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Kobashi Y, Nakayama E, Fukumori N, Shimojima A, Tabira M, Nishimura Y, Mukae M, Muto A, Nakashima N, Okutsu K, Yoshizaki Y, Futagami T, Takamine K, Tamaki H. Homozygous gene disruption in diploid yeast through a single transformation. J Biosci Bioeng 2024; 137:31-37. [PMID: 37981488 DOI: 10.1016/j.jbiosc.2023.11.003] [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: 06/20/2023] [Revised: 10/13/2023] [Accepted: 11/05/2023] [Indexed: 11/21/2023]
Abstract
As industrial shochu yeast is a diploid strain, obtaining a strain with mutations in both allelic genes was considered difficult. We investigated a method for disrupting two copies of a homozygous gene with a single transformation. We designed a disruption cassette containing an intact LYS5 flanked by nonfunctional ura3 gene fragments divided into the 5'- and 3'-regions. These fragments had overlapping sequences that enabled LYS5 removal as well as URA3 regeneration through loop-out. Furthermore, both ends of the disruption cassette had an additional repeat sequence that allowed the cassette to be removed from the chromosome through loop-out. First, 45 bases of 5'- and 3'-regions of target gene sequences were added on both ends of this cassette using polymerase chain reaction; the resultant disruption cassette was introduced into a shochu yeast strain (ura3/ura3 lys5/lys5); then, single allele disrupted strains were selected on Lys drop-out plates; and after cultivation in YPD medium, double-disrupted strains, in which replacement of another allelic gene with disruption cassette by loss of heterozygosity and regeneration of URA3 in one of the cassettes by loop-out, were obtained by selection on Ura and Lys drop-out plates. The disruption cassettes were removed from the double-disrupted strain via loop-out between repeat sequences in the disruption cassette. The strains that lost either URA3 or LYS5 were counter-selected on 5-fluoroorotic acid or α-amino adipic acid plates, respectively. Using this method, we obtained leu2/leu2 and leu2/leu2 his3/his3 strains in shochu yeast, demonstrating the effectiveness and repeatability of this gene disruption technique in diploid yeast Saccharomyces cerevisiae.
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Affiliation(s)
- Yuki Kobashi
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Eri Nakayama
- Graduate School of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Naoki Fukumori
- Graduate School of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Ayane Shimojima
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Manami Tabira
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Yuki Nishimura
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Manami Mukae
- Graduate School of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Ai Muto
- Graduate School of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Naoto Nakashima
- Graduate School of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Kayu Okutsu
- Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Yumiko Yoshizaki
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Taiki Futagami
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Kazunori Takamine
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Hisanori Tamaki
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan.
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Hayashi K, Kajiwara Y, Futagami T, Goto M, Takashita H. Making Traditional Japanese Distilled Liquor, Shochu and Awamori, and the Contribution of White and Black Koji Fungi. J Fungi (Basel) 2021; 7:517. [PMID: 34203379 PMCID: PMC8306306 DOI: 10.3390/jof7070517] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/16/2021] [Accepted: 06/25/2021] [Indexed: 11/30/2022] Open
Abstract
The traditional Japanese single distilled liquor, which uses koji and yeast with designated ingredients, is called "honkaku shochu." It is made using local agricultural products and has several types, including barley shochu, sweet potato shochu, rice shochu, and buckwheat shochu. In the case of honkaku shochu, black koji fungus (Aspergillus luchuensis) or white koji fungus (Aspergillus luchuensis mut. kawachii) is used to (1) saccharify the starch contained in the ingredients, (2) produce citric acid to prevent microbial spoilage, and (3) give the liquor its unique flavor. In order to make delicious shochu, when cultivating koji fungus during the shochu production process, we use a unique temperature control method to ensure that these three important elements, which greatly affect the taste of the produced liquor, are balanced without any excess or deficiency. This review describes in detail the production method of honkaku shochu, a distilled spirit unique to Japan and whose market is expected to expand worldwide, with special attention paid to the koji fungi cultivation step. Furthermore, we describe the history of the koji fungi used today in the production of shochu, and we provide a thorough explanation of the characteristics of each koji fungi. We also report the latest research progress on this topic.
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Affiliation(s)
- Kei Hayashi
- Sanwa Research Institute, Sanwa Shurui Co., Ltd., Usa 879-0495, Japan; (Y.K.); (H.T.)
| | - Yasuhiro Kajiwara
- Sanwa Research Institute, Sanwa Shurui Co., Ltd., Usa 879-0495, Japan; (Y.K.); (H.T.)
| | - Taiki Futagami
- Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan;
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan;
| | - Masatoshi Goto
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan;
- Department of Applied Biochemistry and Food Science, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Hideharu Takashita
- Sanwa Research Institute, Sanwa Shurui Co., Ltd., Usa 879-0495, Japan; (Y.K.); (H.T.)
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Luan MW, Zhang XM, Zhu ZB, Chen Y, Xie SQ. Evaluating Structural Variation Detection Tools for Long-Read Sequencing Datasets in Saccharomyces cerevisiae. Front Genet 2020; 11:159. [PMID: 32211024 PMCID: PMC7075250 DOI: 10.3389/fgene.2020.00159] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/11/2020] [Indexed: 01/01/2023] Open
Abstract
Structural variation (SV) represents a major form of genetic variations that contribute to polymorphic variations, human diseases, and phenotypes in many organisms. Long-read sequencing has been successfully used to identify novel and complex SVs. However, comparison of SV detection tools for long-read sequencing datasets has not been reported. Therefore, we developed an analysis workflow that combined two alignment tools (NGMLR and minimap2) and five callers (Sniffles, Picky, smartie-sv, PBHoney, and NanoSV) to evaluate the SV detection in six datasets of Saccharomyces cerevisiae. The accuracy of SV regions was validated by re-aligning raw reads in diverse alignment tools, SV callers, experimental conditions, and sequencing platforms. The results showed that SV detection between NGMLR and minimap2 was not significant when using the same caller. The PBHoney was with the highest average accuracy (89.04%) and Picky has the lowest average accuracy (35.85%). The accuracy of NanoSV, Sniffles, and smartie-sv was 68.67%, 60.47%, and 57.67%, respectively. In addition, smartie-sv and NanoSV detected the most and least number of SVs, and SV detection from the PacBio sequencing platform was significantly more than that from ONT (p = 0.000173).
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Affiliation(s)
- Mei-Wei Luan
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou, China
| | - Xiao-Ming Zhang
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Huhhot, China
| | - Zi-Bin Zhu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou, China
| | - Ying Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shang-Qian Xie
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou, China
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Watanabe D, Tashiro S, Shintani D, Sugimoto Y, Iwami A, Kajiwara Y, Takashita H, Takagi H. Loss of Rim15p in shochu yeast alters carbon utilization during barley shochu fermentation. Biosci Biotechnol Biochem 2019; 83:1594-1597. [DOI: 10.1080/09168451.2019.1594679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
ABSTRACT
Rim15p of the yeast Saccharomyces cerevisiae is a Greatwall-family protein kinase that inhibits alcoholic fermentation during sake brewing. To elucidate the roles of Rim15p in barley shochu fermentation, RIM15 was deleted in shochu yeast. The disruptant did not improve ethanol yield, but altered sugar and glycerol contents in the mash, suggesting that Rim15p has a novel function in carbon utilization.
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Affiliation(s)
- Daisuke Watanabe
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Satoshi Tashiro
- Research & Development Laboratory, Sanwa Shurui Co. Ltd., Oita, Japan
| | - Dai Shintani
- Research & Development Laboratory, Sanwa Shurui Co. Ltd., Oita, Japan
| | - Yukiko Sugimoto
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Akihiko Iwami
- Research & Development Laboratory, Sanwa Shurui Co. Ltd., Oita, Japan
| | - Yasuhiro Kajiwara
- Research & Development Laboratory, Sanwa Shurui Co. Ltd., Oita, Japan
| | | | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
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Abstract
Completion of the whole genome sequence of a laboratory yeast strain Saccharomyces cerevisiae in 1996 ushered in the development of genome-wide experimental tools and accelerated subsequent genetic study of S. cerevisiae. The study of sake yeast also shared the benefit of such tools as DNA microarrays, gene disruption-mutant collections, and others. Moreover, whole genome analysis of representative sake yeast strain Kyokai no. 7 was performed in the late 2000s, and enabled comparative genomics between sake yeast and laboratory yeast, resulting in some notable finding for of sake yeast genetics. Development of next-generation DNA sequencing and bioinformatics also drastically changed the field of the genetics, including for sake yeast. Genomics and the genome-wide study of sake yeast have progressed under these circumstances during the last two decades, and are summarized in this article. Abbreviations: AFLP: amplified fragment length polymorphism; CGH: comparative genomic hybridization; CNV: copy number variation; DMS: dimethyl succinate; DSW: deep sea water; LOH: loss of heterozygosity; NGS: next generation sequencer; QTL: quantitative trait loci; QTN: quantitative trait nucleotide; SAM: S-adenosyl methionine; SNV: single nucleotide variation.
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Affiliation(s)
- Takeshi Akao
- a National Research Institute of Brewing , Higashi-hiroshima , Japan
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Genomic Sequence of Saccharomyces cerevisiae BAW-6, a Yeast Strain Optimal for Brewing Barley Shochu. GENOME ANNOUNCEMENTS 2018; 6:6/14/e00228-18. [PMID: 29622617 PMCID: PMC5887032 DOI: 10.1128/genomea.00228-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Here, we report the draft genome sequence of Saccharomyces cerevisiae strain BAW-6, which is used for the production of barley shochu, a traditional Japanese spirit. This genomic information can be used to elucidate the genetic basis underlying the high alcohol production capacity and citric acid tolerance of shochu yeast.
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