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Jiang H, Wang H, Wang X, Wang Y, Song R, Yuan S, Fan Z, Meng D. Methyl jasmonate differentially and tissue-specifically regulated the expression of arginine catabolism-related genes and proteins in Agaricus bisporus mushrooms during storage. Fungal Genet Biol 2024; 170:103864. [PMID: 38199492 DOI: 10.1016/j.fgb.2024.103864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/26/2023] [Accepted: 01/07/2024] [Indexed: 01/12/2024]
Abstract
Methyl jasmonate (MeJA)-regulated postharvest quality retention of Agaricus bisporus fruiting bodies is associated with arginine catabolism. However, the mechanism of MeJA-regulated arginine catabolism in edible mushrooms is still unclear. This study aimed to investigate the regulatory modes of MeJA on the expression of arginine catabolism-related genes and proteins in intact and different tissues of A. bisporus mushrooms during storage. Results showed that exogenous MeJA treatment activated endogenous JA biosynthesis in A. bisporus mushrooms, and differentially and tissue-specifically regulated the expression of arginine catabolism-related genes (AbARG, AbODC, AbSPE-SDH, AbSPDS, AbSAMDC, and AbASL) and proteins (AbARG, AbSPE-SDH, AbASL, and AbASS). MeJA caused no significant change in AbASS expression but resulted in a dramatic increase in AbASS protein level. Neither the expression of the AbSAMS gene nor the AbSAMS protein was conspicuously altered upon MeJA treatment. Additionally, MeJA reduced the contents of arginine and ornithine and induced the accumulation of free putrescine and spermidine, which was closely correlated with MeJA-regulated arginine catabolism-related genes and proteins. Hence, the results suggested that the differential and tissue-specific regulation of arginine catabolism-related genes and proteins by MeJA contributed to their selective involvement in the postharvest continuing development and quality retention of button mushrooms.
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Affiliation(s)
- Hanyue Jiang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Huadong Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China; Shandong drug and food vocational college, Weihai 264200, People's Republic of China
| | - Xiuhong Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Yating Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Rui Song
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Shuai Yuan
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Zhenchuan Fan
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Demei Meng
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China; Tianjin Gasin-DH Preservation Technology Co., Ltd, Tianjin 300300, People's Republic of China.
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Lodha T, Narvekar S, Karodi P. Classification of uncultivated anammox bacteria and Candidatus Uabimicrobium into new classes and provisional nomenclature as Candidatus Brocadiia classis nov. and Candidatus Uabimicrobiia classis nov. of the phylum Planctomycetes and novel family Candidatus Scalinduaceae fam. nov to accommodate the genus Candidatus Scalindua. Syst Appl Microbiol 2021; 44:126272. [PMID: 34735804 DOI: 10.1016/j.syapm.2021.126272] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 11/26/2022]
Abstract
The phylum Planctomycetes is metabolically unique group of bacteria divided in two classes Planctomycetia and Phycisphaerae. Anaerobic ammonia-oxidizing (anammox) bacteria are the uncultured representatives of the phylum Planctomycetes. Anammox bacterial genera are placed in the family Candidatus (Ca.) Brocadiaceae of the order Ca. Brocadiales, assigned to the class Planctomycetia. Phylogenetic analysis, showed that the anammox bacteria and Ca. Uabimicrobium form a divergent clade from the rest of the cultured representatives of the phylum Planctomycetes. The phylogenetic study, pairwise distance and Average Amino acid Identity (AAI) showed that anammox bacteria don't belong to the classes Planctomycetia and Phycisphaerae. Anammox bacteria and Ca. Uabimicrobium form a deep-branching third clade in the phylogenetic analysis indicating that it is the most ancient third class within the phylum Planctomycetes. Phenotypic characters also separate anammox bacteria from classes Planctomycetia and Phycisphaerae. Therefore, based on phenotypic, phylogenetic, pairwise distance, AAI and phylogenomic analysis we propose a novel class Ca. Brocadiia to accommodate the order Ca. Brocadiales of anammox bacteria except Ca. Anammoximicrobium. Genera Ca. Jettenia, Ca. Anammoxoglobus, Ca. Kuenenia and Ca. Brocadia show their phylogenetic affiliation to the family Ca. Brocadiaceae. However, Ca. Scalindua showed a distant relationship with the family Ca. Brocadiaceae. Therefore, we suggest the exclusion of the genus Ca. Scalindua from the family Ca. Brocadiaceae; and propose its inclusion under a novel family with a provisional name as Ca. Scalinduaceae fam. nov. Similarly, Ca. Uabimicrobium amporphum showed distinct phylogenetic affiliation, therefore we propose a novel class Ca. Uabimicrobiia classis nov. to accommodate the genus Ca. Uabimicrobium.
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Affiliation(s)
- Tushar Lodha
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411021, India.
| | - Simran Narvekar
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411021, India
| | - Prachi Karodi
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411021, India
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3
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Toplis B, Bosch C, Schwartz IS, Kenyon C, Boekhout T, Perfect JR, Botha A. The virulence factor urease and its unexplored role in the metabolism of Cryptococcus neoformans. FEMS Yeast Res 2021; 20:5850754. [PMID: 32490521 DOI: 10.1093/femsyr/foaa031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 06/01/2020] [Indexed: 12/25/2022] Open
Abstract
Cryptococcal urease is believed to be important for the degradation of exogenous urea that the yeast encounters both in its natural environment and within the human host. Endogenous urea produced by the yeast's own metabolic reactions, however, may also serve as a substrate for the urease enzyme. Using wild-type, urease-deletion mutant and urease-reconstituted strains of Cryptococcus neoformans H99, we studied reactions located up- and downstream from endogenous urea. We demonstrated that urease is important for cryptococcal growth and that, compared to nutrient-rich conditions at 26°C, urease activity is higher under nutrient-limited conditions at 37°C. Compared to cells with a functional urease enzyme, urease-deficient cells had significantly higher intracellular urea levels and also showed more arginase activity, which may act as a potential source of endogenous urea. Metabolic reactions linked to arginase were also affected, since urease-positive and urease-negative cells differed with respect to agmatinase activity, polyamine synthesis, and intracellular levels of proline and reactive oxygen species. Lastly, urease-deficient cells showed higher melanin levels at 26°C than wild-type cells, while the inverse was observed at 37°C. These results suggest that cryptococcal urease is associated with the functioning of key metabolic pathways within the yeast cell.
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Affiliation(s)
- Barbra Toplis
- Department of Microbiology, Stellenbosch University, Matieland 7602, Stellenbosch, South Africa
| | - Caylin Bosch
- Department of Microbiology, Stellenbosch University, Matieland 7602, Stellenbosch, South Africa
| | - Ilan S Schwartz
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G3
| | - Chris Kenyon
- Sexually Transmitted Infection Unit, Institute of Tropical Medicine, 2000 Antwerp, Belgium.,Department of Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, 3584CT Utrecht, The Netherlands.,Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - John R Perfect
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710-1000, North Carolina, USA
| | - Alfred Botha
- Department of Microbiology, Stellenbosch University, Matieland 7602, Stellenbosch, South Africa
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Valenzuela-Cota DF, Morales-Amparano MB, Plascencia-Jatomea M, Martínez-Cruz O, Hernández-García F, Vázquez-Moreno L, Rosas-Burgos EC, Huerta-Ocampo JÁ. Proteomic analysis of the inhibitory effect of the butanolic fraction of Jacquinia macrocarpa on Fusarium verticillioides. Can J Microbiol 2020; 66:535-548. [PMID: 32407666 DOI: 10.1139/cjm-2020-0127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Jacquinia macrocarpa, a plant native to northwestern Mexico, has an inhibitory effect against phytopathogenic fungi. Previous studies have shown that the butanolic extract of J. macrocarpa causes retardation and atrophy in mycelial growth of Fusarium verticillioides. However, the action mechanism of this extract is unknown. We used a proteomics approach to understand the inhibitory effect of J. macrocarpa butanolic extract, based on differential protein accumulation in F. verticillioides. Proteins were extracted from F. verticillioides cultured in Czapek broth with and without 202.12 μg/mL (IC50) of butanolic extract of J. macrocarpa. Thirty-eight protein spots showing statistically significant changes (ANOVA, p < 0.01) and at least a 2-fold change in abundance between experimental conditions were analyzed by mass spectrometry. Identified proteins were grouped into different biological processes according to Gene Ontology, among them were amino acid metabolism, protein folding and stabilization, protein degradation, protein transport, carbohydrate metabolism, oxidative stress response, and miscellaneous. This work is the first report of changes in the proteomic profile of F. verticillioides exposed to the J. macrocarpa extract. This information provides new insights into the inhibitory mechanism of the extract and represents a starting point for dissection of the fungal response against the J. macrocarpa extract components.
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Affiliation(s)
- Daniel F Valenzuela-Cota
- Universidad de Sonora, Blvd. Luis Encinas y Rosales s/n, Col. Centro, C.P. 83000, Hermosillo, Sonora, México
| | - Martha B Morales-Amparano
- Coordinación de Ciencia de los Alimentos, Centro de Investigación en Alimentación y Desarrollo, A.C., Carretera Gustavo Enrique Astiazarán Rosas No. 46, Colonia La Victoria, C.P. 83304, Hermosillo, Sonora, México
| | - Maribel Plascencia-Jatomea
- Universidad de Sonora, Blvd. Luis Encinas y Rosales s/n, Col. Centro, C.P. 83000, Hermosillo, Sonora, México
| | - Oliviert Martínez-Cruz
- Universidad de Sonora, Blvd. Luis Encinas y Rosales s/n, Col. Centro, C.P. 83000, Hermosillo, Sonora, México
| | - Francisca Hernández-García
- Universidad Miguel Hernández de Elche, Carretera de Bienel Km 3.2 s/n, C.P. 03312, Orihuela, Alacant, España
| | - Luz Vázquez-Moreno
- Coordinación de Ciencia de los Alimentos, Centro de Investigación en Alimentación y Desarrollo, A.C., Carretera Gustavo Enrique Astiazarán Rosas No. 46, Colonia La Victoria, C.P. 83304, Hermosillo, Sonora, México
| | - Ema C Rosas-Burgos
- Universidad de Sonora, Blvd. Luis Encinas y Rosales s/n, Col. Centro, C.P. 83000, Hermosillo, Sonora, México
| | - José Á Huerta-Ocampo
- CONACYT-Centro de Investigación en Alimentación y Desarrollo, A.C., Carretera Gustavo Enrique Astiazarán Rosas No. 46, Colonia La Victoria, C.P. 83304, Hermosillo, Sonora, México
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Sakamoto Y. Influences of environmental factors on fruiting body induction, development and maturation in mushroom-forming fungi. FUNGAL BIOL REV 2018. [DOI: 10.1016/j.fbr.2018.02.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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iTRAQ-based quantitative proteome revealed metabolic changes of Flammulina velutipes mycelia in response to cold stress. J Proteomics 2017; 156:75-84. [PMID: 28099886 DOI: 10.1016/j.jprot.2017.01.009] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 01/03/2017] [Accepted: 01/12/2017] [Indexed: 12/26/2022]
Abstract
Temperature is one of the pivotal factors influencing mycelium growth and fruit-body formation of Flammulina velutipes. To gain insights into hyphae growth and fruit-body formation events and facilitate the identification of potential stage-specific biomarker candidates, we investigated the proteome response of F. velutipes mycelia to cold stresses using iTRAQ-coupled two-dimensional liquid chromatography tandem mass spectrometry (2D LC-MS/MS) technique. Among 1198 proteins identified with high confidence, a total of 63 displayed altered expression level after cold stress treatments. In-depth data analysis reveals that differentially expressed proteins were involved in a variety of cellular processes, particularly metabolic processes. Among the 31 up-regulated proteins, 24 (77.42%) were associated with 22 specific KEGG pathways. These up-regulated proteins could possibly serve as potential biomarkers to study the molecular mechanisms of F. velutipes mycelia response to cold stresses. These data of the proteins might provide valuable evidences to better understand the molecular mechanisms of mycelium resistance to cold stress and fruit-body formation in fungi. BIOLOGICAL SIGNIFICANCE Low-temperature is one of the pivotal factors in some Flammulina velutipes industrial processes influencing mycelium growth, inducing primordia and controlling fruit-body development. Preliminary study has indicated that effectively regulating cultivation could augment the yield by controlling optimal cold stress level on mycelia. However, we are still far from understanding the molecular and physiological mechanisms of adaptation of these fungi at cold stress. In the present study, the experiments reported above were undertaken to investigate chronological changes of protein expression during F. velutipes mycelia in response to cold stress by using iTRAQ-coupled 2D LC-MS/MS technique. This result would provide new insights to the underlying mycelium growth and fruit-body formation mechanisms of basidiomycetes under cold stress.
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Mendoza-Mendoza A, Steyaert J, Nieto-Jacobo MF, Holyoake A, Braithwaite M, Stewart A. Identification of growth stage molecular markers in Trichoderma sp. 'atroviride type B' and their potential application in monitoring fungal growth and development in soil. MICROBIOLOGY-SGM 2015; 161:2110-26. [PMID: 26341342 DOI: 10.1099/mic.0.000167] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Several members of the genus Trichoderma are biocontrol agents of soil-borne fungal plant pathogens. The effectiveness of biocontrol agents depends heavily on how they perform in the complex field environment. Therefore, the ability to monitor and track Trichoderma within the environment is essential to understanding biocontrol efficacy. The objectives of this work were to: (a) identify key genes involved in Trichoderma sp. 'atroviride type B' morphogenesis; (b) develop a robust RNA isolation method from soil; and (c) develop molecular marker assays for characterizing morphogenesis whilst in the soil environment. Four cDNA libraries corresponding to conidia, germination, vegetative growth and conidiogenesis were created, and the genes identified by sequencing. Stage specificity of the different genes was confirmed by either Northern blot or quantitative reverse-transcriptase PCR (qRT-PCR) analysis using RNA from the four stages. con10, a conidial-specific gene, was observed in conidia, as well as one gene also involved in subsequent stages of germination (L-lactate/malate dehydrogenase encoding gene). The germination stage revealed high expression rates of genes involved in amino acid and protein biosynthesis, while in the vegetative-growth stage, genes involved in differentiation, including the mitogen-activated protein kinase kinase similar to Kpp7 from Ustilago maydis and the orthologue to stuA from Aspergillus nidulans, were preferentially expressed. Genes involved in cell-wall synthesis were expressed during conidiogenesis. We standardized total RNA isolation from Trichoderma sp. 'atroviride type B' growing in soil and then examined the expression profiles of selected genes using qRT-PCR. The results suggested that the relative expression patterns were cyclic and not accumulative.
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Affiliation(s)
- Artemio Mendoza-Mendoza
- 1 Bio-Protection Research Centre, PO Box 85084, Lincoln University, Lincoln 7647, New Zealand
| | - Johanna Steyaert
- 1 Bio-Protection Research Centre, PO Box 85084, Lincoln University, Lincoln 7647, New Zealand
| | | | - Andrew Holyoake
- 1 Bio-Protection Research Centre, PO Box 85084, Lincoln University, Lincoln 7647, New Zealand
| | - Mark Braithwaite
- 1 Bio-Protection Research Centre, PO Box 85084, Lincoln University, Lincoln 7647, New Zealand
| | - Alison Stewart
- 1 Bio-Protection Research Centre, PO Box 85084, Lincoln University, Lincoln 7647, New Zealand 2 Marrone Bio Innovations, 1540 Drew Avenue, Davis, California 95618, USA
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Eastwood DC, Herman B, Noble R, Dobrovin-Pennington A, Sreenivasaprasad S, Burton KS. Environmental regulation of reproductive phase change in Agaricus bisporus by 1-octen-3-ol, temperature and CO₂. Fungal Genet Biol 2013; 55:54-66. [PMID: 23354075 DOI: 10.1016/j.fgb.2013.01.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 12/03/2012] [Accepted: 01/01/2013] [Indexed: 11/25/2022]
Abstract
Reproductive phase change from vegetative mycelium to the initiation of fruiting in Agaricus bisporus is regulated in large part by the sensing of environmental conditions. A model is proposed in which three separate environmental factors exert control at different stages of the reproductive developmental process change. The eight carbon volatile 1-octen-3-ol controls the early differentiation from vegetative hyphae to multicellular knots; temperature reduction is essential for the later differentiation of primodia; and carbon dioxide level exerts quantitative control on the number of fruiting bodies developed. Analysis of transcriptomic changes during the reproductive phase change was carried out with initiation-specific microarrays, and the newly published A. bisporus genome was used to analyse the promoter regions of differentially regulated genes. Our studies have shown there to be both early and late initiation responses relating to sensing of eight carbon volatiles and temperature respectively. A subset of 45 genes was transcriptionally regulated during the reproductive phase change which exhibited a range of functions including cell structure, nitrogen and carbon metabolism, and sensing and signalling. Three gene clusters linking increased transcription with developmental stage were identified. Analysis of promoter regions revealed cluster-specific conserved motifs indicative of co-ordinated regulation of transcription.
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Affiliation(s)
- Daniel C Eastwood
- Department of Bioscience, University of Swansea, Singleton Park, Swansea SA2 8PP, United Kingdom.
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Jin H, Liu J, Liu J, Huang X. Forms of nitrogen uptake, translocation, and transfer via arbuscular mycorrhizal fungi: a review. SCIENCE CHINA-LIFE SCIENCES 2012; 55:474-82. [PMID: 22744177 DOI: 10.1007/s11427-012-4330-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 04/06/2012] [Indexed: 11/24/2022]
Abstract
Arbuscular mycorrhizal (AM) fungi are obligate symbionts that colonize the roots of more than 80% of land plants. Experiments on the relationship between the host plant and AM in soil or in sterile root-organ culture have provided clear evidence that the extraradical mycelia of AM fungi uptake various forms of nitrogen (N) and transport the assimilated N to the roots of the host plant. However, the uptake mechanisms of various forms of N and its translocation and transfer from the fungus to the host are virtually unknown. Therefore, there is a dearth of integrated models describing the movement of N through the AM fungal hyphae. Recent studies examined Ri T-DNA-transformed carrot roots colonized with AM fungi in (15)N tracer experiments. In these experiments, the activities of key enzymes were determined, and expressions of genes related to N assimilation and translocation pathways were quantified. This review summarizes and discusses the results of recent research on the forms of N uptake, transport, degradation, and transfer to the roots of the host plant and the underlying mechanisms, as well as research on the forms of N and carbon used by germinating spores and their effects on amino acid metabolism. Finally, a pathway model summarizing the entire mechanism of N metabolism in AM fungi is outlined.
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Affiliation(s)
- Hairu Jin
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China.
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10
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Tian C, Kasiborski B, Koul R, Lammers PJ, Bücking H, Shachar-Hill Y. Regulation of the nitrogen transfer pathway in the arbuscular mycorrhizal symbiosis: gene characterization and the coordination of expression with nitrogen flux. PLANT PHYSIOLOGY 2010; 153:1175-87. [PMID: 20448102 PMCID: PMC2899933 DOI: 10.1104/pp.110.156430] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 05/05/2010] [Indexed: 05/19/2023]
Abstract
The arbuscular mycorrhiza (AM) brings together the roots of over 80% of land plant species and fungi of the phylum Glomeromycota and greatly benefits plants through improved uptake of mineral nutrients. AM fungi can take up both nitrate and ammonium from the soil and transfer nitrogen (N) to host roots in nutritionally substantial quantities. The current model of N handling in the AM symbiosis includes the synthesis of arginine in the extraradical mycelium and the transfer of arginine to the intraradical mycelium, where it is broken down to release N for transfer to the host plant. To understand the mechanisms and regulation of N transfer from the fungus to the plant, 11 fungal genes putatively involved in the pathway were identified from Glomus intraradices, and for six of them the full-length coding sequence was functionally characterized by yeast complementation. Two glutamine synthetase isoforms were found to have different substrate affinities and expression patterns, suggesting different roles in N assimilation. The spatial and temporal expression of plant and fungal N metabolism genes were followed after nitrate was added to the extraradical mycelium under N-limited growth conditions using hairy root cultures. In parallel experiments with (15)N, the levels and labeling of free amino acids were measured to follow transport and metabolism. The gene expression pattern and profiling of metabolites involved in the N pathway support the idea that the rapid uptake, translocation, and transfer of N by the fungus successively trigger metabolic gene expression responses in the extraradical mycelium, intraradical mycelium, and host plant.
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Affiliation(s)
- Chunjie Tian
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA.
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11
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Characterization of the post-harvest changes in gene transcription in the gill of the Lentinula edodes fruiting body. Curr Genet 2009; 55:409-23. [PMID: 19488757 DOI: 10.1007/s00294-009-0255-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2009] [Revised: 05/07/2009] [Accepted: 05/13/2009] [Indexed: 01/19/2023]
Abstract
We compared the gene expression patterns of Lentinula edodes fresh fruiting bodies and fruiting bodies 3 days after harvest, by suppression subtractive hybridization, to characterize the physiologic changes that occur after harvest, such as gill browning and cell wall lysis of the fruiting body, which are responsible for the loss of food quality and value. We found increase of transcription levels of several enzyme encoding genes, such as, two phenol oxidases encoding genes (tyr tyrosinase, lcc4 laccase), and several cell wall degradation-related enzyme-encoding genes, such as mixed-linked glucanase (mlg1), chitinases (chi1, chi2), chitin deacetylase (chd1), and chitosanase (cho1), after harvesting. We isolated a putative transcription factor-encoding gene (L. edodes exp1) with high similarity to exp1 from Coprinopsis cinerea, which is involved in autolysis of the cap during spore diffusion. Transcription of L. edodes exp1 increased post-harvest, which suggests that its target genes are up-regulated after harvesting. These enzymes and the transcription factor may be involved in L. edodes fruiting body senescence.
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12
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Eastwood DC, Mead A, Sergeant MJ, Burton KS. Statistical modelling of transcript profiles of differentially regulated genes. BMC Mol Biol 2008; 9:66. [PMID: 18651954 PMCID: PMC2525656 DOI: 10.1186/1471-2199-9-66] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Accepted: 07/23/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The vast quantities of gene expression profiling data produced in microarray studies, and the more precise quantitative PCR, are often not statistically analysed to their full potential. Previous studies have summarised gene expression profiles using simple descriptive statistics, basic analysis of variance (ANOVA) and the clustering of genes based on simple models fitted to their expression profiles over time. We report the novel application of statistical non-linear regression modelling techniques to describe the shapes of expression profiles for the fungus Agaricus bisporus, quantified by PCR, and for E. coli and Rattus norvegicus, using microarray technology. The use of parametric non-linear regression models provides a more precise description of expression profiles, reducing the "noise" of the raw data to produce a clear "signal" given by the fitted curve, and describing each profile with a small number of biologically interpretable parameters. This approach then allows the direct comparison and clustering of the shapes of response patterns between genes and potentially enables a greater exploration and interpretation of the biological processes driving gene expression. RESULTS Quantitative reverse transcriptase PCR-derived time-course data of genes were modelled. "Split-line" or "broken-stick" regression identified the initial time of gene up-regulation, enabling the classification of genes into those with primary and secondary responses. Five-day profiles were modelled using the biologically-oriented, critical exponential curve, y(t) = A + (B + Ct)Rt + epsilon. This non-linear regression approach allowed the expression patterns for different genes to be compared in terms of curve shape, time of maximal transcript level and the decline and asymptotic response levels. Three distinct regulatory patterns were identified for the five genes studied. Applying the regression modelling approach to microarray-derived time course data allowed 11% of the Escherichia coli features to be fitted by an exponential function, and 25% of the Rattus norvegicus features could be described by the critical exponential model, all with statistical significance of p < 0.05. CONCLUSION The statistical non-linear regression approaches presented in this study provide detailed biologically oriented descriptions of individual gene expression profiles, using biologically variable data to generate a set of defining parameters. These approaches have application to the modelling and greater interpretation of profiles obtained across a wide range of platforms, such as microarrays. Through careful choice of appropriate model forms, such statistical regression approaches allow an improved comparison of gene expression profiles, and may provide an approach for the greater understanding of common regulatory mechanisms between genes.
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Affiliation(s)
- Daniel C Eastwood
- Warwick HRI, University of Warwick, Wellesbourne, Warwickshire, CV35 9EF, UK.
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13
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Eastwood DC, Challen MP, Zhang C, Jenkins H, Henderson J, Burton KS. Hairpin-mediated down-regulation of the urea cycle enzyme argininosuccinate lyase in Agaricus bisporus. ACTA ACUST UNITED AC 2008; 112:708-16. [PMID: 18499425 DOI: 10.1016/j.mycres.2008.01.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Revised: 12/18/2007] [Accepted: 01/24/2008] [Indexed: 11/27/2022]
Abstract
A double-stranded (ds) RNA hairpin-mediated down-regulation system was developed for the cultivated mushroom Agaricus bisporus, and the role of the urea cycle enzyme argininosuccinate lyase (asl) in mushroom post-harvest development was investigated. Hairpin expression vectors were constructed to initiate down-regulation of asl and introduced into A. bisporus by Agrobacterium tumefaciens-mediated transformation. Transcripts of asl were significantly reduced (93.1 and 99.9%) in two transformants and hairpin vector transgene sequences were maintained throughout sporophore development. Single and multiple hairpin integration events were observed in Southern analysis. Transformants with down-regulated asl exhibited reduced yield and cap expansion during post-harvest sporophore development. There were no detectable differences in urea levels between the hairpin-transformed and control strains. This is the first report of reduced gene expression resulting from the introduction of dsRNA hairpins in A. bisporus and the applications of this technology will facilitate functional studies in the mushroom.
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Wagemaker MJM, Eastwood DC, Welagen J, van der Drift C, Jetten MSM, Burton K, Van Griensven LJLD, Op den Camp HJM. The role of ornithine aminotransferase in fruiting body formation of the mushroom Agaricus bisporus. ACTA ACUST UNITED AC 2007; 111:909-18. [PMID: 17703933 DOI: 10.1016/j.mycres.2007.05.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Accepted: 05/25/2007] [Indexed: 10/23/2022]
Abstract
The complete oat gene and cDNA from the commercial mushroom, Agaricus bisporus, encoding ornithine aminotransferase (OAT) was characterized. The gene encodes a 466 amino acid protein and provides the first fully reported homobasidiomycete OAT protein sequence. The gene is interrupted by ten introns, and no mitochondrial targeting motif was present pointing to a cytoplasmic localization. The function of the gene was demonstrated by complementation of a Saccharomyces cerevisiae mutant unable to utilize ornithine as a sole source of nitrogen with an A. bisporus oat cDNA construct. Northern analysis of the oat gene together with the pruA gene (encoding Delta(1)-pyrroline-5-carboxylate dehydrogenase) showed that transcripts of both genes were lower during the first stages of fruiting body development. The higher expression of the oat gene in later stages of development, suggests the importance of ornithine metabolism for the redistribution of metabolites in the developing mushroom. Hplc analysis of all amino acids revealed that ornithine levels increased during fruiting body development whereas proline levels fell.
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Affiliation(s)
- Matthijs J M Wagemaker
- Department of Microbiology, IWWR, Radboud University Nijmegen, Toernooiveld 1, NL-6525 ED Nijmegen, The Netherlands
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