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Yu L, An Z, Xie D, Yin D, Xie G, Gao X, Xiao Y, Liu J, Fang Z. From waste to protein: a new strategy of converting composted distilled grain wastes into animal feed. Front Microbiol 2024; 15:1405564. [PMID: 38881654 PMCID: PMC11176434 DOI: 10.3389/fmicb.2024.1405564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 05/16/2024] [Indexed: 06/18/2024] Open
Abstract
Distilled grain waste (DGW) is rich in nutrients and can be a potential resource as animal feed. However, DGW contains as much as 14% lignin, dramatically reducing the feeding value. White-rot fungi such as Pleurotus ostreatus could preferentially degrade lignin with high efficiency. However, lignin derivatives generated during alcohol distillation inhibit P. ostreatus growth. Thus, finding a new strategy to adjust the DGW properties to facilitate P. ostreatus growth is critical for animal feed preparation and DGW recycling. In this study, three dominant indigenous bacteria, including Sphingobacterium thermophilum X1, Pseudoxanthomonas byssovorax X3, and Bacillus velezensis 15F were chosen to generate single and compound microbial inoculums for DGW composting to prepare substrates for P. ostreatus growth. Compared with non-inoculated control or single microbial inoculation, all composite inoculations, especially the three-microbial compound, led to faster organic metabolism, shorter composting process, and improved physicochemical properties of DGW. P. ostreatus growth assays showed the fastest mycelial colonization (20.43 μg·g-1 ergosterol) and extension (9 mm/d), the highest ligninolytic enzyme activities (Lac, 152.68 U·g-1; Lip, 15.56 U·g-1; MnP, 0.34 U·g-1; Xylanase, 10.98 U·g-1; FPase, 0.71 U·g-1), and the highest lignin degradation ratio (30.77%) in the DGW sample after 12 h of composting with the three-microbial compound inoculation when compared to other groups. This sample was relatively abundant in bacteria playing critical roles in amino acid, carbohydrate, energy metabolism, and xenobiotic biodegradation, as suggested by metagenomic analysis. The feed value analysis revealed that P. ostreatus mycelia full colonization in composted DGW led to high fiber content retention and decreased lignin content (final ratio of 5% lignin) but elevated protein concentrations (about 130 g·kg-1 DM). An additional daily weight gain of 0.4 kg/d was shown in cattle feeding experiments by replacing 60% of regular feed with it. These findings demonstrate that compound inoculant consisting of three indigenous microorganisms is efficient to compost DGW and facilitate P. ostreatus growth. P. ostreatus decreased the lignin content of composted DGW during its mycelial growth, improving the quality of DGW for feeding cattle.
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Affiliation(s)
- Lei Yu
- School of Life Sciences, Anhui University, Hefei, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, China
| | - Zichao An
- School of Life Sciences, Anhui University, Hefei, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, China
| | - Dengdeng Xie
- School of Life Sciences, Anhui University, Hefei, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, China
| | - Diao Yin
- School of Life Sciences, Anhui University, Hefei, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, China
| | - Guopai Xie
- Anhui Golden Seed Winery Co., Ltd., Fuyang, China
| | - Xuezhi Gao
- Anhui Golden Seed Winery Co., Ltd., Fuyang, China
| | - Yazhong Xiao
- School of Life Sciences, Anhui University, Hefei, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, China
| | - Juanjuan Liu
- School of Life Sciences, Anhui University, Hefei, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, China
| | - Zemin Fang
- School of Life Sciences, Anhui University, Hefei, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, China
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Nakazawa T, Kawauchi M, Otsuka Y, Han J, Koshi D, Schiphof K, Ramírez L, Pisabarro AG, Honda Y. Pleurotus ostreatus as a model mushroom in genetics, cell biology, and material sciences. Appl Microbiol Biotechnol 2024; 108:217. [PMID: 38372792 PMCID: PMC10876731 DOI: 10.1007/s00253-024-13034-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/11/2024] [Accepted: 01/25/2024] [Indexed: 02/20/2024]
Abstract
Pleurotus ostreatus, also known as the oyster mushroom, is a popular edible mushroom cultivated worldwide. This review aims to survey recent progress in the molecular genetics of this fungus and demonstrate its potential as a model mushroom for future research. The development of modern molecular genetic techniques and genome sequencing technologies has resulted in breakthroughs in mushroom science. With efficient transformation protocols and multiple selection markers, a powerful toolbox, including techniques such as gene knockout and genome editing, has been developed, and numerous new findings are accumulating in P. ostreatus. These include molecular mechanisms of wood component degradation, sexual development, protein secretion systems, and cell wall structure. Furthermore, these techniques enable the identification of new horizons in enzymology, biochemistry, cell biology, and material science through protein engineering, fluorescence microscopy, and molecular breeding. KEY POINTS: • Various genetic techniques are available in Pleurotus ostreatus. • P. ostreatus can be used as an alternative model mushroom in genetic analyses. • New frontiers in mushroom science are being developed using the fungus.
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Affiliation(s)
- Takehito Nakazawa
- Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Moriyuki Kawauchi
- Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Yuitsu Otsuka
- Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Junxian Han
- Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Daishiro Koshi
- Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Kim Schiphof
- Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Lucía Ramírez
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), 31006, Pamplona, Spain
| | - Antonio G Pisabarro
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), 31006, Pamplona, Spain
| | - Yoichi Honda
- Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan.
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Xu H, Nakazawa T, Zhang Y, Oh M, Bao D, Kawauchi M, Sakamoto M, Honda Y. Introducing multiple-gene mutations in Pleurotus ostreatus using a polycistronic tRNA and CRISPR guide RNA strategy. FEMS Microbiol Lett 2022; 369:6776014. [PMID: 36302144 DOI: 10.1093/femsle/fnac102] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/26/2022] [Accepted: 10/25/2022] [Indexed: 12/13/2022] Open
Abstract
The white-rot fungus Pleurotus ostreatus is an agaricomycete that is frequently used in molecular genetics studies as many useful tools are applicable to the fungus. In particular, efficient gene targeting using homologous recombination and CRISPR/Cas9 enables the introduction of a mutation in the gene of interest for functional analysis. Multiple genes encoding various lignocellulose-degrading enzymes are predicted to be present in the genome; therefore, analyses of multiple-gene mutants are required to elucidate the mechanisms underlying lignocellulose degradation by P. ostreatus. Conventional tools for generating multiple-gene mutations in P. ostreatus are laborious and time-consuming. Therefore, more efficient and practical methods are needed. In this study, we introduced CRISPR/Cas9-assisted multiple-gene mutations using a polycistronic tRNA and CRISPR guide RNA approach. The frequency (triple-gene mutation in fcy1, vp2, and 62347) was only 3.3% when a tetracistronic tRNA-sgRNA containing four different sgRNAs targeting fcy1, vp2, vp3, or 62347 was expressed. It increased to 20% (triple-gene mutation in vp1, vp2, and vp3) after a tricistronic tRNA-sgRNA was expressed with replaced/modulated promoter and tRNA sequences. This study demonstrated, for the first time, the applicability of a strategy to induce multiple-gene mutations in P. ostreatus in a transformation experiment.
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Affiliation(s)
- Haibo Xu
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Takehito Nakazawa
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yufan Zhang
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Minji Oh
- Mushroom division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Bisan-ro, Eumseong-gun, Chungcheongbuk-do 22709, Republic of Korea
| | - Dapeng Bao
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Moriyuki Kawauchi
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Masahiro Sakamoto
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yoichi Honda
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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Yamasaki F, Nakazawa T, Oh M, Bao D, Kawauchi M, Sakamoto M, Honda Y. Gene targeting of dikaryotic Pleurotus ostreatus nuclei using the CRISPR/Cas9 system. FEMS Microbiol Lett 2022; 369:6674758. [PMID: 36001999 DOI: 10.1093/femsle/fnac083] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/07/2022] [Accepted: 08/22/2022] [Indexed: 11/14/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9)-assisted gene targeting is a promising method used in molecular breeding. We recently reported the successful introduction of this method in the monokaryotic Pleurotus ostreatus (oyster mushroom), PC9. However, considering their application in mushroom breeding, dikaryotic strains (with targeted gene mutations in both nuclei) need to be generated. This is laborious and time-consuming because a classical crossing technique is used. Herein, we report a technique that targets both nuclei of dikaryotic P. ostreatus, PC9×#64 in a transformation experiment using plasmid-based CRISPR/Cas9, with the aim of developing a method for efficient and rapid molecular breeding. As an example, we targeted strains with low basidiospore production ability through the meiosis-related genes mer3 or msh4. Four different plasmids containing expression cassettes for Cas9 and two different gRNAs targeting mer3 or msh4 were constructed and separately introduced into PC9×#64. Eight of the 38 dikaryotic transformants analyzed produced no basidiospores. Genomic PCR suggested that msh4 or mer3 mutations were introduced into both nuclei of seven out of eight strains. Thus, in this study, we demonstrated simultaneous gene targeting using our CRISPR/Cas9 system, which may be useful for the molecular breeding of cultivated agaricomycetes.
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Affiliation(s)
- Fuga Yamasaki
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Takehito Nakazawa
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Minji Oh
- Mushroom division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Bisan-ro, Eumseong-gun, Chungcheongbuk-do, 22709, Republic of Korea
| | - Dapeng Bao
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Moriyuki Kawauchi
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masahiro Sakamoto
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yoichi Honda
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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CRISPR/Cas9 using a transient transformation system in Ceriporiopsis subvermispora. Appl Microbiol Biotechnol 2022; 106:5575-5585. [PMID: 35902408 DOI: 10.1007/s00253-022-12095-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/15/2022] [Accepted: 07/20/2022] [Indexed: 11/02/2022]
Abstract
Ceriporiopsis subvermispora is a white-rot fungus with great potential for industrial and biotechnological applications, such as the pretreatment of lignocellulose in biorefineries, as it decomposes the lignin in the plant cell wall without causing severe cellulose degradation. A genetic transformation system was recently developed; however, gene-targeting experiments to disrupt or modify the gene(s) of interest remain challenging, and this is a bottleneck for further molecular genetic studies and breeding of C. subvermispora. Herein, we report efficient clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9)-assisted gene mutagenesis in this fungus. Two plasmids expressing Cas9 together with a different pyrG-targeting single-guide RNA were separately introduced into the monokaryotic C. subvermispora strain FP-90031-Sp/1, which frequently generated strains that exhibited resistance to 5-fluoroorotic acid and uridine/uracil auxotrophy. Southern blot analyses and genomic polymerase chain reaction followed by DNA sequencing of some mutants revealed that they were pyrG mutants. We also observed that hygromycin resistance of the pyrG mutants was frequently lost after repeated subcultivations, indicating that a maker-free genome editing occurred successfully. It is also suggested that a gene mutation(s) can be introduced via a transient expression of Cas9 and a single-guide RNA; this feature, together with high-frequency gene targeting using the CRISPR/Cas9 system, would be helpful for studies on lignocellulose-degrading systems in C. subvermispora. KEY POINTS: • Efficient plasmid-based CRISPR/Cas9 was established in C. subvermispora. • The mutations can be introduced via a transient expression of Cas9 and sgRNA. • A maker-free CRISPR/Cas9 is established in this fungus.
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Abstract
Plant-derived biomass is the most abundant biogenic carbon source on Earth. Despite this, only a small clade of organisms known as white-rot fungi (WRF) can efficiently break down both the polysaccharide and lignin components of plant cell walls. This unique ability imparts a key role for WRF in global carbon cycling and highlights their potential utilization in diverse biotechnological applications. To date, research on WRF has primarily focused on their extracellular ‘digestive enzymes’ whereas knowledge of their intracellular metabolism remains underexplored. Systems biology is a powerful approach to elucidate biological processes in numerous organisms, including WRF. Thus, here we review systems biology methods applied to WRF to date, highlight observations related to their intracellular metabolism, and conduct comparative extracellular proteomic analyses to establish further correlations between WRF species, enzymes, and cultivation conditions. Lastly, we discuss biotechnological opportunities of WRF as well as challenges and future research directions.
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