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Tsegaye KN, Alemnew M, Berhane N. Saccharomyces cerevisiae for lignocellulosic ethanol production: a look at key attributes and genome shuffling. Front Bioeng Biotechnol 2024; 12:1466644. [PMID: 39386039 PMCID: PMC11461319 DOI: 10.3389/fbioe.2024.1466644] [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: 07/18/2024] [Accepted: 09/17/2024] [Indexed: 10/12/2024] Open
Abstract
These days, bioethanol research is looking at using non-edible plant materials, called lignocellulosic feedstocks, because they are cheap, plentiful, and renewable. However, these materials are complex and require pretreatment to release fermentable sugars. Saccharomyces cerevisiae, the industrial workhorse for bioethanol production, thrives in sugary environments and can handle high levels of ethanol. However, during lignocellulose fermentation, S. cerevisiae faces challenges like high sugar and ethanol concentrations, elevated temperatures, and even some toxic substances present in the pretreated feedstocks. Also, S. cerevisiae struggles to efficiently convert all the sugars (hexose and pentose) present in lignocellulosic hydrolysates. That's why scientists are exploring the natural variations within Saccharomyces strains and even figuring out ways to improve them. This review highlights why Saccharomyces cerevisiae remains a crucial player for large-scale bioethanol production from lignocellulose and discusses the potential of genome shuffling to create even more efficient yeast strains.
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Affiliation(s)
- Kindu Nibret Tsegaye
- Department of Biology, Gondar College of Teachers Education, Gondar, Ethiopia
- Institute of Biotechnology, University of Gondar, Gondar, Ethiopia
| | - Marew Alemnew
- Institute of Biotechnology, University of Gondar, Gondar, Ethiopia
| | - Nega Berhane
- Institute of Biotechnology, University of Gondar, Gondar, Ethiopia
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Benites-Pariente JS, Samolski I, Ludeña Y, Villena GK. CRISPR/Cas9 mediated targeted knock-in of eglA gene to improve endoglucanase activity of Aspergillus fumigatus LMB-35Aa. Sci Rep 2024; 14:19661. [PMID: 39179646 PMCID: PMC11344075 DOI: 10.1038/s41598-024-70397-4] [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: 05/03/2024] [Accepted: 08/16/2024] [Indexed: 08/26/2024] Open
Abstract
Bioeconomy goals for using biomass feedstock for biofuels and bio-based production has arisen the demand for fungal strains and enzymes for biomass processing. Despite well-known Trichoderma and Aspergillus commercial strains, continuous bioprospecting has revealed the fungal biodiversity potential for production of biomass degrading enzymes. The strain Aspergillus fumigatus LMB-35Aa has revealed a great potential as source of lignocellulose-degrading enzymes. Nevertheless, genetic improvement should be considered to increase its biotechnological potential. Molecular manipulation based on homologous direct recombination (HDR) in filamentous fungi poses a challenge since its low recombination rate. Currently, CRISPR/Cas9-mediated mutagenesis can enable precise and efficient editing of filamentous fungi genomes. In this study, a CRISPR/Cas9-mediated gene editing strategy for improving endoglucanase activity of A. fumigatus LMB-35Aa strain was successfully used, which constitutes the first report of heterologous cellulase production in filamentous fungi using this technology. For this, eglA gene from A. niger ATCC 10,864 was integrated into conidial melanin pksP gene locus, which facilitated the selection of edited events discerned by the emergence of albino colonies. Heterologous production of the EglA enzyme in a biofilm fermentation system resulted in a 40% improvement in endoglucanase activity of the mutant strain compared to the wild type.
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Affiliation(s)
- J S Benites-Pariente
- Laboratorio de Micología y Biotecnología "Marcel Gutiérrez-Correa", Universidad Nacional Agraria la Molina, 15024, Lima, Peru
| | - I Samolski
- Laboratorio de Micología y Biotecnología "Marcel Gutiérrez-Correa", Universidad Nacional Agraria la Molina, 15024, Lima, Peru
| | - Y Ludeña
- Laboratorio de Micología y Biotecnología "Marcel Gutiérrez-Correa", Universidad Nacional Agraria la Molina, 15024, Lima, Peru
| | - G K Villena
- Laboratorio de Micología y Biotecnología "Marcel Gutiérrez-Correa", Universidad Nacional Agraria la Molina, 15024, Lima, Peru.
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Kiyokawa K, Sakuma T, Moriguchi K, Sugiyama M, Akao T, Yamamoto T, Suzuki K. Conversion of polyploid and alloploid Saccharomyces sensu stricto strains to leu2 mutants by genome DNA editing. Appl Microbiol Biotechnol 2024; 108:416. [PMID: 38995331 PMCID: PMC11245423 DOI: 10.1007/s00253-024-13242-y] [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: 01/05/2024] [Revised: 06/06/2024] [Accepted: 06/20/2024] [Indexed: 07/13/2024]
Abstract
A large number of recombinant plasmids for the yeast Saccharomyces cerevisiae have been constructed and accumulated over the past four decades. It is desirable to apply the recombinant plasmid resources to Saccharomyces sensu stricto species group, which contains an increasing number of natural isolate and industrial strains. The application to the group encounters a difficulty. Natural isolates and industrial strains are exclusively prototrophic and polyploid, whereas direct application of most conventional plasmid resources imposes a prerequisite in host yeast strains of an auxotrophic mutation (i.e., leu2) that is rescued by a selection gene (e.g., LEU2) on the recombinant plasmids. To solve the difficulty, we aimed to generate leu2 mutants from yeast strains belonging to the yeast Saccharomyces sensu stricto species group by DNA editing. First, we modified an all-in-one type CRISPR-Cas9 plasmid pML104 by adding an antibiotic-resistance gene and designing guide sequences to target the LEU2 gene and to enable wide application in this yeast group. Then, the resulting CRISPR-Cas9 plasmids were exploited to seven strains belonging to five species of the group, including natural isolate, industrial, and allopolyploid strains. Colonies having the designed mutations in the gene appeared successfully by introducing the plasmids and assisting oligonucleotides to the strains. Most of the plasmids and resultant leu2- mutants produced in this study will be deposited in several repository organizations. KEY POINTS: • All-in-one type CRISPR-Cas9 plasmids targeting LEU2 gene were designed for broad application to Saccharomyces sensu stricto group species strains • Application of the plasmids generated leu2 mutants from strains including natural isolates, industrial, and allopolyploid strains • The easy conversion to leu2 mutants permits free access to recombinant plasmids having a LEU2 gene.
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Affiliation(s)
- Kazuya Kiyokawa
- Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
- Genome Editing Innovation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima, 731-5193, Japan
| | - Tetsushi Sakuma
- Program of Mathematical and Life Sciences and Frontier Development Program for Genome Editing, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Kazuki Moriguchi
- Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Minetaka Sugiyama
- Department of Food Sciences and Biotechnology, Faculty of Life Sciences, Hiroshima Institute of Technology, Hiroshima City, Hiroshima, 731-5193, Japan
| | - Takeshi Akao
- National Research Institute of Brewing, Higashi-Hiroshima City, Hiroshima, 739-0046, Japan
| | - Takashi Yamamoto
- Program of Mathematical and Life Sciences and Frontier Development Program for Genome Editing, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
- Genome Editing Innovation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima, 731-5193, Japan
| | - Katsunori Suzuki
- Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
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Minnaar LS, Kruger F, Fortuin J, Hoffmeester LJ, den Haan R. Engineering Saccharomyces cerevisiae for application in integrated bioprocessing biorefineries. Curr Opin Biotechnol 2024; 85:103030. [PMID: 38091873 DOI: 10.1016/j.copbio.2023.103030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 02/09/2024]
Abstract
After decades of research and development, no organism - natural or engineered - has been described that can produce commodity products through direct microbial conversion to meet industry demands in terms of rates and yields. Variation in lignocellulosic biomass (LCB) feedstocks, the lack of a widely applicable pretreatment method, and the limited economic value of energy products further complicates second-generation biofuel production. Nevertheless, the emergence of advanced genomic editing tools and a more comprehensive understanding of yeast metabolic systems offer promising avenues for the creation of yeast strains tailored to LCB biorefineries. Here, we discuss recent advances toward developing yeast strains that could convert different LCB fractions into a series of economically viable commodity products in a biorefinery.
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Affiliation(s)
- Letitia S Minnaar
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Francois Kruger
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Jordan Fortuin
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Lazzlo J Hoffmeester
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Riaan den Haan
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa.
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