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Hayashi M, Ohnuki S, Tsai Y, Kondo N, Zhou Y, Zhang H, Ishii NT, Ding T, Herbig M, Isozaki A, Ohya Y, Goda K. Is AI essential? Examining the need for deep learning in image-activated sorting of Saccharomyces cerevisiae. LAB ON A CHIP 2023; 23:4232-4244. [PMID: 37650583 DOI: 10.1039/d3lc00556a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Artificial intelligence (AI) has become a focal point across a multitude of societal sectors, with science not being an exception. Particularly in the life sciences, imaging flow cytometry has increasingly integrated AI for automated management and categorization of extensive cell image data. However, the necessity of AI over traditional classification methods when extending imaging flow cytometry to include cell sorting remains uncertain, primarily due to the time constraints between image acquisition and sorting actuation. AI-enabled image-activated cell sorting (IACS) methods remain substantially limited, even as recent advancements in IACS have found success while largely relying on traditional feature gating strategies. Here we assess the necessity of AI for image classification in IACS by contrasting the performance of feature gating, classical machine learning (ML), and deep learning (DL) with convolutional neural networks (CNNs) in the differentiation of Saccharomyces cerevisiae mutant images. We show that classical ML could only yield a 2.8-fold enhancement in target enrichment capability, albeit at the cost of a 13.7-fold increase in processing time. Conversely, a CNN could offer an 11.0-fold improvement in enrichment capability at an 11.5-fold increase in processing time. We further executed IACS on mixed mutant populations and quantified target strain enrichment via downstream DNA sequencing to substantiate the applicability of DL for the proposed study. Our findings validate the feasibility and value of employing DL in IACS for morphology-based genetic screening of S. cerevisiae, encouraging its incorporation in future advancements of similar technologies.
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Affiliation(s)
- Mika Hayashi
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan.
| | - Yating Tsai
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan.
| | - Naoko Kondo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan.
| | - Yuqi Zhou
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Hongqian Zhang
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Natsumi Tiffany Ishii
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Tianben Ding
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Maik Herbig
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Akihiro Isozaki
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
- Department of Mechanical Engineering, College of Science and Engineering, Ritsumeikan University, Shiga 525-8577, 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 113-8654, Japan
| | - Keisuke Goda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
- Department of Bioengineering, University of California, Los Angeles, California 90095, USA
- Institute of Technological Sciences, Wuhan University, Wuhan 430072, China
- CYBO, Tokyo 135-0064, Japan
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2
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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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3
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Itto-Nakama K, Watanabe S, Ohnuki S, Kondo N, Kikuchi R, Nakamura T, Ogasawara W, Kasahara K, Ohya Y. Prediction of ethanol fermentation under stressed conditions using yeast morphological data. J Biosci Bioeng 2023; 135:210-216. [PMID: 36642617 DOI: 10.1016/j.jbiosc.2022.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/09/2022] [Accepted: 12/16/2022] [Indexed: 01/15/2023]
Abstract
A high sugar concentration is used as a starting condition in alcoholic fermentation by budding yeast, which shows changes in intracellular state and cell morphology under conditions of high-sugar stress. In this study, we developed artificial intelligence (AI) models to predict ethanol yields in yeast fermentation cultures under conditions of high-sugar stress using cell morphological data. Our method involves the extraction of high-dimensional morphological data from phase contrast images using image processing software, and predicting ethanol yields by supervised machine learning. The neural network algorithm produced the best performance, with a coefficient of determination (R2) of 0.95, and could predict ethanol yields well even 60 min in the future. Morphological data from cells cultured in low-glucose medium could not be used for accurate prediction under conditions of high-glucose stress. Cells cultured in high-concentration glucose medium were similar in terms of morphology to cells cultured under high osmotic pressure. Feeding experiments revealed that morphological changes differed depending on the fermentation phase. By monitoring the morphology of yeast under stress, it was possible to understand the intracellular physiological conditions, suggesting that analysis of cell morphology can aid the management and stable production of desired biocommodities.
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Affiliation(s)
- Kaori Itto-Nakama
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa, Chiba 277-8562, Japan
| | - Shun Watanabe
- Chitose Laboratory Corp., Biotechnology Research Center, 2-13-3, Nogawahoncho, Miyamae-ku, Kawasaki, Kanagawa 216-0041, Japan
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa, Chiba 277-8562, Japan
| | - Naoko Kondo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa, Chiba 277-8562, Japan
| | - Ryota Kikuchi
- Chitose Laboratory Corp., Biotechnology Research Center, 2-13-3, Nogawahoncho, Miyamae-ku, Kawasaki, Kanagawa 216-0041, Japan; Circular Bioeconomy Development, Office of Society Academia Collaboration for Innovation, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Toru Nakamura
- Chitose Laboratory Corp., Biotechnology Research Center, 2-13-3, Nogawahoncho, Miyamae-ku, Kawasaki, Kanagawa 216-0041, Japan
| | - Wataru Ogasawara
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan; Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Niigata 940-2188, Japan
| | - Ken Kasahara
- Chitose Laboratory Corp., Biotechnology Research Center, 2-13-3, Nogawahoncho, Miyamae-ku, Kawasaki, Kanagawa 216-0041, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa, Chiba 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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Gene loss and compensatory evolution promotes the emergence of morphological novelties in budding yeast. Nat Ecol Evol 2022; 6:763-773. [PMID: 35484218 DOI: 10.1038/s41559-022-01730-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/10/2022] [Indexed: 01/05/2023]
Abstract
Deleterious mutations are generally considered to be irrelevant for morphological evolution. However, they could be compensated by conditionally beneficial mutations, thereby providing access to new adaptive paths. Here we use high-dimensional phenotyping of laboratory-evolved budding yeast lineages to demonstrate that new cellular morphologies emerge exceptionally rapidly as a by-product of gene loss and subsequent compensatory evolution. Unexpectedly, the capacities for invasive growth, multicellular aggregation and biofilm formation also spontaneously evolve in response to gene loss. These multicellular phenotypes can be achieved by diverse mutational routes and without reactivating the canonical regulatory pathways. These ecologically and clinically relevant traits originate as pleiotropic side effects of compensatory evolution and have no obvious utility in the laboratory environment. The extent of morphological diversity in the evolved lineages is comparable to that of natural yeast isolates with diverse genetic backgrounds and lifestyles. Finally, we show that both the initial gene loss and subsequent compensatory mutations contribute to new morphologies, with their synergistic effects underlying specific morphological changes. We conclude that compensatory evolution is a previously unrecognized source of morphological diversity and phenotypic novelties.
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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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6
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High-throughput platform for yeast morphological profiling predicts the targets of bioactive compounds. NPJ Syst Biol Appl 2022; 8:3. [PMID: 35087094 PMCID: PMC8795194 DOI: 10.1038/s41540-022-00212-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 01/05/2022] [Indexed: 01/03/2023] Open
Abstract
Morphological profiling is an omics-based approach for predicting intracellular targets of chemical compounds in which the dose-dependent morphological changes induced by the compound are systematically compared to the morphological changes in gene-deleted cells. In this study, we developed a reliable high-throughput (HT) platform for yeast morphological profiling using drug-hypersensitive strains to minimize compound use, HT microscopy to speed up data generation and analysis, and a generalized linear model to predict targets with high reliability. We first conducted a proof-of-concept study using six compounds with known targets: bortezomib, hydroxyurea, methyl methanesulfonate, benomyl, tunicamycin, and echinocandin B. Then we applied our platform to predict the mechanism of action of a novel diferulate-derived compound, poacidiene. Morphological profiling of poacidiene implied that it affects the DNA damage response, which genetic analysis confirmed. Furthermore, we found that poacidiene inhibits the growth of phytopathogenic fungi, implying applications as an effective antifungal agent. Thus, our platform is a new whole-cell target prediction tool for drug discovery.
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Itto-Nakama K, Watanabe S, Kondo N, Ohnuki S, Kikuchi R, Nakamura T, Ogasawara W, Kasahara K, Ohya Y. AI-based forecasting of ethanol fermentation using yeast morphological data. Biosci Biotechnol Biochem 2021; 86:125-134. [PMID: 34751736 DOI: 10.1093/bbb/zbab188] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/25/2021] [Indexed: 11/12/2022]
Abstract
Several industries require getting information of products as soon as possible during fermentation. However, the trade-off between sensing speed and data quantity presents challenges for forecasting fermentation product yields. In this study, we tried to develop AI models to forecast ethanol yields in yeast fermentation cultures, using cell morphological data. Our platform involves the quick acquisition of yeast morphological images using a non-staining protocol, extraction of high-dimensional morphological data using image processing software, and forecasting of ethanol yields via supervised machine learning. We found that the neural network algorithm produced the best performance, which had a coefficient of determination of > 0.9 even at 30 and 60 min in the future. The model was validated using test data collected using the CalMorph-PC(10) system, which enables rapid image acquisition within 10 min. AI-based forecasting of product yields based on cell morphology will facilitate the management and stable production of desired biocommodities.
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Affiliation(s)
- Kaori Itto-Nakama
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa, Chiba, Japan
| | - Shun Watanabe
- Chitose Laboratory Corp., Biotechnology Research Center, 907 Nogawa, Miyamae-ku, Kawasaki, Kanagawa, Japan
| | - Naoko Kondo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa, Chiba, Japan
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa, Chiba, Japan
| | - Ryota Kikuchi
- Chitose Laboratory Corp., Biotechnology Research Center, 907 Nogawa, Miyamae-ku, Kawasaki, Kanagawa, Japan.,Circular Bioeconomy Development, Office of Society Academia Collaboration for Innovation, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Kyoto, Japan
| | - Toru Nakamura
- NRI System Techno Ltd., 134 Godo-cho, Hodogaya-ku, Yokohama, Kanagawa, Japan
| | - Wataru Ogasawara
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, Japan
| | - Ken Kasahara
- Chitose Laboratory Corp., Biotechnology Research Center, 907 Nogawa, Miyamae-ku, Kawasaki, Kanagawa, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa, Chiba, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan
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Nakagawa Y, Ohnuki S, Kondo N, Itto-Nakama K, Ghanegolmohammadi F, Isozaki A, Ohya Y, Goda K. Are droplets really suitable for single-cell analysis? A case study on yeast in droplets. LAB ON A CHIP 2021; 21:3793-3803. [PMID: 34581379 DOI: 10.1039/d1lc00469g] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Single-cell analysis has become one of the main cornerstones of biotechnology, inspiring the advent of various microfluidic compartments for cell cultivation such as microwells, microtrappers, microcapillaries, and droplets. A fundamental assumption for using such microfluidic compartments is that unintended stress or harm to cells derived from the microenvironments is insignificant, which is a crucial condition for carrying out unbiased single-cell studies. Despite the significance of this assumption, simple viability or growth tests have overwhelmingly been the assay of choice for evaluating culture conditions while empirical studies on the sub-lethal effect on cellular functions have been insufficient in many cases. In this work, we assessed the effect of culturing cells in droplets on the cellular function using yeast morphology as an indicator. Quantitative morphological analysis using CalMorph, an image-analysis program, demonstrated that cells cultured in flasks, large droplets, and small droplets significantly differed morphologically. From these differences, we identified that the cell cycle was delayed in droplets during the G1 phase and during the process of bud growth likely due to the checkpoint mechanism and impaired mitochondrial function, respectively. Furthermore, comparing small and large droplets, cells cultured in large droplets were morphologically more similar to those cultured in a flask, highlighting the advantage of increasing the droplet size. These results highlight a potential source of bias in cell analysis using droplets and reinforce the significance of assessing culture conditions of microfluidic cultivation methods for specific study cases.
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Affiliation(s)
- Yuta Nakagawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Naoko Kondo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Kaori Itto-Nakama
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Farzan Ghanegolmohammadi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Akihiro Isozaki
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8654, Japan.
| | - Keisuke Goda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
- Department of Bioengineering, Samueli School of Engineering, University of California, Los Angeles, 420 Westwood Plaza, California 90095, USA
- Institute of Technological Sciences, Wuhan University, Wuhan, Hubei 430072, China
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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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10
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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: 6] [Impact Index Per Article: 2.0] [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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11
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Liu P, Liu H, Yuan D, Jang D, Yan S, Li M. Separation and Enrichment of Yeast Saccharomyces cerevisiae by Shape Using Viscoelastic Microfluidics. Anal Chem 2020; 93:1586-1595. [DOI: 10.1021/acs.analchem.0c03990] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ping Liu
- School of Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
- Suqian University, Suqian, 223800, China
| | - Hangrui Liu
- Department of Physics and Astronomy, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Dan Yuan
- Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan
| | - Daniel Jang
- School of Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Sheng Yan
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Ming Li
- School of Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
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12
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Kintaka R, Makanae K, Namba S, Kato H, Kito K, Ohnuki S, Ohya Y, Andrews BJ, Boone C, Moriya H. Genetic profiling of protein burden and nuclear export overload. eLife 2020; 9:54080. [PMID: 33146608 PMCID: PMC7673788 DOI: 10.7554/elife.54080] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 11/01/2020] [Indexed: 12/11/2022] Open
Abstract
Overproduction (op) of proteins triggers cellular defects. One of the consequences of overproduction is the protein burden/cost, which is produced by an overloading of the protein synthesis process. However, the physiology of cells under a protein burden is not well characterized. We performed genetic profiling of protein burden by systematic analysis of genetic interactions between GFP-op, surveying both deletion and temperature-sensitive mutants in budding yeast. We also performed genetic profiling in cells with overproduction of triple-GFP (tGFP), and the nuclear export signal-containing tGFP (NES-tGFP). The mutants specifically interacted with GFP-op were suggestive of unexpected connections between actin-related processes like polarization and the protein burden, which was supported by morphological analysis. The tGFP-op interactions suggested that this protein probe overloads the proteasome, whereas those that interacted with NES-tGFP involved genes encoding components of the nuclear export process, providing a resource for further analysis of the protein burden and nuclear export overload.
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Affiliation(s)
- Reiko Kintaka
- Donnelly Center for Cellular and Biomolecular Research, Department of Medical Genetics, University of Toronto, Toronto, Canada
| | - Koji Makanae
- Research Core for Interdisciplinary Sciences, Okayama University, Okayama, Japan
| | - Shotaro Namba
- Matching Program Course, Okayama University, Okayama, Japan
| | - Hisaaki Kato
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Keiji Kito
- Department of Life Sciences, School of Agriculture, Meiji University, Tokyo, Japan
| | - Shinsuke Ohnuki
- Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Yoshikazu Ohya
- Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Brenda J Andrews
- Donnelly Center for Cellular and Biomolecular Research, Department of Medical Genetics, University of Toronto, Toronto, Canada
| | - Charles Boone
- Donnelly Center for Cellular and Biomolecular Research, Department of Medical Genetics, University of Toronto, Toronto, Canada.,RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Hisao Moriya
- Research Core for Interdisciplinary Sciences, Okayama University, Okayama, Japan.,Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
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13
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Isozaki A, Mikami H, Hiramatsu K, Sakuma S, Kasai Y, Iino T, Yamano T, Yasumoto A, Oguchi Y, Suzuki N, Shirasaki Y, Endo T, Ito T, Hiraki K, Yamada M, Matsusaka S, Hayakawa T, Fukuzawa H, Yatomi Y, Arai F, Di Carlo D, Nakagawa A, Hoshino Y, Hosokawa Y, Uemura S, Sugimura T, Ozeki Y, Nitta N, Goda K. A practical guide to intelligent image-activated cell sorting. Nat Protoc 2019; 14:2370-2415. [PMID: 31278398 DOI: 10.1038/s41596-019-0183-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/18/2019] [Indexed: 02/08/2023]
Abstract
Intelligent image-activated cell sorting (iIACS) is a machine-intelligence technology that performs real-time intelligent image-based sorting of single cells with high throughput. iIACS extends beyond the capabilities of fluorescence-activated cell sorting (FACS) from fluorescence intensity profiles of cells to multidimensional images, thereby enabling high-content sorting of cells or cell clusters with unique spatial chemical and morphological traits. Therefore, iIACS serves as an integral part of holistic single-cell analysis by enabling direct links between population-level analysis (flow cytometry), cell-level analysis (microscopy), and gene-level analysis (sequencing). Specifically, iIACS is based on a seamless integration of high-throughput cell microscopy (e.g., multicolor fluorescence imaging, bright-field imaging), cell focusing, cell sorting, and deep learning on a hybrid software-hardware data management infrastructure, enabling real-time automated operation for data acquisition, data processing, intelligent decision making, and actuation. Here, we provide a practical guide to iIACS that describes how to design, build, characterize, and use an iIACS machine. The guide includes the consideration of several important design parameters, such as throughput, sensitivity, dynamic range, image quality, sort purity, and sort yield; the development and integration of optical, microfluidic, electrical, computational, and mechanical components; and the characterization and practical usage of the integrated system. Assuming that all components are readily available, a team of several researchers experienced in optics, electronics, digital signal processing, microfluidics, mechatronics, and flow cytometry can complete this protocol in ~3 months.
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Affiliation(s)
- Akihiro Isozaki
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
| | - Hideharu Mikami
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
| | | | - Shinya Sakuma
- Department of Micro-Nano Mechanical Science and Engineering, Nagoya University, Nagoya, Japan
| | - Yusuke Kasai
- Department of Micro-Nano Mechanical Science and Engineering, Nagoya University, Nagoya, Japan
| | - Takanori Iino
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo, Japan
| | - Takashi Yamano
- Laboratory of Applied Molecular Microbiology, Kyoto University, Kyoto, Japan
| | - Atsushi Yasumoto
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yusuke Oguchi
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
| | - Nobutake Suzuki
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
| | | | | | - Takuro Ito
- Department of Chemistry, The University of Tokyo, Tokyo, Japan.,Japan Science and Technology Agency, Saitama, Japan
| | - Kei Hiraki
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
| | - Makoto Yamada
- Department of Intelligence Science and Technology, Graduate School of Informatics, Kyoto University, Kyoto, Japan
| | - Satoshi Matsusaka
- Clinical Research and Regional Innovation, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Takeshi Hayakawa
- Department of Precision Mechanics, Chuo University, Tokyo, Japan
| | - Hideya Fukuzawa
- Laboratory of Applied Molecular Microbiology, Kyoto University, Kyoto, Japan
| | - Yutaka Yatomi
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Fumihito Arai
- Department of Micro-Nano Mechanical Science and Engineering, Nagoya University, Nagoya, Japan
| | - Dino Di Carlo
- Department of Chemistry, The University of Tokyo, Tokyo, Japan.,Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Mechanical Engineering, University of California, Los Angeles, Los Angeles, CA, USA.,California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Atsuhiro Nakagawa
- Department of Neurosurgery, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Yu Hoshino
- Department of Chemical Engineering, Kyushu University, Fukuoka, Japan
| | - Yoichiroh Hosokawa
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Sotaro Uemura
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
| | - Takeaki Sugimura
- Department of Chemistry, The University of Tokyo, Tokyo, Japan.,Japan Science and Technology Agency, Saitama, Japan
| | - Yasuyuki Ozeki
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo, Japan
| | - Nao Nitta
- Department of Chemistry, The University of Tokyo, Tokyo, Japan.,Japan Science and Technology Agency, Saitama, Japan
| | - Keisuke Goda
- Department of Chemistry, The University of Tokyo, Tokyo, Japan. .,Japan Science and Technology Agency, Saitama, Japan. .,Department of Electrical Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
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14
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Ohnuki S, Kashima M, Yamada T, Ghanegolmohammadi F, Zhou Y, Goshima T, Maruyama JI, Kitamoto K, Hirata D, Akao T, Ohya Y. Genome editing to generate nonfoam-forming sake yeast strains. Biosci Biotechnol Biochem 2019; 83:1583-1593. [PMID: 31189439 DOI: 10.1080/09168451.2019.1631146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Mutations frequently occur during breeding of sake yeasts and result in unexpected phenotypes. Here, genome editing tools were applied to develop an ideal nonfoam-forming sake yeast strain, K7GE01, which had homozygous awa1∆/awa1∆ deletion alleles that were responsible for nonfoam formation and few off-target mutations. High-dimensional morphological phenotyping revealed no detectable morphological differences between the genome-edited strain and its parent, while the canonical nonfoam-forming strain, K701, showed obvious morphological changes. Small-scale fermentation tests also showed differences between components of sake produced by K7GE01 and K701. The K7GE01 strain produced sake with significant differences in the concentrations of ethyl acetate, malic acid, lactic acid, and acetic acid, while K701 produced sake with more differences. Our results indicated genuine phenotypes of awa1∆/awa1∆ in sake yeast isolates and showed the usefulness of genome editing tools for sake yeast breeding.
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Affiliation(s)
- Shinsuke Ohnuki
- a Department of Integrated Biosciences, Graduate School of Frontier Sciences , The University of Tokyo , Kashiwa, Chiba , Japan
| | - Mao Kashima
- a Department of Integrated Biosciences, Graduate School of Frontier Sciences , The University of Tokyo , Kashiwa, Chiba , Japan
| | - Toshikazu Yamada
- a Department of Integrated Biosciences, Graduate School of Frontier Sciences , The University of Tokyo , Kashiwa, Chiba , Japan
| | - Farzan Ghanegolmohammadi
- a Department of Integrated Biosciences, Graduate School of Frontier Sciences , The University of Tokyo , Kashiwa, Chiba , Japan
| | - Yan Zhou
- b National Research Institute of Brewing , Higashi-Hiroshima , Japan
| | - Tetsuya Goshima
- b National Research Institute of Brewing , Higashi-Hiroshima , Japan
| | - Jun-Ichi Maruyama
- c Department of Biotechnology , The University of Tokyo , Tokyo , Japan.,d Collaborative Research Institute for Innovative Microbiology , The University of Tokyo , Tokyo , Japan
| | - Katsuhiko Kitamoto
- e Department of Pharmaceutical and Medical Business Sciences , Nihon Pharmaceutical University , Bunkyo-ku , Japan
| | - Dai Hirata
- f Sake Research Center , Asahi Sake Brewing Co. Ltd ., Nagaoka , Japan.,g Department of Molecular Biotechnology , Graduate School of Advanced Sciences of Matter, Hiroshima University , Higashi-Hiroshima , Japan.,h Sakeology Center , Niigata University , Ikarashi , Japan
| | - Takeshi Akao
- b National Research Institute of Brewing , Higashi-Hiroshima , Japan
| | - Yoshikazu Ohya
- a Department of Integrated Biosciences, Graduate School of Frontier Sciences , The University of Tokyo , Kashiwa, Chiba , Japan.,d Collaborative Research Institute for Innovative Microbiology , The University of Tokyo , Tokyo , Japan.,i AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL) , National Institute of Advanced Industrial Science and Technology (AIST) , Kashiwa, Chiba , Japan
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15
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Cucurbitacin B Exerts Antiaging Effects in Yeast by Regulating Autophagy and Oxidative Stress. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:4517091. [PMID: 31281576 PMCID: PMC6589324 DOI: 10.1155/2019/4517091] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/27/2019] [Accepted: 04/23/2019] [Indexed: 12/28/2022]
Abstract
The budding yeast Saccharomyces cerevisiae has been used as a model organism for the basic mechanism of aging, which provides useful assay systems for measuring both replicative and chronological lifespans. In the course of our screening program for substances that extend replicative lifespan, cucurbitacin B (CuB) was found as a hit compound from a compound library, which contains cerebrosides, phenols, sesquiterpenoid, triterpenoids, and sterols isolated from natural products by our research group. Importantly, it prolonged not only the replicative lifespan but also the chronological lifespan in yeast. CuB increased ATG32 gene expression, suggesting that CuB induces autophagy. Indeed, the GFP signal generated from the cleavage of GFP-Atg8, which is a signature of autophagy, was increased upon CuB treatment. On the other hand, CuB failed to increase the chronological lifespans when either ATG2 or ATG32, essential autophagy genes, was deleted, indicating that the lifespan extension by CuB depends on autophagy induction. Furthermore, CuB significantly increased superoxide dismutase (Sod) activity and the survival rate of yeast under oxidative stress, while it decreased the amount of reactive oxygen species (ROS) and malondialdehyde (MDA) production, indicating that CuB has activity to antagonize oxidative stress. Additionally, CuB did not affect replicative lifespans of sod1, sod2, uth1, and skn7 mutants with the K6001 background, indicating that aging-related genes including SOD1, SOD2, UTH1, and SKN7 participate in the antiaging effect of CuB. These results suggest that CuB exerts antiaging activity by regulating autophagy, ROS, antioxidative ability, and aging-related genes. Finally, we discuss the possible intracellular targets of CuB based on the phenotypic comparison between the CuB and global gene deletion databases.
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16
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Kubo K, Okada H, Shimamoto T, Kimori Y, Mizunuma M, Bi E, Ohnuki S, Ohya Y. Implications of maintenance of mother-bud neck size in diverse vital processes of Saccharomyces cerevisiae. Curr Genet 2019; 65:253-267. [PMID: 30066140 DOI: 10.1007/s00294-018-0872-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/17/2018] [Accepted: 07/25/2018] [Indexed: 11/25/2022]
Abstract
The mother-bud neck is defined as the boundary between the mother cell and bud in budding microorganisms, wherein sequential morphological events occur throughout the cell cycle. This study was designed to quantitatively investigate the morphology of the mother-bud neck in budding yeast Saccharomyces cerevisiae. Observation of yeast cells with time-lapse microscopy revealed an increase of mother-bud neck size through the cell cycle. After screening of yeast non-essential gene-deletion mutants with the image processing software CalMorph, we comprehensively identified 274 mutants with broader necks during S/G2 phase. Among these yeasts, we extensively analyzed 19 representative deletion mutants with defects in genes annotated to six gene ontology terms (polarisome, actin reorganization, endosomal tethering complex, carboxy-terminal domain protein kinase complex, DNA replication, and maintenance of DNA trinucleotide repeats). The representative broad-necked mutants exhibited calcofluor white sensitivity, suggesting defects in their cell walls. Correlation analysis indicated that maintenance of mother-bud neck size is important for cellular processes such as cell growth, system robustness, and replicative lifespan. We conclude that neck-size maintenance in budding yeast is regulated by numerous genes and has several aspects that are physiologically significant.
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Affiliation(s)
- Karen Kubo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Hiroki Okada
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6058, USA
| | - Takuya Shimamoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Yoshitaka Kimori
- Department of Imaging Science, Center for Novel Science Initiatives, National Institutes of Natural Sciences, Okazaki, 444-8787, Japan
- Department of Management and Information Sciences, Faculty of Environmental and Information Sciences, Fukui University of Technology, Gakuen, Fukui City, Fukui, 910-8505, Japan
| | - Masaki Mizunuma
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, 739-8530, Japan
| | - Erfei Bi
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6058, USA
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, 277-8562, Japan.
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, Chiba, 277-8565, Japan.
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17
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Nemoto S, Ohnuki S, Abe F, Ohya Y. Simulated microgravity triggers characteristic morphology and stress response in Saccharomyces cerevisiae. Yeast 2018; 36:85-97. [PMID: 30350382 DOI: 10.1002/yea.3361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 01/20/2023] Open
Abstract
Reduction of gravity results in changes in gene expression and morphology in the budding yeast Saccharomyces cerevisiae. We studied the genes responsible for the morphological changes induced by simulated microgravity (SMG) using the yeast morphology data. We comprehensively captured the features of the morphological changes in yeast cells cultured in SMG with CalMorph, a high-throughput image-processing system. Statistical analysis revealed that 95 of 501 morphological traits were significantly affected, which included changes in bud direction, the ratio of daughter to mother cell size, the random daughter cell shape, the large mother cell size, bright nuclei in the M phase, and the decrease in angle between two nuclei. We identified downregulated genes that impacted the morphological changes in conditions of SMG by focusing on each of the morphological features individually. Gene Ontology (GO)-enrichment analysis indicated that morphological changes under conditions of SMG were caused by cooperative downregulation of 103 genes annotated to six GO terms, which included cytoplasmic ribonucleoprotein granule, RNA elongation, mitotic cell cycle phase transition, nucleocytoplasmic transport, protein-DNA complex subunit organization, and RNA localization. P-body formation was also promoted under conditions of SMG. These results suggest that cooperative downregulation of multiple genes occurs in conditions of SMG.
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Affiliation(s)
- Shota Nemoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Fumiyoshi Abe
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, Sagamihara, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.,AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, Japan
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18
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Ohnuki S, Ohya Y. High-dimensional single-cell phenotyping reveals extensive haploinsufficiency. PLoS Biol 2018; 16:e2005130. [PMID: 29768403 PMCID: PMC5955526 DOI: 10.1371/journal.pbio.2005130] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 04/06/2018] [Indexed: 12/17/2022] Open
Abstract
Haploinsufficiency, a dominant phenotype caused by a heterozygous loss-of-function mutation, has been rarely observed. However, high-dimensional single-cell phenotyping of yeast morphological characteristics revealed haploinsufficiency phenotypes for more than half of 1,112 essential genes under optimal growth conditions. Additionally, 40% of the essential genes with no obvious phenotype under optimal growth conditions displayed haploinsufficiency under severe growth conditions. Haploinsufficiency was detected more frequently in essential genes than in nonessential genes. Similar haploinsufficiency phenotypes were observed mostly in mutants with heterozygous deletion of functionally related genes, suggesting that haploinsufficiency phenotypes were caused by functional defects of the genes. A global view of the gene network was presented based on the similarities of the haploinsufficiency phenotypes. Our dataset contains rich information regarding essential gene functions, providing evidence that single-cell phenotyping is a powerful approach, even in the heterozygous condition, for analyzing complex biological systems. Diploid organisms harboring a wild-type gene and a loss-of-function mutation are called heterozygotes. They are expected to have weak or no individual phenotypes because the mutation is compensated for by the intact allele. The dominant inheritance of phenotypes in heterozygotes is an exceptional phenomenon called haploinsufficiency. Haploinsufficiency was thought to be a rare occurrence; however, a sensitive technique called high-dimensional single-cell phenotyping challenges this perspective. Investigations of single-cell phenotypes revealed that a large extent of the essential genes in yeast exhibit haploinsufficiency. Our analyses also provided crucial information on gene functional networks based on haploinsufficiency phenotypes. This work shows that high-dimensional single-cell phenotyping is a useful tool that can be used to better understand complex biological systems.
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Affiliation(s)
- Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, Chiba, Japan
- * E-mail:
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