during fruit-body development. MYCOSCIENCE 2014. [DOI: 10.1016/j.myc.2013.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Plaza DF, Lin CW, van der Velden NSJ, Aebi M, Künzler M. Comparative transcriptomics of the model mushroom Coprinopsis cinerea reveals tissue-specific armories and a conserved circuitry for sexual development. BMC Genomics 2014; 15:492. [PMID: 24942908 PMCID: PMC4082614 DOI: 10.1186/1471-2164-15-492] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 06/12/2014] [Indexed: 11/12/2022] Open
Abstract
Background It is well known that mushrooms produce defense proteins and secondary metabolites against predators and competitors; however, less is known about the correlation between the tissue-specific expression and the target organism (antagonist) specificity of these molecules. In addition, conserved transcriptional circuitries involved in developing sexual organs in fungi are not characterized, despite the growing number of gene expression datasets available from reproductive and vegetative tissue. The aims of this study were: first, to evaluate the tissue specificity of defense gene expression in the model mushroom Coprinopsis cinerea and, second, to assess the degree of conservation in transcriptional regulation during sexual development in basidiomycetes. Results In order to characterize the regulation in the expression of defense loci and the transcriptional circuitries controlling sexual reproduction in basidiomycetes, we sequenced the poly (A)-positive transcriptome of stage 1 primordia and vegetative mycelium of C. cinerea A43mutB43mut. Our data show that many genes encoding predicted and already characterized defense proteins are differentially expressed in these tissues. The predicted specificity of these proteins with regard to target organisms suggests that their expression pattern correlates with the type of antagonists these tissues are confronted with. Accordingly, we show that the stage 1 primordium-specific protein CC1G_11805 is toxic to insects and nematodes. Comparison of our data to analogous data from Laccaria bicolor and Schizophyllum commune revealed that the transcriptional regulation of nearly 70 loci is conserved and probably subjected to stabilizing selection. A Velvet domain-containing protein was found to be up-regulated in all three fungi, providing preliminary evidence of a possible role of the Velvet protein family in sexual development of basidiomycetes. The PBS-soluble proteome of C. cinerea primordia and mycelium was analyzed by shotgun LC-MS. This proteome data confirmed the presence of intracellular defense proteins in primordia. Conclusions This study shows that the exposure of different tissues in fungi to different types of antagonists shapes the expression pattern of defense loci in a tissue-specific manner. Furthermore, we identify a transcriptional circuitry conserved among basidiomycetes during fruiting body formation that involves, amongst other transcription factors, the up-regulation of a Velvet domain-containing protein. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-492) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Markus Künzler
- Department of Biology, Institute of Microbiology, ETH Zürich, Zürich, Switzerland.
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Zhou Y, Chen L, Fan X, Bian Y. De novo assembly of Auricularia polytricha transcriptome using Illumina sequencing for gene discovery and SSR marker identification. PLoS One 2014; 9:e91740. [PMID: 24626227 PMCID: PMC3953639 DOI: 10.1371/journal.pone.0091740] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 02/13/2014] [Indexed: 11/18/2022] Open
Abstract
Auricularia polytricha (Mont.) Sacc., a type of edible black-brown mushroom with a gelatinous and modality-specific fruiting body, is in high demand in Asia due to its nutritional and medicinal properties. Illumina Solexa sequenceing technology was used to generate very large transcript sequences from the mycelium and the mature fruiting body of A. polytricha for gene discovery and molecular marker development. De novo assembly generated 36,483 ESTs with an N50 length of 636 bp. A total of 28,108 ESTs demonstrated significant hits with known proteins in the nr database, and 94.03% of the annotated ESTs showed the greatest similarity to A. delicata, a related species of A. polytricha. Functional categorization of the Gene Ontology (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed the conservation of genes involved in various biological processes in A. polytricha. Gene expression profile analysis indicated that a total of 2,057 ESTs were differentially expressed, including 1,020 ESTs that were up-regulated in the mycelium and 1,037 up-regulated in the fruiting body. Functional enrichment showed that the ESTs associated with biosynthesis, metabolism and assembly of proteins were more active in fruiting body development. The expression patterns of homologous transcription factors indicated that the molecular mechanisms of fruiting body formation and development were not exactly the same as for other agarics. Interestingly, an EST encoding tyrosinase was significantly up-regulated in the fruiting body, indicating that melanins accumulated during the processes of the formation of the black-brown color of the fruiting body in A. polytricha development. In addition, a total of 1,715 potential SSRs were detected in this transcriptome. The transcriptome analysis of A. polytricha provides valuable sequence resources and numerous molecular markers to facilitate further functional genomics studies and genetic researches on this fungus.
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Affiliation(s)
- Yan Zhou
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lianfu Chen
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiuzhi Fan
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yinbing Bian
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
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Abstract
Proteins with membrane-attack complex/perforin (MACPF) domains are found in almost all kingdoms of life, and they have a variety of biological roles, including defence and attack, organism development, and cell adhesion and signalling. The distribution of these proteins in fungi appears to be restricted to some Pezizomycotina and Basidiomycota species only, in correlation with another group of proteins with unknown biological function, known as aegerolysins. These two protein groups coincide in only a few species, and they might operate in concert as cytolytic bi-component pore-forming agents. Representative proteins here include pleurotolysin B, which has a MACPF domain, and the aegerolysin-like protein pleurotolysin A, and the very similar ostreolysin A, which have been purified from oyster mushroom (Pleurotus ostreatus). These have been shown to act in concert to perforate natural and artificial lipid membranes with high cholesterol and sphingomyelin content. The aegerolysin-like proteins provide the membrane cholesterol/sphingomyelin selectivity and recruit oligomerised pleurotolysin B molecules, to create a membrane-inserted pore complex. The resulting protein structure has been imaged with electron microscopy, and it has a 13-meric rosette-like structure, with a central lumen that is ~4-5 nm in diameter. The opened transmembrane pore is non-selectively permeable for ions and smaller neutral solutes, and is a cause of cytolysis of a colloid-osmotic type. The biological significance of these proteins for the fungal life-style is discussed.
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Islam MT, Mohamedali A, Garg G, Khan JM, Gorse AD, Parsons J, Marshall P, Ranganathan S, Baker MS. Unlocking the puzzling biology of the black Périgord truffle Tuber melanosporum. J Proteome Res 2013; 12:5349-56. [PMID: 24147936 DOI: 10.1021/pr400650c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The black Périgord truffle (Tuber melanosporum Vittad.) is a highly prized food today, with its unique scent (i.e., perfume) and texture. Despite these attributes, it remains relatively poorly studied, lacking "omics" information to characterize its biology and biochemistry, especially changes associated with freshness and the proteins/metabolites responsible for its organoleptic properties. In this study, we have functionally annotated the truffle proteome from the 2010 T. melanosporum genome comprising 12,771 putative nonredundant proteins. Using sequential BLAST search strategies, we identified homologues for 2587 proteins with 2486 (96.0%) fungal homologues (available from http://biolinfo.org/protannotator/blacktruffle.php). A combined 1D PAGE and high-accuracy LC-MS/MS proteomic study was employed to validate the results of the functional annotation and identified 836 (6.5%) proteins, of which 47.5% (i.e., 397) were present in our bioinformatics studies. Our study, functionally annotating 6487 black Périgord truffle proteins and confirming 836 by proteomic experiments, is by far the most comprehensive study to date contributing significantly to the scientific community. This study has resulted in the functional characterization of novel proteins to increase our biological understanding of this organism and to uncover potential biomarkers of authenticity, freshness, and perfume maturation.
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Affiliation(s)
- Mohammad Tawhidul Islam
- Department of Chemistry and Biomolecular Sciences, Macquarie University , NSW 2109, Australia
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Cheng CK, Au CH, Wilke SK, Stajich JE, Zolan ME, Pukkila PJ, Kwan HS. 5'-Serial Analysis of Gene Expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea. BMC Genomics 2013; 14:195. [PMID: 23514374 PMCID: PMC3606632 DOI: 10.1186/1471-2164-14-195] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 03/08/2013] [Indexed: 12/02/2022] Open
Abstract
Background The transition from the vegetative mycelium to the primordium during fruiting body development is the most complex and critical developmental event in the life cycle of many basidiomycete fungi. Understanding the molecular mechanisms underlying this process has long been a goal of research on basidiomycetes. Large scale assessment of the expressed transcriptomes of these developmental stages will facilitate the generation of a more comprehensive picture of the mushroom fruiting process. In this study, we coupled 5'-Serial Analysis of Gene Expression (5'-SAGE) to high-throughput pyrosequencing from 454 Life Sciences to analyze the transcriptomes and identify up-regulated genes among vegetative mycelium (Myc) and stage 1 primordium (S1-Pri) of Coprinopsis cinerea during fruiting body development. Results We evaluated the expression of >3,000 genes in the two respective growth stages and discovered that almost one-third of these genes were preferentially expressed in either stage. This identified a significant turnover of the transcriptome during the course of fruiting body development. Additionally, we annotated more than 79,000 transcription start sites (TSSs) based on the transcriptomes of the mycelium and stage 1 primoridum stages. Patterns of enrichment based on gene annotations from the GO and KEGG databases indicated that various structural and functional protein families were uniquely employed in either stage and that during primordial growth, cellular metabolism is highly up-regulated. Various signaling pathways such as the cAMP-PKA, MAPK and TOR pathways were also identified as up-regulated, consistent with the model that sensing of nutrient levels and the environment are important in this developmental transition. More than 100 up-regulated genes were also found to be unique to mushroom forming basidiomycetes, highlighting the novelty of fruiting body development in the fungal kingdom. Conclusions We implicated a wealth of new candidate genes important to early stages of mushroom fruiting development, though their precise molecular functions and biological roles are not yet fully known. This study serves to advance our understanding of the molecular mechanisms of fruiting body development in the model mushroom C. cinerea.
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Affiliation(s)
- Chi Keung Cheng
- Food Research Centre and Food and Nutrition Sciences Programme, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, S.A.R., Hong Kong
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