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Yoda T. Materials evaluation using cell-sized liposomes. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:5509-5518. [PMID: 39109603 DOI: 10.1039/d4ay00803k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
Cell membranes play a vital role in delineating the internal cellular environment from the external surroundings, going beyond mere compartmentalization. Researchers have delved into the structural organization, properties, and functional roles of biological membranes, paving the way for their application in substance identification, detection, and quantification. This review introduces various studies and their implications for future research. It underscores the advantages of employing cell-sized liposomes, which enable real-time observation for rapid detection and analysis of diverse materials. The utility of cell-sized liposomes extends to their size, dynamic shape changes, and phase-separation, offering valuable insights into the evaluation of targeted materials.
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Affiliation(s)
- Tsuyoshi Yoda
- Industrial Research Institute, Aomori Prefectural Industrial Technology Research Center, 221-10 Yamaguchi Nogi, Aomori City, Aomori, 030-0142, Japan.
- The United Graduate School of Agricultural Sciences, Iwate University, 3-18-8, Ueda, Morioka City, Iwate 020-8550, Japan
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2
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Shibata Y, Yamada T, Ikeda Y, Kanai M, Fujii T, Akao T, Goshima T, Isogai A, Takahashi T. Effect of S-adenosyl-methionine accumulation on hineka odor in sake brewed with a non-Kyokai yeast. J Biosci Bioeng 2024; 137:268-273. [PMID: 38310037 DOI: 10.1016/j.jbiosc.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 02/05/2024]
Abstract
Hineka is a type of off-flavor of sake and is attributed to the presence of several compounds, including a major one called dimethyl trisulfide (DMTS). The production of the main precursor of DMTS involves yeast methionine salvage pathway. The DMTS-producing potential (DMTS-pp) of sake brewed using the Km67 strain, a non-Kyokai sake yeast, is lower than that of sake brewed using Kyokai yeast; however, the detailed mechanism is unclear. We focused on S-adenosyl-methionine (SAM) and aimed to elucidate the mechanism that prevents DMTS production in sake brewed using the Km67 strain. We revealed that SAM is involved in DMTS production in sake, and that the conversion of SAM to the DMTS precursor occurs through an enzymatic reaction rather than a chemical reaction. Based on previous reports on ADO1 and MDE1 genes, sake brewing tests were performed using the Km67 Δmde1, Δado1, and Δmde1Δado1 strains. A comparison of the SAM content of pressed sake cakes and DMTS-pp of sake produced using the Km67 Δado1 strain showed an increase in both SAM content and DMTS-pp compared to those produced using the parent strain. However, the Km67 Δmde1Δado1 strain showed little increase in DMTS-pp compared to the Km67 Δmde1 strain, despite an increase in SAM content. These results suggest that SAM accumulation in yeast plays a role in the production of DMTS in sake through the methionine salvage pathway. Moreover, the low SAM-accumulation characteristic of the Km67 strain contributes to low DMTS production in sake.
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Affiliation(s)
- Yusuke Shibata
- General Research Laboratory, Kiku-Masamune Sake Brewing Co. Ltd., 1-8-6 Uozaki-nishimachi, Higashinada-ku, Kobe, Hyogo 658-0026, Japan.
| | - Tasuku Yamada
- General Research Laboratory, Kiku-Masamune Sake Brewing Co. Ltd., 1-8-6 Uozaki-nishimachi, Higashinada-ku, Kobe, Hyogo 658-0026, Japan
| | - Yuriko Ikeda
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashihiroshima, Hiroshima 739-0046, Japan
| | - Muneyoshi Kanai
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashihiroshima, Hiroshima 739-0046, Japan
| | - Tsutomu Fujii
- Faculty of Food and Agricultural Sciences, Fukushima University, 1 Kanayagawa, Fukushima 960-1296, Japan
| | - Takeshi Akao
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashihiroshima, Hiroshima 739-0046, Japan
| | - Tetsuya Goshima
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashihiroshima, Hiroshima 739-0046, Japan
| | - Atsuko Isogai
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashihiroshima, Hiroshima 739-0046, Japan
| | - Toshinari Takahashi
- General Research Laboratory, Kiku-Masamune Sake Brewing Co. Ltd., 1-8-6 Uozaki-nishimachi, Higashinada-ku, Kobe, Hyogo 658-0026, Japan
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3
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Nakagawa T, Yoshimura A, Sawai Y, Hisamatsu K, Akao T, Masaki K. Japanese sake making using wild yeasts isolated from natural environments. Biosci Biotechnol Biochem 2024; 88:231-236. [PMID: 38364793 DOI: 10.1093/bbb/zbae003] [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: 09/29/2023] [Accepted: 01/04/2024] [Indexed: 02/18/2024]
Abstract
Saccharomyces cerevisiae is one of the most important microorganisms for the food industry, including Japanese sake, beer, wine, bread, and other products. For sake making, Kyokai sake yeast strains are considered one of the best sake yeast strains because these strains possess fermentation properties that are suitable for the quality of sake required. In recent years, the momentum for the development of unique sake, which is distinct from conventional sake, has grown, and there is now a demand to develop unique sake yeasts that have different sake making properties than Kyokai sake yeast strains. In this minireview, we focus on "wild yeasts," which inhabit natural environments, and introduce basic research on the wild yeasts for sake making, such as their genetic and sake fermentation aspects. Finally, we also discuss the molecular breeding of wild yeast strains for sake fermentation and the possibility for sake making using wild yeasts.
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Affiliation(s)
- Tomoyuki Nakagawa
- The Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | | | - Yoshinori Sawai
- Gifu Prefectural Research Institute for Food Sciences, Gifu, Japan
| | | | - Takeshi Akao
- National Research Institute of Brewing, Higashihiroshima, Hiroshima, Japan
| | - Kazuo Masaki
- National Research Institute of Brewing, Higashihiroshima, Hiroshima, Japan
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4
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Watanabe D. Sake yeast symbiosis with lactic acid bacteria and alcoholic fermentation. Biosci Biotechnol Biochem 2024; 88:237-241. [PMID: 38006236 DOI: 10.1093/bbb/zbad167] [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: 09/30/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
The yeast Saccharomyces cerevisiae plays a pivotal role in the production of fermented foods by converting sugars in ingredients into ethanol through alcoholic fermentation. However, how accurate is our understanding of its biological significance? Although yeast is essential to produce alcoholic beverages and bioethanol, yeast does not yield ethanol for humankind. Yeast obtains energy in the form of ATP for its own vital processes through alcoholic fermentation, which generates ethanol as a byproduct. The production of ethanol may have more significance for yeast, since many other organisms do not produce ethanol, a highly toxic substance, to obtain energy. The key to address this issue has not been found using conventional microbiology, where yeasts are isolated and cultured in pure form. This review focuses on a possible novel role of yeast alcohol fermentation, which is revealed through our recent studies of microbial interactions.
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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
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5
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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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6
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Hotta N, Kotaka A, Matsumura K, Sasano Y, Hata Y, Harada T, Sugiyama M, Harashima S, Ishida H. Effect of yeast chromosome II aneuploidy on malate production in sake brewing. J Biosci Bioeng 2024; 137:24-30. [PMID: 37989703 DOI: 10.1016/j.jbiosc.2023.10.007] [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: 05/11/2022] [Revised: 10/08/2023] [Accepted: 10/31/2023] [Indexed: 11/23/2023]
Abstract
Chromosome aneuploidy is a common phenomenon in industrial yeast. Aneuploidy is considered one of the strategies to enhance the industrial properties of Saccharomyces cerevisiae strains. However, the effects of chromosomal aneuploidy on the brewing properties of sake have not been extensively studied. In this study, sake brewing was performed using a series of genome-wide segmental duplicated laboratory S. cerevisiae strains, and the effects of each segmentally duplicated region on sake brewing were investigated. We found that the duplication of specific chromosomal regions affected the production of organic acids and aromatic compounds in sake brewing. As organic acids significantly influence the taste of sake, we focused on the segmental duplication of chromosome II that alters malate levels. Sake yeast Kyokai No. 901 strains with segmental chromosome II duplication were constructed using a polymerase chain reaction-mediated chromosomal duplication method, and sake was brewed using the resultant aneuploid sake yeast strains. The results showed the possibility of developing sake yeast strains exhibiting low malate production without affecting ethanol production capacity. Our study revealed that aneuploidy in yeast alters the brewing properties; in particular, the aneuploidy of chromosome II alters malate production in sake brewing. In conclusion, aneuploidization can be a novel and useful tool to breed sake yeast strains with improved traits, possessing industrial significance.
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Affiliation(s)
- Natsuki Hotta
- Research Institute, Gekkeikan Sake Co., Ltd., 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto 612-8385, Japan.
| | - Atsushi Kotaka
- Research Institute, Gekkeikan Sake Co., Ltd., 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto 612-8385, Japan
| | - Kengo Matsumura
- Research Institute, Gekkeikan Sake Co., Ltd., 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto 612-8385, Japan
| | - Yu Sasano
- Department of Applied Microbial Technology, Faculty of Biotechnology and Life Science, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Yoji Hata
- Research Institute, Gekkeikan Sake Co., Ltd., 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto 612-8385, Japan
| | - Tomoka Harada
- Department of Food Sciences and Biotechnology, Faculty of Life Sciences, Hiroshima Institute of Technology, 2-1-1 Miyake, Saeki-ku, Hiroshima 731-5193, Japan
| | - Minetaka Sugiyama
- Department of Food Sciences and Biotechnology, Faculty of Life Sciences, Hiroshima Institute of Technology, 2-1-1 Miyake, Saeki-ku, Hiroshima 731-5193, Japan
| | - Satoshi Harashima
- Department of Applied Microbial Technology, Faculty of Biotechnology and Life Science, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Hiroki Ishida
- Research Institute, Gekkeikan Sake Co., Ltd., 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto 612-8385, Japan
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Klinkaewboonwong N, Ohnuki S, Chadani T, Nishida I, Ushiyama Y, Tomiyama S, Isogai A, Goshima T, Ghanegolmohammadi F, Nishi T, Kitamoto K, Akao T, Hirata D, Ohya Y. Targeted Mutations Produce Divergent Characteristics in Pedigreed Sake Yeast Strains. Microorganisms 2023; 11:1274. [PMID: 37317248 DOI: 10.3390/microorganisms11051274] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/29/2023] [Accepted: 05/09/2023] [Indexed: 06/16/2023] Open
Abstract
Modification of the genetic background and, in some cases, the introduction of targeted mutations can play a critical role in producing trait characteristics during the breeding of crops, livestock, and microorganisms. However, the question of how similar trait characteristics emerge when the same target mutation is introduced into different genetic backgrounds is unclear. In a previous study, we performed genome editing of AWA1, CAR1, MDE1, and FAS2 on the standard sake yeast strain Kyokai No. 7 to breed a sake yeast with multiple excellent brewing characteristics. By introducing the same targeted mutations into other pedigreed sake yeast strains, such as Kyokai strains No. 6, No. 9, and No. 10, we were able to create sake yeasts with the same excellent brewing characteristics. However, we found that other components of sake made by the genome-edited yeast strains did not change in the exact same way. For example, amino acid and isobutanol contents differed among the strain backgrounds. We also showed that changes in yeast cell morphology induced by the targeted mutations also differed depending on the strain backgrounds. The number of commonly changed morphological parameters was limited. Thus, divergent characteristics were produced by the targeted mutations in pedigreed sake yeast strains, suggesting a breeding strategy to generate a variety of sake yeasts with excellent brewing characteristics.
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Affiliation(s)
- Norapat Klinkaewboonwong
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Tomoya Chadani
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Ikuhisa Nishida
- Sakeology Center, Niigata University, 2-8050, Ikarashi, Niigata 950-2181, Japan
| | - Yuto Ushiyama
- Sakeology Course, Graduate School of Science and Technology, Niigata University, 2-8050, Ikarashi, Niigata 950-2181, Japan
| | - Saki Tomiyama
- Sakeology Course, Graduate School of Science and Technology, Niigata University, 2-8050, Ikarashi, Niigata 950-2181, Japan
| | - Atsuko Isogai
- National Research Institute of Brewing, Higashi-Hiroshima, Hiroshima 739-0046, Japan
- Program of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Tetsuya Goshima
- National Research Institute of Brewing, Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Farzan Ghanegolmohammadi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tomoyuki Nishi
- Sake Research Center, Asahi Sake Brewing Co., Ltd., Nagaoka, Niigata 949-5494, Japan
| | - Katsuhiko Kitamoto
- Department of Pharmaceutical and Medical Business Sciences, Nihon Pharmaceutical University, Bunkyo-ku, Tokyo 113-0034, Japan
| | - Takeshi Akao
- National Research Institute of Brewing, Higashi-Hiroshima, Hiroshima 739-0046, Japan
- Program of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Dai Hirata
- Sakeology Center, Niigata University, 2-8050, Ikarashi, Niigata 950-2181, Japan
- Sakeology Course, Graduate School of Science and Technology, Niigata University, 2-8050, Ikarashi, Niigata 950-2181, Japan
- Program of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
- Sake Research Center, Asahi Sake Brewing Co., Ltd., Nagaoka, Niigata 949-5494, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
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Negoro H, Ishida H. Development of sake yeast breeding and analysis of genes related to its various phenotypes. FEMS Yeast Res 2022; 22:6825454. [PMID: 36370450 DOI: 10.1093/femsyr/foac057] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/21/2022] [Accepted: 11/10/2022] [Indexed: 11/13/2022] Open
Abstract
Sake is a traditional Japanese alcoholic beverage made from rice and water, fermented by the filamentous fungi Aspergillus oryzae and the yeast Saccharomyces cerevisiae. Yeast strains, also called sake yeasts, with high alcohol yield and the ability to produce desired flavor compounds in the sake, have been isolated from the environment for more than a century. Furthermore, numerous methods to breed sake yeasts without genetic modification have been developed. The objectives of breeding include increasing the efficiency of production, improving the aroma and taste, enhancing safety, imparting functional properties, and altering the appearance of sake. With the recent development of molecular biology, the suitable sake brewing characteristics in sake yeasts, and the causes of acquisition of additional phenotypes in bred yeasts have been elucidated genetically. This mini-review summarizes the history and lineage of sake yeasts, their genetic characteristics, the major breeding methods used, and molecular biological analysis of the acquired strains. The data in this review on the metabolic mechanisms of sake yeasts and their genetic profiles will enable the development of future strains with superior phenotypes.
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Affiliation(s)
- Hiroaki Negoro
- Research Institute, Gekkeikan Sake Co. Ltd., 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto 612-8385, Japan
| | - Hiroki Ishida
- Research Institute, Gekkeikan Sake Co. Ltd., 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto 612-8385, Japan
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9
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Ghanegolmohammadi F, Ohnuki S, Ohya Y. Assignment of unimodal probability distribution models for quantitative morphological phenotyping. BMC Biol 2022; 20:81. [PMID: 35361198 PMCID: PMC8969357 DOI: 10.1186/s12915-022-01283-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 03/17/2022] [Indexed: 01/02/2023] Open
Abstract
Background Cell morphology is a complex and integrative readout, and therefore, an attractive measurement for assessing the effects of genetic and chemical perturbations to cells. Microscopic images provide rich information on cell morphology; therefore, subjective morphological features are frequently extracted from digital images. However, measured datasets are fundamentally noisy; thus, estimation of the true values is an ultimate goal in quantitative morphological phenotyping. Ideal image analyses require precision, such as proper probability distribution analyses to detect subtle morphological changes, recall to minimize artifacts due to experimental error, and reproducibility to confirm the results. Results Here, we present UNIMO (UNImodal MOrphological data), a reliable pipeline for precise detection of subtle morphological changes by assigning unimodal probability distributions to morphological features of the budding yeast cells. By defining the data type, followed by validation using the model selection method, examination of 33 probability distributions revealed nine best-fitting probability distributions. The modality of the distribution was then clarified for each morphological feature using a probabilistic mixture model. Using a reliable and detailed set of experimental log data of wild-type morphological replicates, we considered the effects of confounding factors. As a result, most of the yeast morphological parameters exhibited unimodal distributions that can be used as basic tools for powerful downstream parametric analyses. The power of the proposed pipeline was confirmed by reanalyzing morphological changes in non-essential yeast mutants and detecting 1284 more mutants with morphological defects compared with a conventional approach (Box–Cox transformation). Furthermore, the combined use of canonical correlation analysis permitted global views on the cellular network as well as new insights into possible gene functions. Conclusions Based on statistical principles, we showed that UNIMO offers better predictions of the true values of morphological measurements. We also demonstrated how these concepts can provide biologically important information. This study draws attention to the necessity of employing a proper approach to do more with less. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01283-6.
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Affiliation(s)
- Farzan Ghanegolmohammadi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Bldg. FSB-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba Prefecture, 277-8562, Japan.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Bldg. FSB-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba Prefecture, 277-8562, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Bldg. FSB-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba Prefecture, 277-8562, Japan. .,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
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Ghanegolmohammadi F, Okada H, Liu Y, Itto-Nakama K, Ohnuki S, Savchenko A, Bi E, Yoshida S, Ohya Y. Defining Functions of Mannoproteins in Saccharomyces cerevisiae by High-Dimensional Morphological Phenotyping. J Fungi (Basel) 2021; 7:jof7090769. [PMID: 34575807 PMCID: PMC8466635 DOI: 10.3390/jof7090769] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/12/2021] [Accepted: 09/14/2021] [Indexed: 12/24/2022] Open
Abstract
Mannoproteins are non-filamentous glycoproteins localized to the outermost layer of the yeast cell wall. The physiological roles of these structural components have not been completely elucidated due to the limited availability of appropriate tools. As the perturbation of mannoproteins may affect cell morphology, we investigated mannoprotein mutants in Saccharomyces cerevisiae via high-dimensional morphological phenotyping. The mannoprotein mutants were morphologically classified into seven groups using clustering analysis with Gaussian mixture modeling. The pleiotropic phenotypes of cluster I mutant cells (ccw12Δ) indicated that CCW12 plays major roles in cell wall organization. Cluster II (ccw14Δ, flo11Δ, srl1Δ, and tir3Δ) mutants exhibited altered mother cell size and shape. Mutants of cluster III and IV exhibited no or very small morphological defects. Cluster V (dse2Δ, egt2Δ, and sun4Δ) consisted of endoglucanase mutants with cell separation defects due to incomplete septum digestion. The cluster VI mutant cells (ecm33Δ) exhibited perturbation of apical bud growth. Cluster VII mutant cells (sag1Δ) exhibited differences in cell size and actin organization. Biochemical assays further confirmed the observed morphological defects. Further investigations based on various omics data indicated that morphological phenotyping is a complementary tool that can help with gaining a deeper understanding of the functions of mannoproteins.
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Affiliation(s)
- Farzan Ghanegolmohammadi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan or (F.G.); (Y.L.); (K.I.-N.); (S.O.); (A.S.)
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hiroki Okada
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (H.O.); (E.B.)
| | - Yaxuan Liu
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan or (F.G.); (Y.L.); (K.I.-N.); (S.O.); (A.S.)
| | - Kaori Itto-Nakama
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan or (F.G.); (Y.L.); (K.I.-N.); (S.O.); (A.S.)
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan or (F.G.); (Y.L.); (K.I.-N.); (S.O.); (A.S.)
| | - Anna Savchenko
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan or (F.G.); (Y.L.); (K.I.-N.); (S.O.); (A.S.)
- Cardiovascular Research Institute Maastricht, Maastricht University Medical Center, ER 6229 Maastricht, The Netherlands
| | - Erfei Bi
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (H.O.); (E.B.)
| | - Satoshi Yoshida
- School of International Liberal Studies, Nishi-Waseda Campus, Waseda University, Tokyo 169-8050, Japan;
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan or (F.G.); (Y.L.); (K.I.-N.); (S.O.); (A.S.)
- Correspondence:
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11
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Genome Editing to Generate Sake Yeast Strains with Eight Mutations That Confer Excellent Brewing Characteristics. Cells 2021; 10:cells10061299. [PMID: 34073778 PMCID: PMC8225151 DOI: 10.3390/cells10061299] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/16/2021] [Accepted: 05/21/2021] [Indexed: 01/23/2023] Open
Abstract
Sake yeast is mostly diploid, so the introduction of recessive mutations to improve brewing characteristics requires considerable effort. To construct sake yeast with multiple excellent brewing characteristics, we used an evidence-based approach that exploits genome editing technology. Our breeding targeted the AWA1, CAR1, MDE1, and FAS2 genes. We introduced eight mutations into standard sake yeast to construct a non-foam-forming strain that makes sake without producing carcinogens or an unpleasant odor, while producing a sweet ginjo aroma. Small-scale fermentation tests showed that the desired sake could be brewed with our genome-edited strains. The existence of a few unexpected genetic perturbations introduced during breeding proved that genome editing technology is extremely effective for the serial breeding of sake yeast.
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12
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Yoda T, Saito T. Size of Cells and Physicochemical Properties of Membranes are Related to Flavor Production during Sake Brewing in the Yeast Saccharomyces cerevisiae. MEMBRANES 2020; 10:membranes10120440. [PMID: 33352892 PMCID: PMC7766171 DOI: 10.3390/membranes10120440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/17/2022]
Abstract
Ethyl caproate (EC) and isoamyl acetate (IA) are key flavor components of sake. Recently, attempts have been made to increase the content of good flavor components, such as EC and IA, in sake brewing. However, the functions of EC and IA in yeast cells remain poorly understood. Therefore, we investigated the effects of EC and IA using cell-sized lipid vesicles. We also investigated lipid vesicles containing EC and/or caproic acid (CA) as well as IA and/or isoamyl alcohol (IAA). CA and IAA are precursors of EC and IA, respectively, and are important flavors in sake brewing. The size of a vesicle is influenced by flavor compounds and their precursors in a concentration-dependent manner. We aimed to establish the conditions in which the vesicles contained more flavors simultaneously and with different ratios. Interestingly, vesicles were largest in a mixture of 50% of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) with 25% EC and 25% CA or a mixture of 50% DOPC with 25% IA and 25% IAA. The impact of flavor additives on membrane fluidity was also studied using Laurdan generalized polarization. During the production process, flavors may regulate the fluidity of lipid membranes.
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Affiliation(s)
- Tsuyoshi Yoda
- Aomori Prefectural Industrial Technology Research Center, Hirosaki Industrial Research Institute, 1-1-8 Ougi-machi, Hirosaki, Aomori 036-8104, Japan;
- The United Graduate School of Agricultural Sciences, Iwate University, 3-18-8, Ueda, Morioka 020-8550, Japan
- Correspondence: ; Tel.: +81-172-55-6740
| | - Tomoaki Saito
- Aomori Prefectural Industrial Technology Research Center, Hirosaki Industrial Research Institute, 1-1-8 Ougi-machi, Hirosaki, Aomori 036-8104, Japan;
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13
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Yamasaki R, Goshima T, Oba K, Kanai M, Ohdoi R, Hirata D, Akao T. Development of sake yeast haploid set with diverse brewing properties using sake yeast strain Hiroshima no. 6 exhibiting sexual reproduction. J Biosci Bioeng 2020; 129:706-714. [PMID: 32085973 DOI: 10.1016/j.jbiosc.2020.01.005] [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: 12/18/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 10/25/2022]
Abstract
Among sake yeast strains, Kyokai no. 7 (K7) and its closely related strains (K7 group) are predominantly used because of their excellent brewing properties. In the sake industrial sector, the need for various types of yeast strains is high. Although crossbreeding is an effective method for generating genetic diversity that should result in diverse characteristics, most K7 group strains lack normal sporulation ability, including the ability to undergo meiotic chromosomal recombination, which leads to difficulties in crossbreeding. Accordingly, the improvement of sake yeast strains primarily depends on mutagenesis and suitable selection in a stepwise manner. Our recent study revealed that the long-preserved sake yeast strain Hiroshima no. 6 (H6) does not belong to the K7 group despite genetically being extremely similar. In addition, H6 exhibited normal sporulation. Thus, we isolated haploid cells from H6 and mated them with previously isolated haploid cells of K7 group strains. The crossbred diploid strains had normal sporulation ability; hence, we performed tetrad analysis. The brewing characteristics of the obtained haploid set were extremely diverse. Principal component analysis based on the volatile and organic acid components measured using small-scale sake brewing tests revealed that the haploid strains derived from each diploid strain displayed a characteristic distribution. Thus, we demonstrated the availability of genetic crossbreeding using H6 with sporulation ability to facilitate both the development of novel sake yeast strains with many desirable characteristics and analyses of the function of sake yeast.
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Affiliation(s)
- Risa Yamasaki
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-Hiroshima 739-0046, Japan; Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan; Food Technology Research Center, Hiroshima Prefectural Technology Research Institute, 12-70 Hijiyamahonmachi, Minami-Ku, Hiroshima 732-0816, Japan
| | - Tetsuya Goshima
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-Hiroshima 739-0046, Japan
| | - Kenji Oba
- Food Technology Research Center, Hiroshima Prefectural Technology Research Institute, 12-70 Hijiyamahonmachi, Minami-Ku, Hiroshima 732-0816, Japan
| | - Muneyoshi Kanai
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-Hiroshima 739-0046, Japan
| | - Ritsushi Ohdoi
- Food Technology Research Center, Hiroshima Prefectural Technology Research Institute, 12-70 Hijiyamahonmachi, Minami-Ku, Hiroshima 732-0816, Japan
| | - Dai Hirata
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan; Sakeology Center, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan; Sake Research Center, Asahi Sake Brewing Co., Ltd., 880-1 Asahi, Nagaoka, Niigata 949-5494, Japan
| | - Takeshi Akao
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-Hiroshima 739-0046, Japan; Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan.
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14
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Novel mutagenesis and screening technologies for food microorganisms: advances and prospects. Appl Microbiol Biotechnol 2020; 104:1517-1531. [DOI: 10.1007/s00253-019-10341-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/19/2019] [Accepted: 12/28/2019] [Indexed: 12/19/2022]
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15
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Yamasaki R, Goshima T, Oba K, Isogai A, Ohdoi R, Hirata D, Akao T. Characteristic analysis of the fermentation and sporulation properties of the traditional sake yeast strain Hiroshima no.6. Biosci Biotechnol Biochem 2019; 84:842-853. [PMID: 31868109 DOI: 10.1080/09168451.2019.1706441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
General sake yeasts (e.g., Kyokai no.7, K7) show high fermentation ability and low sporulation frequency. Former is related to stress-response defect due to the loss-of-function of MSN4 and RIM15. Later is mainly caused by low IME1 expression, leading to difficulty in breeding and genetic analysis. Sake yeast Hiroshima no.6 (H6), which had been applied for sake fermentation, has sporulation ability. However, its detailed properties have not been unveiled. Here we present that the fermentation ability of H6 is suitable for sake brewing, and the precursor of dimethyl trisulfide in sake from H6 is low. MSN4 but not RIM15 of H6 has the same mutation as K7. Our phylogenetic analysis indicated that H6 is closely related to the K7 group. Unlike K7, H6 showed normal sporulation frequency in a partially RIM15-dependent manner, and IME1 in H6 was expressed. H6 possesses excellent properties as a partner strain for breeding by crossing.
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Affiliation(s)
- Risa Yamasaki
- National Research Institute of Brewing, Higashi-Hiroshima, Japan.,Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Food Technology Research Center, Hiroshima Prefectural Technology Research Institute, Hiroshima, Japan
| | - Tetsuya Goshima
- National Research Institute of Brewing, Higashi-Hiroshima, Japan
| | - Kenji Oba
- Food Technology Research Center, Hiroshima Prefectural Technology Research Institute, Hiroshima, Japan
| | - Atsuko Isogai
- National Research Institute of Brewing, Higashi-Hiroshima, Japan.,Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Ritsushi Ohdoi
- Food Technology Research Center, Hiroshima Prefectural Technology Research Institute, Hiroshima, Japan
| | - Dai Hirata
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Sake Research Center, Asahi Sake Brewing Co., Niigata, Japan.,Sakeology Center, Niigata University, Niigata, Japan
| | - Takeshi Akao
- National Research Institute of Brewing, Higashi-Hiroshima, Japan.,Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
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