1
|
Kikuta H, Aramaki T, Mabu S, Akada R, Hoshida H. The presence of an intron relieves gene repression caused by promoter-proximal four-bp specific sequences in yeast. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194982. [PMID: 37659722 DOI: 10.1016/j.bbagrm.2023.194982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/24/2023] [Accepted: 08/24/2023] [Indexed: 09/04/2023]
Abstract
Introns can enhance gene expression in eukaryotic cells in a process called intron-mediated enhancement (IME). The levels of enhancement are affected not only by the intron sequence but also by coding sequences (CDSs). However, the parts of CDSs responsible for mediating IME have not yet been identified. In this study, we identified an IME-mediating sequence by analyzing three pairs of IME-sensitive and -insensitive CDSs in Saccharomyces cerevisiae. Expression of the CDSs yCLuc, yRoGLU1, and KmBGA1 was enhanced by the presence of an intron (i.e., they were IME sensitive), but the expression of each corresponding codon-changed CDS, which encoded the identical amino acid sequence, was not enhanced (i.e., they were IME insensitive). Interestingly, the IME-insensitive CDSs showed higher expression levels that were like intron-enhanced expression of IME-sensitive CDSs, suggesting that expression of IME-sensitive CDSs was repressed. A four-nucleotide sequence (TCTT) located in the promoter-proximal position of either the untranslated or coding region was found to be responsible for repression in IME-sensitive CDSs, and repression caused by the TCTT sequence was relieved by the presence of an intron. Further, it was found that the expression of intron-containing yeast-native genes, UBC4 and MPT5, was repressed by TCTT in the CDS but relieved by the introns. These results indicate that TCTT sequences in promoter-proximal positions repress gene expression and that introns play a role in relieving gene repression caused by sequences such as TCTT.
Collapse
Affiliation(s)
- Hiroki Kikuta
- Division of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube 755-8611, Japan
| | - Takahiro Aramaki
- Division of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube 755-8611, Japan
| | - Shingo Mabu
- Division of Electrical, Electronic and Information Engineering, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube 755-8611, Japan
| | - Rinji Akada
- Division of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube 755-8611, Japan; Research Center for Thermotolerant Microbial Resources, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8315, Japan; Yamaguchi University Biomedical Engineering Center, 2-16-1 Tokiwadai, Ube 755-8611, Japan
| | - Hisashi Hoshida
- Division of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube 755-8611, Japan; Research Center for Thermotolerant Microbial Resources, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8315, Japan; Yamaguchi University Biomedical Engineering Center, 2-16-1 Tokiwadai, Ube 755-8611, Japan.
| |
Collapse
|
2
|
Arellano-Caicedo C, Ohlsson P, Bengtsson M, Beech JP, Hammer EC. Habitat complexity affects microbial growth in fractal maze. Curr Biol 2023; 33:1448-1458.e4. [PMID: 36933553 DOI: 10.1016/j.cub.2023.02.064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 01/09/2023] [Accepted: 02/21/2023] [Indexed: 03/19/2023]
Abstract
The great variety of earth's microorganisms and their functions are attributed to the heterogeneity of their habitats, but our understanding of the impact of this heterogeneity on microbes is limited at the microscale. In this study, we tested how a gradient of spatial habitat complexity in the form of fractal mazes influenced the growth, substrate degradation, and interactions of the bacterial strain Pseudomonas putida and the fungal strain Coprinopsis cinerea. These strains responded in opposite ways: complex habitats strongly reduced fungal growth but, in contrast, increased the abundance of bacteria. Fungal hyphae did not reach far into the mazes and forced bacteria to grow in deeper regions. Bacterial substrate degradation strongly increased with habitat complexity, even more than bacterial biomass, up to an optimal depth, while the most remote parts of the mazes showed both decreased biomass and substrate degradation. These results suggest an increase in enzymatic activity in confined spaces, where areas may experience enhanced microbial activity and resource use efficiency. Very remote spaces showing a slower turnover of substrates illustrate a mechanism which may contribute to the long-term storage of organic matter in soils. We demonstrate here that the sole effect of spatial microstructures affects microbial growth and substrate degradation, leading to differences in local microscale spatial availability. These differences might add up to considerable changes in nutrient cycling at the macroscale, such as contributing to soil organic carbon storage.
Collapse
Affiliation(s)
| | - Pelle Ohlsson
- Department of Biomedical Engineering, Lund University, Ole Römers väg 3, 223 63 Lund, Sweden
| | - Martin Bengtsson
- Department of Biomedical Engineering, Lund University, Ole Römers väg 3, 223 63 Lund, Sweden
| | - Jason P Beech
- Division of Solid State Physics, Lund University, Sölvegatan 16, 223 63 Lund, Sweden
| | - Edith C Hammer
- Department of Biology, Lund University, Sölvegatan 35, 223 62 Lund, Sweden; Centre for Environmental and Climate Science, CEC, Lund University, Sölvegatan 37, 223 62 Lund, Sweden
| |
Collapse
|
3
|
Zhang Q, Shu F, Chen X, Liu W, Bian Y, Kang H. Construction of nucleus-directed fluorescent reporter systems and its application to verification of heterokaryon formation in Morchella importuna. Front Microbiol 2022; 13:1051013. [PMID: 36478869 PMCID: PMC9720127 DOI: 10.3389/fmicb.2022.1051013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/04/2022] [Indexed: 08/26/2023] Open
Abstract
INTRODUCTION Morchella importuna (M. importuna) is a rare fungus with high nutrition value and distinct flavor. Despite the successful artificial cultivation, its genetic characteristics and biological processes such as life cycle, reproductive system, and trophic mode remain poorly understood. METHODS Considering this, we constructed pEH2B and pMH2B vectors by fusing M. importuna endogenous histone protein H2B with fluorescent proteins eGFP or mCherry, respectively. Based on the constructed pEH2B and pMH2B vectors, nuclear fluorescence localization was performed via Agrobacterium tumefaciens-mediated transformation (ATMT). These two vectors were both driven by two endogenous promoters glyceraldehyde 3-phosphate dehydrogenase (GPD) and ubiquitin (UBI). The vector-based reporter systems were tested by the paired culture of two genetically modified strains pEH2B-labeled M04M24 (24e, MAT1-1-1) and pMH2B-abeled M04M26 (26m, MAT1-2-1). RESULTS The fluorescence observation and molecular identification results indicated the successful hyphal fusion and heterokaryon formation. We found that the expression of the reporter genes was stable, and it did not interfere with the growth of the fungus. DISCUSSION Our constructed nucleus-directed fluorescent systems in M. importuna can be used for monitoring the dynamic development and reproductive processes in living cells and also for monitoring the interaction between morels and plant roots. Therefore, morels exhibit the potential to be a candidate organism used for the research on basic biology and genetics of ascomycetes.
Collapse
Affiliation(s)
- Qianqian Zhang
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Fang Shu
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xin Chen
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Wei Liu
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yinbing Bian
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Heng Kang
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| |
Collapse
|
4
|
Kemppainen M, Pardo A. Nucleus-directed fluorescent reporter system for promoter studies in the ectomycorrhizal fungus Laccaria bicolor. J Microbiol Methods 2021; 190:106341. [PMID: 34610385 DOI: 10.1016/j.mimet.2021.106341] [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: 08/09/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 11/19/2022]
Abstract
Currently ectomycorrhizal research suffers from a lack of molecular tools specifically adapted to study gene expression in fungal symbionts. Considering that, we designed pReNuK, a cloning vector for transcriptional promoter studies in the ectomycorrhizal basidiomycete Laccaria bicolor. The pReNuK vector offers the use of a nuclear localizing and chromatin incorporating histone H2B-mCherry fluorescent reporter protein and it is specifically optimized for efficient transgene expression in Laccaria. Moreover, pReNuK is designed to work in concert with Agrobacterium-mediated transformation under hygromycin B resistance selection. The functionality of the pReNuK reporter system was tested with the constitutive Laccaria glyceraldehyde 3-phosphate dehydrogenase gene promoter and further validated with the nitrogen source regulated nitrate reductase gene promoter. The expression of the nucleus-directed H2B-mCherry reporter is highly stable in time. Moreover, the transformation of Laccaria with pReNuK and the expression of the reporter do not have negative effects on the growth of the fungus. The pReNuK offers a novel tool for studying in vivo gene expression regulation in Laccaria, the leading fungal model for ectomycorrhizal research.
Collapse
Affiliation(s)
- Minna Kemppainen
- Laboratory of Molecular Mycology, Institute of Basic and Applied Microbiology, Department of Science and Technology, National University of Quilmes and CONICET, Bernal, Province of Buenos Aires, Argentina.
| | - Alejandro Pardo
- Laboratory of Molecular Mycology, Institute of Basic and Applied Microbiology, Department of Science and Technology, National University of Quilmes and CONICET, Bernal, Province of Buenos Aires, Argentina
| |
Collapse
|
5
|
Arellano-Caicedo C, Ohlsson P, Bengtsson M, Beech JP, Hammer EC. Habitat geometry in artificial microstructure affects bacterial and fungal growth, interactions, and substrate degradation. Commun Biol 2021; 4:1226. [PMID: 34702996 PMCID: PMC8548513 DOI: 10.1038/s42003-021-02736-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 10/01/2021] [Indexed: 11/25/2022] Open
Abstract
Microhabitat conditions determine the magnitude and speed of microbial processes but have been challenging to investigate. In this study we used microfluidic devices to determine the effect of the spatial distortion of a pore space on fungal and bacterial growth, interactions, and substrate degradation. The devices contained channels differing in bending angles and order. Sharper angles reduced fungal and bacterial biomass, especially when angles were repeated in the same direction. Substrate degradation was only decreased by sharper angles when fungi and bacteria were grown together. Investigation at the cellular scale suggests that this was caused by fungal habitat modification, since hyphae branched in sharp and repeated turns, blocking the dispersal of bacteria and the substrate. Our results demonstrate how the geometry of microstructures can influence microbial activity. This can be transferable to soil pore spaces, where spatial occlusion and microbial feedback on microstructures is thought to explain organic matter stabilization.
Collapse
Affiliation(s)
| | - Pelle Ohlsson
- Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Martin Bengtsson
- Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Jason P Beech
- Division of Solid State Physics, Lund University, Lund, Sweden
| | | |
Collapse
|
6
|
You H, Sun B, Li N, Xu JW. Efficient expression of heterologous genes by the introduction of the endogenous glyceraldehyde-3-phosphate dehydrogenase gene intron 1 in Ganoderma lucidum. Microb Cell Fact 2021; 20:164. [PMID: 34419069 PMCID: PMC8379801 DOI: 10.1186/s12934-021-01654-8] [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: 05/11/2021] [Accepted: 08/12/2021] [Indexed: 11/18/2022] Open
Abstract
Background Ganoderma lucidum, a well-known medicinal mushroom, has received wide attention as a promising cell factory for producing bioactive compounds. However, efficient expression of heterologous genes remains a major challenge in Ganoderma, hindering metabolic regulation research and molecular breeding of this species. Results We show that the presence of glyceraldehyde-3-phosphate dehydrogenase gene (gpd) intron 1 at the 5′ end of, the 3′ end of, or within the heterologous phosphinothricin-resistant gene (bar) is efficient for its expression in G. lucidum. The enhanced expression of bar is exhibited by the higher accumulation of mRNA and increased amounts of protein. Moreover, the insertion of the gpd intron 1 in the β-glucuronidase gene (gus) elevates its mRNA accumulation and enzyme activity, which facilitates the use of this reporter gene in Ganoderma. Conclusions This study has demonstrated the importance of the introduction of gpd intron 1 for the efficient expression of bar and gus in G. lucidum. The presence of the gpd intron 1 in heterologous genes increases levels of mRNA accumulation and protein expression in basidiomycete Ganoderma. The developed method may be utilized in upregulating the expression of other heterologous genes in Ganoderma. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01654-8.
Collapse
Affiliation(s)
- Hao You
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Bin Sun
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Na Li
- Faculty of Science, Kunming University of Science and Technology, Kunming, 650500, China
| | - Jun-Wei Xu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
| |
Collapse
|
7
|
de Mattos-Shipley KMJ, Foster GD, Bailey AM. Cprp-An Unusual, Repetitive Protein Which Impacts Pleuromutilin Biosynthesis in the Basidiomycete Clitopilus passeckerianus. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:655323. [PMID: 37744150 PMCID: PMC10512284 DOI: 10.3389/ffunb.2021.655323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/04/2021] [Indexed: 09/26/2023]
Abstract
Interrogation of an EST database for Clitopilus passeckerianus identified a putative homolog to the unusual stress response gene from yeast; ddr48, as being upregulated under pleuromutilin production conditions. Silencing of this gene, named cprp, produced a population of transformants which demonstrated significantly reduced pleuromutilin production. Attempts to complement a Saccharomyces cerevisiae ddr48 mutant strain (strain Y16748) with cprp were hampered by the lack of a clearly identifiable mutant phenotype, but interestingly, overexpression of either ddr48 or cprp in S. cerevisiae Y16748 led to a conspicuous and comparable reduction in growth rate. This observation, combined with the known role of DDR48 proteins from a range of fungal species in nutrient starvation and stress responses, raises the possibility that this family of proteins plays a role in triggering oligotrophic growth. Localization studies via the production of a Cprp:GFP fusion protein in C. passeckerianus showed clear localization adjacent to the hyphal septa and, to a lesser extent, cell walls, which is consistent with the identification of DDR48 as a cell wall-associated protein in various yeast species. To our knowledge this is the first study demonstrating that a DDR48-like protein plays a role in the regulation of a secondary metabolite, and represents the first DDR48-like protein from a basidiomycete. Potential homologs can be identified across much of the Dikarya, suggesting that this unusual protein may play a central role in regulating both primary and secondary metabolism in fungi.
Collapse
Affiliation(s)
| | | | - Andy M. Bailey
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| |
Collapse
|
8
|
Alberti F, Kaleem S, Weaver JA. Recent developments of tools for genome and metabolome studies in basidiomycete fungi and their application to natural product research. Biol Open 2020; 9:bio056010. [PMID: 33268478 PMCID: PMC7725599 DOI: 10.1242/bio.056010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Basidiomycota are a large and diverse phylum of fungi. They can make bioactive metabolites that are used or have inspired the synthesis of antibiotics and agrochemicals. Terpenoids are the most abundant class of natural products encountered in this taxon. Other natural product classes have been described, including polyketides, peptides, and indole alkaloids. The discovery and study of natural products made by basidiomycete fungi has so far been hampered by several factors, which include their slow growth and complex genome architecture. Recent developments of tools for genome and metabolome studies are allowing researchers to more easily tackle the secondary metabolome of basidiomycete fungi. Inexpensive long-read whole-genome sequencing enables the assembly of high-quality genomes, improving the scaffold upon which natural product gene clusters can be predicted. CRISPR/Cas9-based engineering of basidiomycete fungi has been described and will have an important role in linking natural products to their genetic determinants. Platforms for the heterologous expression of basidiomycete genes and gene clusters have been developed, enabling natural product biosynthesis studies. Molecular network analyses and publicly available natural product databases facilitate data dereplication and natural product characterisation. These technological advances combined are prompting a revived interest in natural product discovery from basidiomycete fungi.This article has an associated Future Leader to Watch interview with the first author of the paper.
Collapse
Affiliation(s)
- Fabrizio Alberti
- School of Life Sciences and Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Saraa Kaleem
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Jack A Weaver
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| |
Collapse
|
9
|
Li M, Chang P, Pan X, Imanaka T, Igarashi Y, Luo F. Efficient expressions of reporter genes in the industrial filamentous fungus Sclerotium rolfsii mediated by Agrobacterium tumefaciens. Fungal Biol 2020; 124:932-939. [PMID: 33059845 DOI: 10.1016/j.funbio.2020.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 05/28/2020] [Accepted: 08/03/2020] [Indexed: 10/23/2022]
Abstract
Sclerotium rolfsii (teleomorph Athelia rolfsii) is one of the plant pathogenic basidiomycetes, which causes severe stem-rot disease in hundreds of plants and produces important metabolites, such as scleroglucan and TF-specific lectin. However, further molecular biological research on this filamentous fungus is severely plateaued out due to the lack of genetic methods. In this study, the A. tumefaciens strain LBA4404 harboring a binary vector containing the basta resistance gene fused with three reporters (DsRed, tdTomato, and GUSPlus) respectively, driven by the SrGPD promoter, was used for genetic transformation of S. rolfsii. The results showed that the three reporter genes were all effectively expressed in S. rolfsii. This study also showed that the intron of the SrGPD promoter is not necessary for transgene expression in this fungus. Besides, we showed that these reporters' signals could be observed easily but in a short time window. The efficient Agrobacterium-mediated transformation system and the three reporter gene plasmids for S. rolfsii developed in this study are of significance in overcoming current limitations of no available transformation and genetic manipulation techniques in S. rolfsii, facilitating further genetic manipulations and gene function exploration.
Collapse
Affiliation(s)
- Meilin Li
- College of Resources and Environment, Southwest University, 2 Tiansheng Road, Chongqing, 400715, China
| | - Peng Chang
- College of Resources and Environment, Southwest University, 2 Tiansheng Road, Chongqing, 400715, China; Chongqing Key Lab of Bio-resource Development for Bioenergy, Southwest University, 2 Tiansheng Road, Chongqing, 400715, China.
| | - Xiaohong Pan
- College of Resources and Environment, Southwest University, 2 Tiansheng Road, Chongqing, 400715, China
| | - Tadayuki Imanaka
- College of Resources and Environment, Southwest University, 2 Tiansheng Road, Chongqing, 400715, China; Chongqing Key Lab of Bio-resource Development for Bioenergy, Southwest University, 2 Tiansheng Road, Chongqing, 400715, China
| | - Yasuo Igarashi
- College of Resources and Environment, Southwest University, 2 Tiansheng Road, Chongqing, 400715, China; Chongqing Key Lab of Bio-resource Development for Bioenergy, Southwest University, 2 Tiansheng Road, Chongqing, 400715, China.
| | - Feng Luo
- College of Resources and Environment, Southwest University, 2 Tiansheng Road, Chongqing, 400715, China; Chongqing Key Lab of Bio-resource Development for Bioenergy, Southwest University, 2 Tiansheng Road, Chongqing, 400715, China.
| |
Collapse
|
10
|
Characterization of the effects of terminators and introns on recombinant gene expression in the basidiomycete Ceriporiopsis subvermispora. J Microbiol 2020; 58:1037-1045. [DOI: 10.1007/s12275-020-0213-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 01/06/2023]
|
11
|
Kemppainen M, Chowdhury J, Lundberg-Felten J, Pardo A. Fluorescent protein expression in the ectomycorrhizal fungus Laccaria bicolor: a plasmid toolkit for easy use of fluorescent markers in basidiomycetes. Curr Genet 2020; 66:791-811. [PMID: 32170354 DOI: 10.1007/s00294-020-01060-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/22/2020] [Accepted: 02/04/2020] [Indexed: 10/24/2022]
Abstract
For long time, studies on ectomycorrhiza (ECM) have been limited by inefficient expression of fluorescent proteins (FPs) in the fungal partner. To convert this situation, we have evaluated the basic requirements of FP expression in the model ECM homobasidiomycete Laccaria bicolor and established eGFP and mCherry as functional FP markers. Comparison of intron-containing and intronless FP-expression cassettes confirmed that intron-processing is indispensable for efficient FP expression in Laccaria. Nuclear FP localization was obtained via in-frame fusion of FPs between the intron-containing genomic gene sequences of Laccaria histone H2B, while cytosolic FP expression was produced by incorporating the intron-containing 5' fragment of the glyceraldehyde-3-phosphate dehydrogenase encoding gene. In addition, we have characterized the consensus Kozak sequence of strongly expressed genes in Laccaria and demonstrated its boosting effect on transgene mRNA accumulation. Based on these results, an Agrobacterium-mediated transformation compatible plasmid set was designed for easy use of FPs in Laccaria. The four cloning plasmids presented here allow fast and highly flexible construction of C-terminal in-frame fusions between the sequences of interest and the two FPs, expressed either from the endogenous gene promoter, allowing thus evaluation of the native regulation modes of the gene under study, or alternatively, from the constitutive Agaricus bisporus gpdII promoter for enhanced cellular protein localization assays. The molecular tools described here for cell-biological studies in Laccaria can also be exploited in studies of other biotrophic or saprotrophic basidiomycete species susceptible to genetic transformation.
Collapse
Affiliation(s)
- Minna Kemppainen
- Laboratory of Molecular Mycology, Institute of Basic and Applied Microbiology, Department of Science and Technology, Nacional University of Quilmes and CONICET, Bernal, Buenos Aires, Argentina.
| | - Jamil Chowdhury
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Judith Lundberg-Felten
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Alejandro Pardo
- Laboratory of Molecular Mycology, Institute of Basic and Applied Microbiology, Department of Science and Technology, Nacional University of Quilmes and CONICET, Bernal, Buenos Aires, Argentina
| |
Collapse
|
12
|
Liu K, Sun B, You H, Tu JL, Yu X, Zhao P, Xu JW. Dual sgRNA-directed gene deletion in basidiomycete Ganoderma lucidum using the CRISPR/Cas9 system. Microb Biotechnol 2020; 13:386-396. [PMID: 31958883 PMCID: PMC7017817 DOI: 10.1111/1751-7915.13534] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 12/28/2019] [Accepted: 12/29/2019] [Indexed: 12/12/2022] Open
Abstract
Ganoderma lucidum is an important medicinal mushroom in traditional Chinese medicine. However, the lack of adequate genetic tools has hindered molecular genetic research in and the genetic modification of this species. Here, we report that the presence of an intron is necessary for the efficient expression of the heterologous phosphinothricin-resistance and green fluorescent protein genes in G. lucidum. Moreover, we improved the CRISPR/Cas9-mediated gene disruption frequency in G. lucidum by adding an intron upstream of the Cas9 gene. Our results showed that the disruption frequency of the orotidine 5'-monophosphate decarboxylase gene (ura3) in transformants containing the glyceraldehyde-3-phosphate dehydrogenase gene intron in the Cas9 plasmid is 14-18 in 107 protoplasts, which is 10.6 times higher than that in transformants without any intron sequence. Furthermore, genomic fragment deletions in the ura3 and GL17624 genes were achieved via a dual sgRNA-directed CRISPR/Cas9 system in G. lucidum. We achieved a ura3 deletion frequency of 36.7% in G. lucidum. The developed method provides a powerful platform to generate gene deletion mutants and will facilitate functional genomic studies in G. lucidum.
Collapse
Affiliation(s)
- Ke Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Bin Sun
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Hao You
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Jun-Liang Tu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Xuya Yu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Peng Zhao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Jun-Wei Xu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| |
Collapse
|
13
|
Yin C, Fan X, Ma K, Chen Z, Shi D, Yao F, Gao H, Ma A. Identification and characterization of a novel light-induced promoter for recombinant protein production in Pleurotus ostreatus. J Microbiol 2019; 58:39-45. [PMID: 31686390 DOI: 10.1007/s12275-020-9230-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 09/26/2019] [Accepted: 09/29/2019] [Indexed: 11/30/2022]
Abstract
A lectin gene (plectin) with a high level of expression was previously identified by comparative transcriptome analysis of Pleurotus ostreatus. In this study, we cloned a 733-bp DNA fragment from the start codon of the plectin gene. Sequence analysis showed that the plectin promoter (Plp) region contained several eukaryotic transcription factor binding motifs, such as the TATA-box, four possible CAAT-box, light respon-siveness motifs and MeJA-responsiveness motifs. To deter-mine whether the Plp promoter was a light-regulated promoter, we constructed an expression vector with the fused egfp-hph fragment under the control of the Plp promoter and transformed P. ostreatus mycelia via Agrobacterium tunte-faciens. PCR and Southern blot analyses confirmed the Plp-egfp-hph fragment was integrated into the chromosomal DNA of transformants. qRT-PCR, egfp visualization, and intracellular egfp determination experiments showed the Plp promoter could be a light-induced promoter that may be suitable for P. ostreatus genetic engineering. This study lays the foundation for gene homologous expression in P. ostreatus.
Collapse
Affiliation(s)
- Chaomin Yin
- Institute of Agro-Products Processing and Nuclear-Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, 430064, P. R. China. .,National Research and Development Center for Edible Fungi Processing (Wuhan), Wuhan, 430064, P. R. China.
| | - Xiuzhi Fan
- Institute of Agro-Products Processing and Nuclear-Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, 430064, P. R. China
| | - Kun Ma
- Institute of Agro-Products Processing and Nuclear-Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, 430064, P. R. China
| | - Zheya Chen
- Institute of Agro-Products Processing and Nuclear-Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, 430064, P. R. China
| | - Defang Shi
- Institute of Agro-Products Processing and Nuclear-Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, 430064, P. R. China
| | - Fen Yao
- Institute of Agro-Products Processing and Nuclear-Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, 430064, P. R. China
| | - Hong Gao
- Institute of Agro-Products Processing and Nuclear-Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, 430064, P. R. China.,National Research and Development Center for Edible Fungi Processing (Wuhan), Wuhan, 430064, P. R. China
| | - Aimin Ma
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| |
Collapse
|
14
|
Shang J, Yang R, Tang L, Li Y, Li Y, Mao W, Gong M, Wang Y, Honda Y, Bao D. Differential expression of two gpd genes in the cultivated mushroom Pleurotus eryngii using RNA sequencing analysis. MYCOSCIENCE 2019. [DOI: 10.1016/j.myc.2019.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
15
|
Heterologous expression of Zn-binding peptide RaZBP1 from Russula bresadolae does not overcome Zn and Cd detoxification mechanisms in Hebeloma mesophaeum. Folia Microbiol (Praha) 2019; 64:835-844. [DOI: 10.1007/s12223-019-00696-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 03/11/2019] [Indexed: 10/26/2022]
|
16
|
Niu X, Pei M, Liang C, Lv Y, Wu X, Zhang R, Lu G, Yu F, Zhu H, Qin W. Genetic Transformation and Green Fluorescent Protein Labeling in Ceratocystis paradoxa from Coconut. Int J Mol Sci 2019; 20:ijms20102387. [PMID: 31091742 PMCID: PMC6566578 DOI: 10.3390/ijms20102387] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/11/2019] [Accepted: 05/11/2019] [Indexed: 11/17/2022] Open
Abstract
Ceratocystis paradoxa, the causal agent of stem-bleeding disease of the coconut palm, causes great losses to the global coconut industry. As the mechanism of pathogenicity of C. paradoxa has not been determined, an exogenous gene marker was introduced into the fungus. In this study, pCT74-sGFP, which contains the green fluorescent protein (GFP) gene, and the hygromycin B resistance gene as a selective marker, was used as an expression vector. Several protoplast release buffers were compared to optimize protoplast preparation. The plasmid pCT74-sGFP was successfully transformed into the genome of C. paradoxa, which was verified using polymerase chain reaction and green fluorescence detection. The transformants did not exhibit any obvious differences from the wild-type isolates in terms of growth and morphological characteristics. Pathogenicity tests showed that the transformation process did not alter the virulence of the X-3314 C. paradoxa strain. This is the first report on the polyethylene glycol-mediated transformation of C. paradoxa carrying a ‘reporter’ gene GFP that was stably and efficiently expressed in the transformants. These findings provide a basis for future functional genomics studies of C. paradoxa and offer a novel opportunity to track the infection process of C. paradoxa.
Collapse
Affiliation(s)
- Xiaoqing Niu
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China.
| | - Mengtian Pei
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Chenyu Liang
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yuexiao Lv
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Xinyi Wu
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Ruina Zhang
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Guodong Lu
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Fengyu Yu
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China.
| | - Hui Zhu
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China.
| | - Weiquan Qin
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China.
| |
Collapse
|
17
|
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.
Collapse
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.
| |
Collapse
|
18
|
Poyedinok NL, Blume YB. Advances, Problems, and Prospects of Genetic Transformation of Fungi. CYTOL GENET+ 2018. [DOI: 10.3103/s009545271802007x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
19
|
Idnurm A, Bailey AM, Cairns TC, Elliott CE, Foster GD, Ianiri G, Jeon J. A silver bullet in a golden age of functional genomics: the impact of Agrobacterium-mediated transformation of fungi. Fungal Biol Biotechnol 2017; 4:6. [PMID: 28955474 PMCID: PMC5615635 DOI: 10.1186/s40694-017-0035-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/18/2017] [Indexed: 11/10/2022] Open
Abstract
The implementation of Agrobacterium tumefaciens as a transformation tool revolutionized approaches to discover and understand gene functions in a large number of fungal species. A. tumefaciens mediated transformation (AtMT) is one of the most transformative technologies for research on fungi developed in the last 20 years, a development arguably only surpassed by the impact of genomics. AtMT has been widely applied in forward genetics, whereby generation of strain libraries using random T-DNA insertional mutagenesis, combined with phenotypic screening, has enabled the genetic basis of many processes to be elucidated. Alternatively, AtMT has been fundamental for reverse genetics, where mutant isolates are generated with targeted gene deletions or disruptions, enabling gene functional roles to be determined. When combined with concomitant advances in genomics, both forward and reverse approaches using AtMT have enabled complex fungal phenotypes to be dissected at the molecular and genetic level. Additionally, in several cases AtMT has paved the way for the development of new species to act as models for specific areas of fungal biology, particularly in plant pathogenic ascomycetes and in a number of basidiomycete species. Despite its impact, the implementation of AtMT has been uneven in the fungi. This review provides insight into the dynamics of expansion of new research tools into a large research community and across multiple organisms. As such, AtMT in the fungi, beyond the demonstrated and continuing power for gene discovery and as a facile transformation tool, provides a model to understand how other technologies that are just being pioneered, e.g. CRISPR/Cas, may play roles in fungi and other eukaryotic species.
Collapse
Affiliation(s)
- Alexander Idnurm
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Andy M. Bailey
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Timothy C. Cairns
- Department of Applied and Molecular Microbiology, Technische Universität Berlin, Berlin, Germany
| | - Candace E. Elliott
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Gary D. Foster
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Giuseppe Ianiri
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, USA
| | - Junhyun Jeon
- College of Life and Applied Sciences, Yeungnam University, Gyeongsan, South Korea
| |
Collapse
|
20
|
Al-Salihi SAA, Scott TA, Bailey AM, Foster GD. Improved vectors for Agrobacterium mediated genetic manipulation of Hypholoma spp. and other homobasidiomycetes. J Microbiol Methods 2017; 142:4-9. [PMID: 28843436 DOI: 10.1016/j.mimet.2017.08.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 08/17/2017] [Accepted: 08/22/2017] [Indexed: 12/01/2022]
Abstract
The basidiomycete fungi Hypholoma fasciculare and H. sublateritium are both prolific producers of sesquiterpenes and triterpenes, some of which have relevant pharmaceutical properties. Although H. sublateritium has been transformed in the past, the low reported efficiencies highlighted the need for establishing an effective simple transformation system for these valuable species. We have optimized Agrobacterium tumefaciens-mediated transformation through testing various parameters in these two Hypholoma species, showing that a mixture of homogenized mycelia and Agrobacterium (strain LBA4404) co-cultivated for 84h at 25°C is optimal for efficient transformation in these basidiomycetes. This study also reveals the requirements for transgene expression, with the first report of GFP expression in these Hypholoma, the need for an intron for such transgene expression, and further demonstrates the functionality of the expression vector by its use in Clitopilus passeckerianus. This development of transformation system and expression constructs, can facilitate further genetic investigation such as gene functionality in these fungi.
Collapse
Affiliation(s)
- Suhad A A Al-Salihi
- Molecular Plant Pathology and Fungal Biology Group, University of Bristol, School of Biological Sciences, 24 Tyndall Avenue Bristol, BS8 1TQ, UK
| | - Thomas A Scott
- Molecular Plant Pathology and Fungal Biology Group, University of Bristol, School of Biological Sciences, 24 Tyndall Avenue Bristol, BS8 1TQ, UK
| | - Andy M Bailey
- Molecular Plant Pathology and Fungal Biology Group, University of Bristol, School of Biological Sciences, 24 Tyndall Avenue Bristol, BS8 1TQ, UK
| | - Gary D Foster
- Molecular Plant Pathology and Fungal Biology Group, University of Bristol, School of Biological Sciences, 24 Tyndall Avenue Bristol, BS8 1TQ, UK.
| |
Collapse
|
21
|
Sugano SS, Suzuki H, Shimokita E, Chiba H, Noji S, Osakabe Y, Osakabe K. Genome editing in the mushroom-forming basidiomycete Coprinopsis cinerea, optimized by a high-throughput transformation system. Sci Rep 2017; 7:1260. [PMID: 28455526 PMCID: PMC5430836 DOI: 10.1038/s41598-017-00883-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 03/08/2017] [Indexed: 11/09/2022] Open
Abstract
Mushroom-forming basidiomycetes produce a wide range of metabolites and have great value not only as food but also as an important global natural resource. Here, we demonstrate CRISPR/Cas9-based genome editing in the model species Coprinopsis cinerea. Using a high-throughput reporter assay with cryopreserved protoplasts, we identified a novel promoter, CcDED1pro, with seven times stronger activity in this assay than the conventional promoter GPD2. To develop highly efficient genome editing using CRISPR/Cas9 in C. cinerea, we used the CcDED1pro to express Cas9 and a U6-snRNA promoter from C. cinerea to express gRNA. Finally, CRISPR/Cas9-mediated GFP mutagenesis was performed in a stable GFP expression line. Individual genome-edited lines were isolated, and loss of GFP function was detected in hyphae and fruiting body primordia. This novel method of high-throughput CRISPR/Cas9-based genome editing using cryopreserved protoplasts should be a powerful tool in the study of edible mushrooms.
Collapse
Affiliation(s)
- Shigeo S Sugano
- Center for Collaboration among Agriculture, Industry, and Commerce, Tokushima University, Tokushima, Japan
| | - Hiroko Suzuki
- Center for Collaboration among Agriculture, Industry, and Commerce, Tokushima University, Tokushima, Japan
| | - Eisuke Shimokita
- Center for Collaboration among Agriculture, Industry, and Commerce, Tokushima University, Tokushima, Japan.,Tokushima Prefectural Agriculture, Forestry and Fisheries Technology Support Center, Tokushima, Japan
| | - Hirofumi Chiba
- Center for Collaboration among Agriculture, Industry, and Commerce, Tokushima University, Tokushima, Japan.,Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Sumihare Noji
- Center for Collaboration among Agriculture, Industry, and Commerce, Tokushima University, Tokushima, Japan
| | - Yuriko Osakabe
- Center for Collaboration among Agriculture, Industry, and Commerce, Tokushima University, Tokushima, Japan.,Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Keishi Osakabe
- Center for Collaboration among Agriculture, Industry, and Commerce, Tokushima University, Tokushima, Japan. .,Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan.
| |
Collapse
|
22
|
de Mattos-Shipley K, Ford K, Alberti F, Banks A, Bailey A, Foster G. The good, the bad and the tasty: The many roles of mushrooms. Stud Mycol 2016; 85:125-157. [PMID: 28082758 PMCID: PMC5220184 DOI: 10.1016/j.simyco.2016.11.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Fungi are often inconspicuous in nature and this means it is all too easy to overlook their importance. Often referred to as the "Forgotten Kingdom", fungi are key components of life on this planet. The phylum Basidiomycota, considered to contain the most complex and evolutionarily advanced members of this Kingdom, includes some of the most iconic fungal species such as the gilled mushrooms, puffballs and bracket fungi. Basidiomycetes inhabit a wide range of ecological niches, carrying out vital ecosystem roles, particularly in carbon cycling and as symbiotic partners with a range of other organisms. Specifically in the context of human use, the basidiomycetes are a highly valuable food source and are increasingly medicinally important. In this review, seven main categories, or 'roles', for basidiomycetes have been suggested by the authors: as model species, edible species, toxic species, medicinal basidiomycetes, symbionts, decomposers and pathogens, and two species have been chosen as representatives of each category. Although this is in no way an exhaustive discussion of the importance of basidiomycetes, this review aims to give a broad overview of the importance of these organisms, exploring the various ways they can be exploited to the benefit of human society.
Collapse
Affiliation(s)
- K.M.J. de Mattos-Shipley
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - K.L. Ford
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - F. Alberti
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
- School of Life Sciences and Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - A.M. Banks
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
- School of Biology, Devonshire Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - A.M. Bailey
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - G.D. Foster
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| |
Collapse
|
23
|
Ford KL, Baumgartner K, Henricot B, Bailey AM, Foster GD. A native promoter and inclusion of an intron is necessary for efficient expression of GFP or mRFP in Armillaria mellea. Sci Rep 2016; 6:29226. [PMID: 27384974 PMCID: PMC4935854 DOI: 10.1038/srep29226] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 06/14/2016] [Indexed: 12/21/2022] Open
Abstract
Armillaria mellea is a significant pathogen that causes Armillaria root disease on numerous hosts in forests, gardens and agricultural environments worldwide. Using a yeast-adapted pCAMBIA0380 Agrobacterium vector, we have constructed a series of vectors for transformation of A. mellea, assembled using yeast-based recombination methods. These have been designed to allow easy exchange of promoters and inclusion of introns. The vectors were first tested by transformation into basidiomycete Clitopilus passeckerianus to ascertain vector functionality then used to transform A. mellea. We show that heterologous promoters from the basidiomycetes Agaricus bisporus and Phanerochaete chrysosporium that were used successfully to control the hygromycin resistance cassette were not able to support expression of mRFP or GFP in A. mellea. The endogenous A. mellea gpd promoter delivered efficient expression, and we show that inclusion of an intron was also required for transgene expression. GFP and mRFP expression was stable in mycelia and fluorescence was visible in transgenic fruiting bodies and GFP was detectable in planta. Use of these vectors has been successful in giving expression of the fluorescent proteins GFP and mRFP in A. mellea, providing an additional molecular tool for this pathogen.
Collapse
Affiliation(s)
- Kathryn L. Ford
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, United Kingdom
| | - Kendra Baumgartner
- United States Department of Agriculture-Agricultural Research Service, 363 Hutchison Hall, University of California, One Shields Avenue, Davis, CA 95616, United States
| | - Béatrice Henricot
- The Royal Horticultural Society, Wisley, Woking, Surrey, GU23 6QB, United Kingdom
| | - Andy M. Bailey
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, United Kingdom
| | - Gary D. Foster
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, United Kingdom
| |
Collapse
|
24
|
Paradoxical performance of tryptophan synthase gene trp1 (+) in transformations of the basidiomycete Coprinopsis cinerea. Appl Microbiol Biotechnol 2016; 100:8789-807. [PMID: 27368741 DOI: 10.1007/s00253-016-7693-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/14/2016] [Accepted: 06/17/2016] [Indexed: 10/21/2022]
Abstract
Several transformation strains of Coprinopsis cinerea carry the defective tryptophan synthase allele trp1-1,1-6 which can be complemented by introduction of the trp1 (+) wild-type gene. Regularly in C. cinerea, single-trp1 (+)-vector transformations yield about half the numbers of clones than cotransformations with a non-trp1 (+)-plasmid done in parallel. The effect is also observed with the orthologous Schizophyllum commune trpB (+) gene shown here to function as a selection marker in C. cinerea. Parts of single-trp1 (+) - or single-trpB (+) -vector transformants are apparently lost. This paradoxical phenomenon relates to de-regulation of aromatic amino acid biosynthesis pathways. Adding tryptophan precursors to protoplast regeneration agar or feeding with other aromatic amino acids increases loss of single-trp1 (+)-vector transformants and also sets off loss of clones in cotransformation with a non-trp1 (+)-plasmid. Feedback control by tryptophan and cross-pathway control by tyrosine and phenylalanine are both active in the process. We deduce from the observations that more cotransformants than single-vector transformants are obtained by in average less disturbance of the tryptophan biosynthesis pathway. DNA in C. cinerea transformation usually integrates into the genome at multiple ectopic places. Integration events for a single vector per nucleus should statistically be 2-fold higher in single-vector transformations than in cotransformations in which the two different molecules compete for the same potential integration sites. Integration of more trp1 (+) copies into the genome might more likely lead to sudden tryptophan overproduction with subsequent rigid shut-down of the pathway. Blocking ectopic DNA integration in a Δku70 mutant abolished the effect of doubling clone numbers in cotransformations due to preferred single trp1 (+) integration by homologous recombination at its native genomic site.
Collapse
|
25
|
Heneghan MN, Burns C, Costa AMSB, Burton KS, Challen MP, Bailey AM, Foster GD. Functional analysis of Agaricus bisporus serine proteinase 1 reveals roles in utilization of humic rich substrates and adaptation to the leaf-litter ecological niche. Environ Microbiol 2016; 18:4687-4696. [PMID: 27113919 PMCID: PMC5215592 DOI: 10.1111/1462-2920.13350] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 04/19/2016] [Indexed: 12/03/2022]
Abstract
Agaricus bisporus is a secondary decomposer fungus and an excellent model for the adaptation, persistence and growth of fungi in humic‐rich environments such as soils of temperate woodland and pastures. The A. bisporus serine proteinase SPR1 is induced by humic acids and is highly expressed during growth on compost. Three Spr1 gene silencing cassettes were constructed around sense, antisense and non‐translatable‐stop strategies (pGRsensehph, pGRantihph and pGRstophph). Transformation of A. bisporus with these cassettes generated cultures showing a reduction in extracellular proteinase activity as demonstrated by the reduction, or abolition, of a clearing zone on plate‐based bioassays. These lines were then assessed by detailed enzyme assay, RT‐qPCR and fruiting. Serine proteinase activity in liquid cultures was reduced in 83% of transformants. RT‐qPCR showed reduced Spr1 mRNA levels in all transformants analysed, and these correlated with reduced enzyme activity. When fruiting was induced, highly‐silenced transformant AS5 failed to colonize the compost, whilst for those that did colonize the compost, 60% gave a reduction in mushroom yield. Transcriptional, biochemical and developmental observations, demonstrate that SPR1 has an important role in nutrient acquisition in compost and that SPR1 is a key enzyme in the adaptation of Agaricus to the humic‐rich ecological niche formed during biomass degradation.
Collapse
Affiliation(s)
- Mary N Heneghan
- School of Biological Sciences, Life Sciences Building, 24 Tyndall Avenue, University of Bristol, Bristol, BS8 1TQ, UK.,Department of Life Sciences, Institute of Technology, Sligo, Ash Lane, Sligo, Ireland
| | - Claire Burns
- School of Biological Sciences, Life Sciences Building, 24 Tyndall Avenue, University of Bristol, Bristol, BS8 1TQ, UK
| | - Ana M S B Costa
- School of Biological Sciences, Life Sciences Building, 24 Tyndall Avenue, University of Bristol, Bristol, BS8 1TQ, UK.,Warwick HRI, University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK
| | - Kerry S Burton
- Warwick HRI, University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK
| | - Michael P Challen
- Warwick HRI, University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK
| | - Andy M Bailey
- School of Biological Sciences, Life Sciences Building, 24 Tyndall Avenue, University of Bristol, Bristol, BS8 1TQ, UK
| | - Gary D Foster
- School of Biological Sciences, Life Sciences Building, 24 Tyndall Avenue, University of Bristol, Bristol, BS8 1TQ, UK
| |
Collapse
|
26
|
An aryl-alcohol oxidase of Pleurotus sapidus: heterologous expression, characterization, and application in a 2-enzyme system. Appl Microbiol Biotechnol 2016; 100:8021-30. [DOI: 10.1007/s00253-016-7567-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 04/12/2016] [Accepted: 04/18/2016] [Indexed: 10/21/2022]
|
27
|
Homologous and Heterologous Expression of Basidiomycete Genes Related to Plant Biomass Degradation. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
28
|
Arimoto M, Yamagishi K, Wang J, Tanaka K, Miyoshi T, Kamei I, Kondo R, Mori T, Kawagishi H, Hirai H. Molecular breeding of lignin-degrading brown-rot fungus Gloeophyllum trabeum by homologous expression of laccase gene. AMB Express 2015; 5:81. [PMID: 26695948 PMCID: PMC4688280 DOI: 10.1186/s13568-015-0173-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/11/2015] [Indexed: 11/10/2022] Open
Abstract
The basidiomycete Gloeophyllum trabeum KU-41 can degrade Japanese cedar wood efficiently. To construct a strain better suited for biofuel production from Japanese cedar wood, we developed a gene transformation system for G. trabeum KU-41 using the hygromycin phosphotransferase-encoding gene (hpt) as a marker. The endogenous laccase candidate gene (Gtlcc3) was fused with the promoter of the G. trabeum glyceraldehyde-3-phosphate dehydrogenase-encoding gene and co-transformed with the hpt-bearing pAH marker plasmid. We obtained 44 co-transformants, and identified co-transformant L#61, which showed the highest laccase activity among all the transformants. Moreover, strain L#61 was able to degrade lignin in Japanese cedar wood-containing medium, in contrast to wild-type G. trabeum KU-41 and to a typical white-rot fungus Phanerochaete chrysosporium. By using strain L#61, direct ethanol production from Japanese cedar wood was improved compared to wild type. To our knowledge, this study is the first report of the molecular breeding of lignin-degrading brown-rot fungus and direct ethanol production from softwoods by co-transformation with laccase overproduction constructs.
Collapse
Affiliation(s)
- Misa Arimoto
- Department of Applied Biological Chemistry, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
| | - Kenji Yamagishi
- NARO National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan.
| | - Jianqiao Wang
- Department of Applied Biological Chemistry, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
| | - Kanade Tanaka
- Integrative Technology Research Institute, Teijin Limited, Iwakuni, 740-8511, Japan.
| | - Takanori Miyoshi
- New Business Development Business Unit, Teijin Limited, Tokyo, 100-8585, Japan.
| | - Ichiro Kamei
- Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan.
| | - Ryuichiro Kondo
- Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan.
| | - Toshio Mori
- Department of Applied Biological Chemistry, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
| | - Hirokazu Kawagishi
- Department of Applied Biological Chemistry, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
- Graduate School of Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan.
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan.
| | - Hirofumi Hirai
- Department of Applied Biological Chemistry, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan.
| |
Collapse
|
29
|
Nishikawa R, Yoshida M, Noda T, Okuhara T, Taguchi G, Inatomi S, Shimosaka M. pFungiway: a series of plasmid vectors used for gene manipulation in fungi. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1166-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
|
30
|
A reliable in vitro fruiting system for Armillaria mellea for evaluation of Agrobacterium tumefaciens transformation vectors. Fungal Biol 2015; 119:859-869. [DOI: 10.1016/j.funbio.2015.06.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 06/16/2015] [Accepted: 06/22/2015] [Indexed: 12/27/2022]
|
31
|
Development of a transformation system for the edible mushroom Grifola frondosa: Demonstrating heterologous gene expression and RNAi-mediated gene silencing. MYCOSCIENCE 2015. [DOI: 10.1016/j.myc.2014.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
32
|
The Xanthomonas oryzae pv. oryzae PilZ Domain Proteins Function Differentially in Cyclic di-GMP Binding and Regulation of Virulence and Motility. Appl Environ Microbiol 2015; 81:4358-67. [PMID: 25911481 DOI: 10.1128/aem.04044-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/10/2015] [Indexed: 12/17/2022] Open
Abstract
The PilZ domain proteins have been demonstrated to be one of the major types of receptors mediating cyclic di-GMP (c-di-GMP) signaling pathways in several pathogenic bacteria. However, little is known about the function of PilZ domain proteins in c-di-GMP regulation of virulence in the bacterial blight pathogen of rice Xanthomonas oryzae pv. oryzae. Here, the roles of PilZ domain proteins PXO_00049 and PXO_02374 in c-di-GMP binding, regulation of virulence and motility, and subcellular localization were characterized in comparison with PXO_02715, identified previously as an interactor with the c-di-GMP receptor Filp to regulate virulence. The c-di-GMP binding motifs in the PilZ domains were conserved in PXO_00049 and PXO_02374 but were less well conserved in PXO_02715. PXO_00049 and PXO_02374 but not PXO_02715 proteins bound to c-di-GMP with high affinity in vitro, and the R(141) and R(10) residues in the PilZ domains of PXO_00049 and PXO_02374, respectively, were crucial for c-di-GMP binding. Gene deletion of PXO_00049 and PXO_02374 resulted in significant increases in virulence and hrp gene transcription, indicating their negative regulation of virulence via type III secretion system expression. All mutants showed significant changes in sliding motility but not exopolysaccharide production and biofilm formation. In trans expression of the full-length open reading frame (ORF) of each gene in the relevant mutants led to restoration of the phenotype to wild-type levels. Moreover, PXO_00049 and PXO_02374 displayed mainly multisite subcellular localizations, whereas PXO_02715 showed nonpolar distributions in the X. oryzae pv. oryzae cells. Therefore, this study demonstrated the different functions of the PilZ domain proteins in mediation of c-di-GMP regulation of virulence and motility in X. oryzae pv. oryzae.
Collapse
|
33
|
Phytochelatin synthase is required for tolerating metal toxicity in a basidiomycete yeast and is a conserved factor involved in metal homeostasis in fungi. Fungal Biol Biotechnol 2015; 2. [PMID: 25926993 PMCID: PMC4410428 DOI: 10.1186/s40694-015-0013-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background Phytochelatin synthase (PCS) is an enzyme that catalyzes the biosynthesis of phytochelatin from glutathione. Phytochelatins protect cells against the toxic effects of non-essential heavy metals, such as cadmium, and hence growth is restricted in the presence of these metals in mutants in PCS-encoding genes. PCS genes from fungi have been characterized in only two species in the Ascomycota, and these genes are considered sparsely distributed in the fungal kingdom. Results A gene encoding a putative PCS was identified in Sporobolomyces sp. strain IAM 13481, a fungus that is a member of the Pucciniomycotina subphylum of the Basidiomycota. The function of this PCS1 gene was assessed by heterologous expression in the Ascomycota yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, and by mutating the gene in Sporobolomyces. The gene is required for tolerance to toxic concentrations of non-essential cadmium as well as the essential metal copper. Pcs1 homologs in fungi and other eukaryotes have putative targeting sequences for mitochondrial localization: the S. pombe homolog was fused to green fluorescent protein and it co-localized with a mitochondrial dye. Evaluation of the presence or absence of PCS and PCS-like homologs in the genome sequences of fungi indicates that they have a wide distribution, and the absence in most Ascomycota and Basidiomycota (the Dikarya) species can be explained by a small number of gene losses. Conclusions The ecology of the species within the fungi carrying putative PCS genes, the phenotypes of phytochelatin synthase mutants in two major fungal lineages, and the presence of homologs in many non-Dikarya lineages parallel what is seen in the plant and animal kingdoms. That is, PCS is a protein present early during the evolution of the fungi and whose role is not solely dedicated to combating toxic concentrations of non-essential metals. Electronic supplementary material The online version of this article (doi:10.1186/s40694-015-0013-3) contains supplementary material, which is available to authorized users.
Collapse
|
34
|
Kim S, Ha BS, Ro HS. Current technologies and related issues for mushroom transformation. MYCOBIOLOGY 2015; 43:1-8. [PMID: 25892908 PMCID: PMC4397374 DOI: 10.5941/myco.2015.43.1.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 03/02/2015] [Indexed: 06/04/2023]
Abstract
Mushroom transformation requires a series of experimental steps, including generation of host strains with a desirable selective marker, design of vector DNA, removal of host cell wall, introduction of foreign DNA across the cell membrane, and integration into host genomic DNA or maintenance of an autonomous vector DNA inside the host cell. This review introduces limitations and obstacles related to transformation technologies along with possible solutions. Current methods for cell wall removal and cell membrane permeabilization are summarized together with details of two popular technologies, Agrobacterium tumefaciens-mediated transformation and restriction enzyme-mediated integration.
Collapse
Affiliation(s)
- Sinil Kim
- Division of Applied Life Science and Research Institute for Life Science, Gyeongsang National University, Jinju 660-701, Korea
| | - Byeong-Suk Ha
- Division of Applied Life Science and Research Institute for Life Science, Gyeongsang National University, Jinju 660-701, Korea
| | - Hyeon-Su Ro
- Division of Applied Life Science and Research Institute for Life Science, Gyeongsang National University, Jinju 660-701, Korea
| |
Collapse
|
35
|
Yin C, Zheng L, Zhu J, Chen L, Ma A. Characterization of the highly active fragment of glyceraldehyde-3-phosphate dehydrogenase gene promoter for recombinant protein expression in Pleurotus ostreatus. FEMS Microbiol Lett 2015; 362:fnv010. [DOI: 10.1093/femsle/fnv010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
|
36
|
Han F, Kang LZ, Zeng XL, Ye ZW, Guo LQ, Lin JF. Bioproduction of baccatin III, an advanced precursor of paclitaxol, with transgenic Flammulina velutipes expressing the 10-deacetylbaccatin III-10-O-acetyl transferase gene. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2014; 94:2376-2383. [PMID: 24403190 DOI: 10.1002/jsfa.6562] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 11/06/2013] [Accepted: 01/08/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND 10-Deacetylbaccatin III (10-DAB) and baccatin III are intermediates in the biosynthesis of Taxol (an anti-cancer drug) and useful precursors for semi-synthesis of the drug. In this study, a bioconversion system was established for the production of baccatin III, an advanced precursor of paclitaxel, in the transgenic mushroom Flammulina velutipes expressing the 10-deacetylbaccatin III-10β-O-acetyltransferase gene. The expression vector pgFvs-TcDBAT containing the 10-deacetylbaccatin III-10β-O-acetyltransferase (DBAT) gene was constructed and transformed into the cells of F. velutipes by polyethylene glycol-mediated protoplast transformation. RESULTS Polymerase chain reaction and Southern blotting analysis verified the successful integration of the exogenous DBAT gene into the genome of F. velutipes. Reverse transcription polymerase chain reaction and enzyme activity analyses confirmed that the DBAT gene was expressed in F. velutipes, and DBAT is able to convert substrate into baccatin III. CONCLUSION The DBAT gene from the plant Taxus chinensis can be functionally expressed in F. velutipes. Transgenic F. velutipes expressing the DBAT gene is able to produce the target product, baccatin III. This is the first report about the transformation and expression of paclitaxel biosynthetic gene in the edible mushroom F. velutipes. This represents a significant step towards bio-production of paclitaxel and its advanced precursor baccatin III in an edible fungus.
Collapse
Affiliation(s)
- Fei Han
- Department of Bioengineering, College of Food Science, South China Agriculture University, Guangzhou, Guangdong, 510640, China; Guangdong Shantou Institute of Quality and Metrology Supervision Testing, Shantou, 515041, China
| | | | | | | | | | | |
Collapse
|
37
|
Stanley CE, Stöckli M, van Swaay D, Sabotič J, Kallio PT, Künzler M, deMello AJ, Aebi M. Probing bacterial–fungal interactions at the single cell level. Integr Biol (Camb) 2014; 6:935-45. [DOI: 10.1039/c4ib00154k] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
38
|
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]
|
39
|
Physical methods for genetic transformation of fungi and yeast. Phys Life Rev 2014; 11:184-203. [DOI: 10.1016/j.plrev.2014.01.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 01/21/2014] [Indexed: 01/27/2023]
|
40
|
Goebels C, Thonn A, Gonzalez-Hilarion S, Rolland O, Moyrand F, Beilharz TH, Janbon G. Introns regulate gene expression in Cryptococcus neoformans in a Pab2p dependent pathway. PLoS Genet 2013; 9:e1003686. [PMID: 23966870 PMCID: PMC3744415 DOI: 10.1371/journal.pgen.1003686] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 06/17/2013] [Indexed: 11/18/2022] Open
Abstract
Most Cryptococccus neoformans genes are interrupted by introns, and alternative splicing occurs very often. In this study, we examined the influence of introns on C. neoformans gene expression. For most tested genes, elimination of introns greatly reduces mRNA accumulation. Strikingly, the number and the position of introns modulate the gene expression level in a cumulative manner. A screen for mutant strains able to express functionally an intronless allele revealed that the nuclear poly(A) binding protein Pab2 modulates intron-dependent regulation of gene expression in C. neoformans. PAB2 deletion partially restored accumulation of intronless mRNA. In addition, our results demonstrated that the essential nucleases Rrp44p and Xrn2p are implicated in the degradation of mRNA transcribed from an intronless allele in C. neoformans. Double mutant constructions and over-expression experiments suggested that Pab2p and Xrn2p could act in the same pathway whereas Rrp44p appears to act independently. Finally, deletion of the RRP6 or the CID14 gene, encoding the nuclear exosome nuclease and the TRAMP complex associated poly(A) polymerase, respectively, has no effect on intronless allele expression. Cryptococcus neoformans is a major human pathogen responsible for deadly infection in immunocompromised patients. The analysis of its genome previously revealed that most of its genes are interrupted by introns. Here, we demonstrate that introns modulate gene expression in a cumulative manner. We also demonstrate that introns can play a positive or a negative role in this process. We identify a nuclear poly(A) binding protein (Pab2p) as implicated in the intron-dependent control of gene expression in C. neoformans. We also demonstrate that the essential nucleases Rrp44p and Xrn2p are implicated in two independent pathways controlling the intron-dependent regulation of gene expression in C. neoformans. Xrn2p regulation seems to depend on Pab2p whereas Rrp44p acts independently. In contrast, the other exosome nuclease Rrp6p and the TRAMP associated poly(A) polymerase Cid14p do not appear to be implicated in this regulation. Our results provide new insights into the regulation of gene expression in eukaryotes and more specifically into the biology and virulence of C. neoformans.
Collapse
Affiliation(s)
- Carolin Goebels
- Institut Pasteur, Unité des Aspergillus, Département Parasitologie et Mycologie, Paris, France
| | - Aline Thonn
- Institut Pasteur, Unité des Aspergillus, Département Parasitologie et Mycologie, Paris, France
| | - Sara Gonzalez-Hilarion
- Institut Pasteur, Unité des Aspergillus, Département Parasitologie et Mycologie, Paris, France
| | - Olga Rolland
- Institut Pasteur, Unité des Aspergillus, Département Parasitologie et Mycologie, Paris, France
| | - Frederique Moyrand
- Institut Pasteur, Unité des Aspergillus, Département Parasitologie et Mycologie, Paris, France
| | - Traude H. Beilharz
- Monash University, Department of Biochemistry and Molecular Biology, Clayton, Australia
| | - Guilhem Janbon
- Institut Pasteur, Unité des Aspergillus, Département Parasitologie et Mycologie, Paris, France
- * E-mail:
| |
Collapse
|
41
|
A DNA damage checkpoint pathway coordinates the division of dikaryotic cells in the ink cap mushroom Coprinopsis cinerea. Genetics 2013; 195:47-57. [PMID: 23792951 DOI: 10.1534/genetics.113.152231] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The fungal fruiting body or mushroom is a multicellular structure essential for sexual reproduction. It is composed of dikaryotic cells that contain one haploid nucleus from each mating partner sharing the same cytoplasm without undergoing nuclear fusion. In the mushroom, the pileus bears the hymenium, a layer of cells that includes the specialized basidia in which nuclear fusion, meiosis, and sporulation occur. Coprinopsis cinerea is a well-known model fungus used to study developmental processes associated with the formation of the fruiting body. Here we describe that knocking down the expression of Atr1 and Chk1, two kinases shown to be involved in the response to DNA damage in a number of eukaryotic organisms, dramatically impairs the ability to develop fruiting bodies in C. cinerea, as well as other developmental decisions such as sclerotia formation. These developmental defects correlated with the impairment in silenced strains to sustain an appropriated dikaryotic cell cycle. Dikaryotic cells in which chk1 or atr1 genes were silenced displayed a higher level of asynchronous mitosis and as a consequence aberrant cells carrying an unbalanced dose of nuclei. Since fruiting body initiation is dependent on the balanced mating-type regulator doses present in the dikaryon, we believe that the observed developmental defects were a consequence of the impaired cell cycle in the dikaryon. Our results suggest a connection between the DNA damage response cascade, cell cycle regulation, and developmental processes in this fungus.
Collapse
|
42
|
Lin YJ, Huang LH, Huang CT. Enhancement of heterologous gene expression in Flammulina velutipes using polycistronic vectors containing a viral 2A cleavage sequence. PLoS One 2013; 8:e59099. [PMID: 23516605 PMCID: PMC3597617 DOI: 10.1371/journal.pone.0059099] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 02/12/2013] [Indexed: 01/06/2023] Open
Abstract
Agrobacterium tumefaciens-mediated transformation for edible mushrooms has been previously established. However, the enhancement of heterologous protein production and the expression of multi-target genes remains a challenge. In this study, heterologous protein expression in the enoki mushroom Flammulina velutipes was notably enhanced using 2A peptide-mediated cleavage to co-express multiple copies of single gene. The polycistronic expression vectors were constructed by connecting multi copies of the enhanced green fluorescent protein (egfp) gene using 2A peptides derived from porcine teschovirus-1. The P2A peptides properly self-cleaved as shown by the formation of the transformants with antibiotic resistant capacity and exciting green fluorescence levels after introducing the vectors into F. velutipes mycelia. The results of western blot analysis, epifluorescent microscopy and EGFP production showed that heterologous protein expression in F. velutipes using the polycistronic strategy increased proportionally as the gene copy number increased from one to three copies. In contrast, much lower EGFP levels were detected in the F. velutipes transformants harboring four copies of the egfp gene due to mRNA instability. The polycistronic strategy using 2A peptide-mediated cleavage developed in this study can not only be used to express single gene in multiple copies, but also to express multiple genes in a single reading frame. It is a promising strategy for the application of mushroom molecular pharming.
Collapse
Affiliation(s)
- Yu-Ju Lin
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Li-Hsin Huang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Ching-Tsan Huang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
- * E-mail:
| |
Collapse
|
43
|
Dumesic PA, Natarajan P, Chen C, Drinnenberg IA, Schiller BJ, Thompson J, Moresco JJ, Yates JR, Bartel DP, Madhani HD. Stalled spliceosomes are a signal for RNAi-mediated genome defense. Cell 2013; 152:957-68. [PMID: 23415457 DOI: 10.1016/j.cell.2013.01.046] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 11/13/2012] [Accepted: 01/17/2013] [Indexed: 11/29/2022]
Abstract
Using the yeast Cryptococcus neoformans, we describe a mechanism by which transposons are initially targeted for RNAi-mediated genome defense. We show that intron-containing mRNA precursors template siRNA synthesis. We identify a Spliceosome-Coupled And Nuclear RNAi (SCANR) complex required for siRNA synthesis and demonstrate that it physically associates with the spliceosome. We find that RNAi target transcripts are distinguished by suboptimal introns and abnormally high occupancy on spliceosomes. Functional investigations demonstrate that the stalling of mRNA precursors on spliceosomes is required for siRNA accumulation. Lariat debranching enzyme is also necessary for siRNA production, suggesting a requirement for processing of stalled splicing intermediates. We propose that recognition of mRNA precursors by the SCANR complex is in kinetic competition with splicing, thereby promoting siRNA production from transposon transcripts stalled on spliceosomes. Disparity in the strength of expression signals encoded by transposons versus host genes offers an avenue for the evolution of genome defense.
Collapse
Affiliation(s)
- Phillip A Dumesic
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Amore A, Honda Y, Faraco V. Copper induction of enhanced green fluorescent protein expression inPleurotus ostreatusdriven by laccasepoxa1bpromoter. FEMS Microbiol Lett 2012; 337:155-63. [DOI: 10.1111/1574-6968.12023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Revised: 10/01/2012] [Accepted: 10/02/2012] [Indexed: 10/27/2022] Open
Affiliation(s)
- Antonella Amore
- Department of Chemical Sciences; University of Naples ‘Federico II’; Complesso Universitario Monte S. Angelo; Napoli; Italy
| | - Yoichi Honda
- Graduate School of Agriculture; Kyoto University; Kyoto; Japan
| | | |
Collapse
|
45
|
Amore A, Honda Y, Faraco V. Enhanced Green Fluorescent Protein Expression in Pleurotus ostreatus for In Vivo Analysis of Fungal Laccase Promoters. Appl Biochem Biotechnol 2012; 168:761-9. [DOI: 10.1007/s12010-012-9816-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 07/30/2012] [Indexed: 10/28/2022]
|
46
|
Yin Y, Liu Y, Jin H, Wang S, Zhao S, Geng X, Li M, Xu F. Polyethylene glycol-mediated transformation of fused egfp-hph gene under the control of gpd promoter in Pleurotus eryngii. Biotechnol Lett 2012; 34:1895-900. [DOI: 10.1007/s10529-012-0985-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 06/19/2012] [Indexed: 11/29/2022]
|
47
|
Characterization of glyceraldehyde-3-phosphate dehydrogenase gene RtGPD1 and development of genetic transformation method by dominant selection in oleaginous yeast Rhodosporidium toruloides. Appl Microbiol Biotechnol 2012; 97:719-29. [DOI: 10.1007/s00253-012-4223-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 06/01/2012] [Accepted: 06/02/2012] [Indexed: 10/28/2022]
|
48
|
Kemppainen MJ, Pardo AG. Gene knockdown by ihpRNA-triggering in the ectomycorrhizal basidiomycete fungus Laccaria bicolor. Bioeng Bugs 2012; 1:354-8. [PMID: 21326837 DOI: 10.4161/bbug.1.5.12385] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 05/07/2010] [Accepted: 05/11/2010] [Indexed: 11/19/2022] Open
Abstract
Ectomycorrhiza (ECM) is a mutualistic association between fungi and the roots of the vast majority of trees. These include numerous ecologically and economically relevant species and the participating fungal symbionts are predominantly filamentous basidiomycetes. In natural ecosystems the plant nutrient uptake from soil takes place via the extraradical mycelia of these ECM mycosimbionts as a trade for plant photosyntates. The symbiotic phase in the life cycle of ECM basidiomycetes is the dikaryotic hyphae. Therefore, studies on symbiotic relevant gene functions require the inactivation of both gene copies in these dikaryotic fungi. RNA silencing is a eukaryotic sequence homology-dependent degradation of target RNAs which is believed to have evolved as a protection mechanism against invading nucleic acids. In different eukaryotic organisms, including fungi, the RNA silencing pathway can be artificially triggered to target and degrade gene transcripts of interest, resulting in gene knock-down. Most importantly, RNA silencing can act at the cytosolic level affecting mRNAs originating from several gene copies and different nuclei thus offering an efficient means of altering gene expression in dikaryotic organisms. Therefore, the pHg/pSILBAγ silencing vector was constructed for efficient RNA silencing triggering in the model mycorrhizal fungus Laccaria bicolor. This cloning vector carries the Agaricus bisporus gpdII-promoter, two multiple cloning sites separated by a L. bicolor nitrate reductase intron and the Aspergillus nidulans trpC terminator. pSILBAγ allows an easy two-step PCR-cloning of hairpin sequences to be expressed in basidiomycetes. With one further cloning step into pHg, a pCAMBIA1300-based binary vector carrying a hygromycin resistance cassette, makes the pHg/pSILBAγ plasmid compatible with Agrobacterium-mediated transformation. The pHg/pSILBAγ-system results in predominantly single integrations of RNA silencing triggering T-DNAs in the fungal genome and the integration sites of the transgenes can be resolved by plasmid rescue. Besides the optimized use in L. bicolor, general consideration was taken to build a vector system with maximum compatibility with other homobasidiomycetes and different transformation techniques.
Collapse
Affiliation(s)
- Minna J Kemppainen
- Laboratorio de Micología Molecular, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Provincia de Buenos Aires, Argentina
| | | |
Collapse
|
49
|
Frandsen RJN. A guide to binary vectors and strategies for targeted genome modification in fungi using Agrobacterium tumefaciens-mediated transformation. J Microbiol Methods 2011; 87:247-62. [DOI: 10.1016/j.mimet.2011.09.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 09/09/2011] [Accepted: 09/09/2011] [Indexed: 01/31/2023]
|
50
|
Protease inhibitors clitocypin and macrocypin are differentially expressed within basidiomycete fruiting bodies. Biochimie 2011; 93:1685-93. [DOI: 10.1016/j.biochi.2011.05.034] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 05/31/2011] [Indexed: 11/18/2022]
|