1
|
Tong Z, Han X, Duan X, Lin J, Chen J, Xiao J, Gan Y, Gan B, Yan J. Genome-Wide Identification and Expression Analysis of the Cys2His2 Zinc Finger Protein Gene Family in Flammulina filiformis. J Fungi (Basel) 2024; 10:644. [PMID: 39330404 PMCID: PMC11433517 DOI: 10.3390/jof10090644] [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: 08/12/2024] [Revised: 09/06/2024] [Accepted: 09/09/2024] [Indexed: 09/28/2024] Open
Abstract
Zinc finger proteins (ZFPs) are essential transcription factors in eukaryotes, particularly the extensively studied C2H2 family, which is known for its involvement in various biological processes. This research provides a thorough examination and analysis of the C2H2-ZFP gene family in Flammulina filiformis. Using bioinformatics tools, 58 FfC2H2-ZFP genes spread across 11 chromosomes were identified and scrutinized in detail for their gene structures, protein characteristics, and phylogenetic relationships. The study of phylogenetics and synteny sheds light on the evolutionary relationships among C2H2-ZFPs in F. filiformis and other fungi, revealing a complex evolutionary past. The identification of conserved cis-regulatory elements in the gene promoter regions suggests intricate functionalities, particularly in the developmental and stress response pathways. By utilizing RNA-seq and qRT-PCR techniques, the expression patterns of these genes were explored across different developmental stages and tissues of F. filiformis, unveiling distinct expression profiles. Notably, significant expression variations were observed in the stipe elongation region and pilei of various sizes, indicating potential roles in fruiting body morphogenesis. This study enhances our knowledge of the C2H2-ZFP gene family in F. filiformis and lays the groundwork for future investigations into their regulatory mechanisms and applications in fungal biology and biotechnology.
Collapse
Affiliation(s)
- Zongjun Tong
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610000, China
| | - Xing Han
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610000, China
- Chengdu Agricultural Science and Technology Center, Chengdu 610095, China
| | - Xinlian Duan
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610000, China
| | - Junbin Lin
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610000, China
- Chengdu Agricultural Science and Technology Center, Chengdu 610095, China
| | - Jie Chen
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610000, China
- Chengdu Agricultural Science and Technology Center, Chengdu 610095, China
| | - Jihong Xiao
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610000, China
| | - Ying Gan
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610000, China
- Chengdu Agricultural Science and Technology Center, Chengdu 610095, China
| | - Bingcheng Gan
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610000, China
| | - Junjie Yan
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610000, China
| |
Collapse
|
2
|
Deng B, Zhang B, Xi L, Chang M, Meng J, Feng C, Liu J, Xu J. The Tissue Browning and Concomitant Toughening of Yellow Flammulina filiformis Stipes Is Caused by Oxidative Damage-Mediated Metabolic Disorder and Cell Wall Glycan Remodeling. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:16593-16603. [PMID: 37890451 DOI: 10.1021/acs.jafc.3c04398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/29/2023]
Abstract
The browning and associated toughening of fruiting body stipes are the main causes of declines in the commercial production of yellow Flammulina filiformis. The dynamic metabolic changes from the top to bottom stipe sections of yellow F. filiformis fruiting bodies were investigated by integrating physiological, transcriptomic, and metabolomic analyses. The results indicated that oxidative stress levels gradually increased accompanying the degree of tissue browning and toughening from the top to bottom sections of F. filiformis stipes. In-depth analysis showed that there were remarkable changes in the expression of genes, and the content of metabolites correlated with the primary and secondary metabolism of F. filiformis stipes. Interestingly, the expression levels of genes participating in chitosan biosynthesis and the degree of deacetylation of chitosan increased from top to bottom in F. filiformis stipes, implying that cell wall glycan remodeling may contribute to concomitant toughening of the browning of F. filiformis stipes.
Collapse
Affiliation(s)
- Bing Deng
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, Shanxi, China
- Key Laboratory of Shanxi Province for Loess Plateau Edible Fungi, Taigu 030801, Shanxi, China
| | - Benfeng Zhang
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Linhao Xi
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Mingchang Chang
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, Shanxi, China
- Shanxi Engineering Research Center of Edible Fungi, Taigu 030801, Shanxi, China
| | - Junlong Meng
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, Shanxi, China
- Shanxi Engineering Research Center of Edible Fungi, Taigu 030801, Shanxi, China
| | - Cuiping Feng
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, Shanxi, China
- Key Laboratory of Shanxi Province for Loess Plateau Edible Fungi, Taigu 030801, Shanxi, China
| | - Jingyu Liu
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, Shanxi, China
- Key Laboratory of Shanxi Province for Loess Plateau Edible Fungi, Taigu 030801, Shanxi, China
| | - Jin Xu
- College of Horticulture, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| |
Collapse
|
3
|
Hou L, Yan K, Dong S, Guo L, Liu J, Wang S, Chang M, Meng J. Transcriptome Analysis Revealed That Hydrogen Peroxide-Regulated Oxidative Phosphorylation Plays an Important Role in the Formation of Pleurotus ostreatus Cap Color. J Fungi (Basel) 2023; 9:823. [PMID: 37623594 PMCID: PMC10455351 DOI: 10.3390/jof9080823] [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: 06/14/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
Pleurotus ostreatus is widely cultivated in China. H2O2, as a signaling molecule, can regulate the formation of cap color, but its regulatory pathway is still unclear, severely inhibiting the breeding of dark-colored strains. In this study, 614 DEGs specifically regulated by H2O2 were identified by RNA-seq analysis. GO-enrichment analysis shows that DEGs can be significantly enriched in multiple pathways related to ATP synthesis, mainly including proton-transporting ATP synthesis complex, coupling factor F(o), ATP biosynthetic process, nucleoside triphosphate metabolic processes, ATP metabolic process, purine nucleoside triphosphate biosynthetic and metabolic processes, and purine ribonuclease triphosphate biosynthetic metabolic processes. Further KEGG analysis revealed that 23 DEGs were involved in cap color formation through the oxidative phosphorylation pathway. They were enriched in Complexes I, III, IV, and V in the respiratory chain. Further addition of exogenous uncoupling agents and ATP synthase inhibitors clarifies the important role of ATP synthesis in color formation. In summary, H2O2 may upregulate the expression of complex-encoding genes in the respiratory chain and promote ATP synthesis, thereby affecting the formation of cap color. The results of this study lay the foundation for the breeding of dark-colored strains of P. ostreatus and provide a basis for the color-formation mechanism of edible fungi.
Collapse
Affiliation(s)
- Ludan Hou
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, China; (L.H.); (K.Y.); (S.D.); (L.G.); (J.L.); (S.W.)
- Shanxi Key Laboratory of Edible Fungi for Loess Plateau, Taigu 030801, China
| | - Kexing Yan
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, China; (L.H.); (K.Y.); (S.D.); (L.G.); (J.L.); (S.W.)
| | - Shuai Dong
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, China; (L.H.); (K.Y.); (S.D.); (L.G.); (J.L.); (S.W.)
| | - Lifeng Guo
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, China; (L.H.); (K.Y.); (S.D.); (L.G.); (J.L.); (S.W.)
| | - Jingyu Liu
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, China; (L.H.); (K.Y.); (S.D.); (L.G.); (J.L.); (S.W.)
- Shanxi Key Laboratory of Edible Fungi for Loess Plateau, Taigu 030801, China
| | - Shurong Wang
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, China; (L.H.); (K.Y.); (S.D.); (L.G.); (J.L.); (S.W.)
- Shanxi Research Center for Engineering Technology of Edible Fungi, Taigu 030801, China
| | - Mingchang Chang
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, China; (L.H.); (K.Y.); (S.D.); (L.G.); (J.L.); (S.W.)
- Shanxi Research Center for Engineering Technology of Edible Fungi, Taigu 030801, China
| | - Junlong Meng
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, China; (L.H.); (K.Y.); (S.D.); (L.G.); (J.L.); (S.W.)
- Shanxi Research Center for Engineering Technology of Edible Fungi, Taigu 030801, China
| |
Collapse
|
4
|
Transcriptome Profiling Reveals Candidate Genes Related to Stipe Gradient Elongation of Flammulina filiformis. J Fungi (Basel) 2022; 9:jof9010064. [PMID: 36675885 PMCID: PMC9862757 DOI: 10.3390/jof9010064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023] Open
Abstract
Stipe gradient elongation is an important and remarkable feature in the development of most mushroom fruiting bodies. However, its molecular mechanism has rarely been described. Here, the decreasing trend of stipe elongation and increasing trend of cell length in a gradient from the top to the base of the stipe were determined in a model basidiomycete mushroom: Flammulina filiformis. According to RNA-seq results, 1409 differentially expressed genes (DEGs) were identified among elongation region (ER), transition region (TR), and stable region (SR) samples, including 26 transcription factors (TFs). Based on Short Time-series Expression Miner (STEM) clustering of DEGs, clusters 1 and 3, with obvious expression trends that were consistent with or in contrast to the elongation rate, were screened. The cluster 1 DEGs were mainly involved in the GO cellular component category and KEGG genetic information processing class; however, the cluster 3 DEGs were mainly involved in metabolic processes. Furthermore, qRT-PCR confirmed that key genes of the long-chain fatty acid synthesis pathway were involved in stipe gradient elongation and regulated by NADPH oxidase-derived ROS signaling molecules. These findings provide an essential basis for understanding the molecular mechanism of stipe gradient elongation.
Collapse
|
5
|
Liu Y, Ma X, Long Y, Yao S, Wei C, Han X, Gan B, Yan J, Xie B. Effects of β-1,6-Glucan Synthase Gene ( FfGS6) Overexpression on Stress Response and Fruit Body Development in Flammulina filiformis. Genes (Basel) 2022; 13:1753. [PMID: 36292637 PMCID: PMC9601887 DOI: 10.3390/genes13101753] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/20/2022] [Accepted: 09/26/2022] [Indexed: 12/29/2023] Open
Abstract
β-1, 6-glucan synthase is a key enzyme of β-1, 6-glucan synthesis, which plays a vital role in the cell wall cross-linking of fungi. However, the role of the β-1, 6-glucan synthase gene in the development of the fruiting body and the stress response of macrofungi is largely unknown. In this study, four overexpression transformants of the β-1, 6-glucan synthase gene (FfGS6) were successfully obtained, and gene function was studied in Flammulina filiformis. The overexpression of FfGS6 can increase the width of mycelium cells and improve the tolerance ability under mechanical injury and oxidative stress. Moreover, FfGS6 gene expression fluctuated in up-regulation during the recovery process of mycelium injury but showed a negative correlation with H2O2 concentration. Fruiting body phenotype tests showed that mycelia's recovery ability after scratching improved when the FfGS6 gene was overexpressed. However, primordia formation and the stipe elongation ability were significantly inhibited. Our findings indicate that FfGS6 is involved in regulating mycelial cell morphology, the mycelial stress response, and fruit body development in F. filiformis.
Collapse
Affiliation(s)
- Yuanyuan Liu
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinbin Ma
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ying Long
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sen Yao
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chuanzheng Wei
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xing Han
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610213, China
| | - Bingcheng Gan
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610213, China
| | - Junjie Yan
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610213, China
| | - Baogui Xie
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| |
Collapse
|
6
|
Yao S, Wei C, Lin H, Zhang P, Liu Y, Deng Y, Huang Q, Xie B. Cystathionine Gamma-Lyase Regulate Psilocybin Biosynthesis in Gymnopilus dilepis Mushroom via Amino Acid Metabolism Pathways. J Fungi (Basel) 2022; 8:870. [PMID: 36012858 PMCID: PMC9410116 DOI: 10.3390/jof8080870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 12/02/2022] Open
Abstract
As a potential medicine for the treatment of depression, psilocybin has gradually attracted attention. To elucidate the molecular mechanism regulating psilocybin synthesis in Gymnopilus dilepis, ultra-performance liquid chromatography (UPLC) was used to detect the changes in psilocybin content after S-adenosyl-l-homocysteine (SAH) treatment and the changes of psilocybin content in different parts (stipe and pileus), and RNA-Seq was used to explore the mechanism of psilocybin content changes. In this study, the psilocybin content in G. dilepis mycelia treated with SAH was significantly lower than that in the control group, and the content of psilocybin in the stipe was significantly higher than that in the pileus. Transcriptome analysis revealed that differential expression genes (DEGs) were associated with cysteine and methionine metabolism. In particular, the transcription levels of genes encoding Cystathionine gamma-lyase (CTH) in different treatments and different parts were positively correlated with psilocybin content. In addition, we found that the exogenous addition of CTH activity inhibitor (DL-propargylglycine, PAG) could reduce the content of psilocybin and L-serine, and the content of psilocybin and L-serine returned to normal levels after L-cysteine supplementation, suggesting that psilocybin synthesis may be positively correlated with L-cysteine or CTH, and L-cysteine regulates the synthesis of psilocybin by affecting L-serine and 4-hydroxy-L-tryptophan. In conclusion, this study revealed a new molecular mechanism that affects psilocybin biosynthesis, which can provide a theoretical basis for improving psilocybin synthesis and the possibility for the development of biomedicine.
Collapse
Affiliation(s)
- Sen Yao
- Mycological Research Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chuanzheng Wei
- Mycological Research Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hui Lin
- Mycological Research Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Peng Zhang
- Mycological Research Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuanyuan Liu
- Mycological Research Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Youjin Deng
- Mycological Research Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qianhui Huang
- College of Life Science, Ningde Normal University, Ningde 352100, China
| | - Baogui Xie
- Mycological Research Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| |
Collapse
|