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Khanh HC, Kaothien-Nakayama P, Zou Z, Nakayama H. Metabolic pathway engineering of high-salinity-induced overproduction of L-proline improves high-salinity stress tolerance of an ectoine-deficient Halomonas elongata. Appl Environ Microbiol 2024:e0119524. [PMID: 39158316 DOI: 10.1128/aem.01195-24] [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: 06/23/2024] [Accepted: 07/25/2024] [Indexed: 08/20/2024] Open
Abstract
Halophilic bacteria have adapted to survive in high-salinity environments by accumulating amino acids and their derivatives as organic osmolytes. L-Proline (Pro) is one such osmolyte that is also being used as a feed stimulant in the aquaculture industry. Halomonas elongata OUT30018 is a moderately halophilic bacterium that accumulates ectoine (Ect), but not Pro, as an osmolyte. Due to its ability to utilize diverse biomass-derived carbon and nitrogen sources for growth, H. elongata OUT30018 is used in this work to create a strain that overproduces Pro, which could be used as a sustainable Pro-rich feed additive. To achieve this, we replaced the coding region of H. elongata OUT30018's Ect biosynthetic operon with the artificial self-cloned proBm1AC gene cluster that encodes the Pro biosynthetic enzymes: feedback-inhibition insensitive mutant γ-glutamate kinase (γ-GKD118N/D119N), γ-glutamyl phosphate reductase, and pyrroline-5-carboxylate reductase. Additionally, the putA gene, which encodes the key enzyme of Pro catabolism, was deleted from the genome to generate H. elongata HN6. While the Ect-deficient H. elongata KA1 could not grow in minimal media containing more than 4% NaCl, H. elongata HN6 thrived in the medium containing 8% NaCl by accumulating Pro in the cell instead of Ect, reaching a concentration of 353.1 ± 40.5 µmol/g cell fresh weight, comparable to the Ect accumulated in H. elongata OUT30018 in response to salt stress. With its genetic background, H. elongata HN6 has the potential to be developed into a Pro-rich cell factory for upcycling biomass waste into single-cell feed additives, contributing to a more sustainable aquaculture industry.IMPORTANCEWe report here the evidence for de novo biosynthesis of Pro to be used as a major osmolyte in an ectoine-deficient Halomonas elongata. Remarkably, the concentration of Pro accumulated in H. elongata HN6 (∆ectABC::mCherry-proBm1AC ∆putA) is comparable to that of ectoine accumulated in H. elongata OUT30018 in response to high-salinity stress. We also found that among the two γ-glutamate kinase mutants (γ-GKD118N/D119N and γ-GKD154A/E155A) designed to resemble the two known Escherichia coli feedback-inhibition insensitive γ-GKD107N and γ-GKE143A, the γ-GKD118N/D119N mutant is the only one that became insensitive to feedback inhibition by Pro in H. elongata. As Pro is one of the essential feed additives for the poultry and aquaculture industries, the genetic makeup of the engineered H. elongata HN6 would allow for the sustainable upcycling of high-salinity waste biomass into a Pro-rich single-cell eco-feed.
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Affiliation(s)
- Huynh Cong Khanh
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Japan
- College of Environment and Natural Resources, Can Tho University, Can Tho, Vietnam
| | - Pulla Kaothien-Nakayama
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Japan
| | - Ziyan Zou
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Japan
| | - Hideki Nakayama
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Japan
- Graduate School of Integrated Science and Technology, Nagasaki University, Nagasaki, Japan
- Organization for Marine Science and Technology, Nagasaki University, Nagasaki, Japan
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Flores-Cosío G, García-Béjar JA, Sandoval-Nuñez D, Amaya-Delgado L. Stress response and adaptation mechanisms in Kluyveromyces marxianus. ADVANCES IN APPLIED MICROBIOLOGY 2024; 126:27-62. [PMID: 38637106 DOI: 10.1016/bs.aambs.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Kluyveromyces marxianus is a non-Saccharomyces yeast that has gained importance due to its great potential to be used in the food and biotechnology industries. In general, K. marxianus is a known yeast for its ability to assimilate hexoses and pentoses; even this yeast can grow in disaccharides such as sucrose and lactose and polysaccharides such as agave fructans. Otherwise, K. marxianus is an excellent microorganism to produce metabolites of biotechnological interest, such as enzymes, ethanol, aroma compounds, organic acids, and single-cell proteins. However, several studies highlighted the metabolic trait variations among the K. marxianus strains, suggesting genetic diversity within the species that determines its metabolic functions; this diversity can be attributed to its high adaptation capacity against stressful environments. The outstanding metabolic characteristics of K. marxianus have motivated this yeast to be a study model to evaluate its easy adaptability to several environments. This chapter will discuss overview characteristics and applications of K. marxianus and recent insights into the stress response and adaptation mechanisms used by this non-Saccharomyces yeast.
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Affiliation(s)
- G Flores-Cosío
- Industrial Biotechnology Unit, Center for Research and Assistance in Technology and Design of the State of Jalisco, Camino Arenero, Col. El Bajio, C.P., Zapopan Jalisco, A.C, Mexico
| | - J A García-Béjar
- Industrial Biotechnology Unit, Center for Research and Assistance in Technology and Design of the State of Jalisco, Camino Arenero, Col. El Bajio, C.P., Zapopan Jalisco, A.C, Mexico
| | - D Sandoval-Nuñez
- Industrial Biotechnology Unit, Center for Research and Assistance in Technology and Design of the State of Jalisco, Camino Arenero, Col. El Bajio, C.P., Zapopan Jalisco, A.C, Mexico
| | - L Amaya-Delgado
- Industrial Biotechnology Unit, Center for Research and Assistance in Technology and Design of the State of Jalisco, Camino Arenero, Col. El Bajio, C.P., Zapopan Jalisco, A.C, Mexico.
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Khotimah H, Astuti RI, Rafi M, Yuliana ND. Metabolomics Study Reveals Biomarker L-Proline as Potential Stress-Protectant Compound for High-Temperature Bioethanol Fermentation by Yeast Pichia kudriavzevii 1P4. Appl Biochem Biotechnol 2023; 195:5180-5198. [PMID: 37103737 DOI: 10.1007/s12010-023-04554-2] [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] [Accepted: 04/18/2023] [Indexed: 04/28/2023]
Abstract
High-temperature ethanol fermentation (> 40 °C) can be applied as effective bioprocess technology to increase ethanol production. Thermotolerant yeast Pichia kudriavzevii 1P4 showed the ability to produce ethanol at optimum 37 °C. Thus, this study evaluated the ethanol productivity of isolate 1P4 at high-temperature ethanol fermentation (42 and 45 °C) and the identification of metabolite biomarkers using untargeted metabolomics with liquid chromatography-tandem mass spectrometry (LC-MS/MS). 1P4 showed tolerance to temperature stress up to 45 °C and thus relevant for high-temperature fermentation. As measured by gas chromatography (GC), bioethanol production of 1P4 at 30, 37, 42, and 45 °C was 5.8 g/l, 7.1 g/l, 5.1 g/l, and 2.8 g/l, respectively. The classification of biomarker compounds was based on orthogonal projection analysis to latent structure discriminant analysis (OPLS-DA), resulting in L-proline being a suspected biomarker compound for isolate 1P4 tolerance against high-temperature stress. Indeed, supplementation of L-proline on fermentation medium supported the growth of 1P4 at high temperatures (> 40 °C) than without L-proline. The bioethanol production with the addition of the L-proline resulted in the highest ethanol concentration (7.15 g/l) at 42 °C. Supplementation of L-proline as a stress-protective compound increased ethanol productivity at high-temperature fermentation of 42 and 45 °C by 36.35% and 83.33%, respectively, compared without the addition of L-proline. Preliminary interpretation of these results indicates that bioprocess engineering through supplementation of stress-protective compounds L-proline increases the fermentation efficiency of isolate 1P4 at higher temperatures (42 °C and 45 °C).
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Affiliation(s)
- Husnul Khotimah
- Graduate School of Biotechnology, IPB University, Bogor, West Java, 16680, Indonesia
| | - Rika Indri Astuti
- Department of Biology, IPB University, Bogor, West Java, 16680, Indonesia.
- Biotechnology Research Center, IPB University, Bogor, West Java, Indonesia.
| | - Mohamad Rafi
- Department of Chemistry, IPB University, Bogor, West Java, 16680, Indonesia
- Advance Research Laboratory, IPB University, Bogor, West Java, 16680, Indonesia
| | - Nancy Dewi Yuliana
- Department of Food Science and Technology, IPB University, Bogor, West Java, 16680, Indonesia
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Nishimura A, Takasaki Y, Isogai S, Toyokawa Y, Tanahashi R, Takagi H. Role of Gln79 in Feedback Inhibition of the Yeast γ-Glutamyl Kinase by Proline. Microorganisms 2021; 9:microorganisms9091902. [PMID: 34576795 PMCID: PMC8472793 DOI: 10.3390/microorganisms9091902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/04/2021] [Accepted: 09/06/2021] [Indexed: 11/16/2022] Open
Abstract
Awamori, the traditional distilled alcoholic beverage of Okinawa, Japan, is brewed with the yeast Saccharomyces cerevisiae. During the distillation process after the fermentation, enormous quantities of distillation residues containing yeast cells must be disposed of, and this has recently been recognized as a major problem both environmentally and economically. Proline, a multifunctional amino acid, has the highest water retention capacity among amino acids. Therefore, distillation residues with large amounts of proline could be useful in cosmetics. Here, we isolated a yeast mutant with high levels of intracellular proline and found a missense mutation (Gln79His) on the PRO1 gene encoding the γ-glutamyl kinase Pro1, a limiting enzyme in proline biosynthesis. The amino acid change of Gln79 to His in Pro1 resulted in desensitization to the proline-mediated feedback inhibition of GK activity, leading to the accumulation of proline in cells. Biochemical and in silico analyses showed that the amino acid residue at position 79 is involved in the stabilization of the proline binding pocket in Pro1 via a hydrogen-bonding network, which plays an important role in feedback inhibition. Our current study, therefore, proposed a possible mechanism underlying the feedback inhibition of γ-glutamyl kinase activity. This mechanism can be applied to construct proline-accumulating yeast strains to effectively utilize distillation residues.
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Takagi H. Molecular mechanisms and highly functional development for stress tolerance of the yeast Saccharomyces cerevisiae. Biosci Biotechnol Biochem 2021; 85:1017-1037. [PMID: 33836532 DOI: 10.1093/bbb/zbab022] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 01/25/2021] [Indexed: 12/25/2022]
Abstract
In response to environmental stress, microorganisms adapt to drastic changes while exerting cellular functions by controlling gene expression, metabolic pathways, enzyme activities, and protein-protein interactions. Microbial cells that undergo a fermentation process are subjected to stresses, such as high temperature, freezing, drying, changes in pH and osmotic pressure, and organic solvents. Combinations of these stresses that continue over long terms often inhibit cells' growth and lead to their death, markedly limiting the useful functions of microorganisms (eg their fermentation ability). Thus, high stress tolerance of cells is required to improve productivity and add value to fermented/brewed foods and biofuels. This review focuses on stress tolerance mechanisms, including l-proline/l-arginine metabolism, ubiquitin system, and transcription factors, and the functional development of the yeast Saccharomyces cerevisiae, which has been used not only in basic science as a model of higher eukaryotes but also in fermentation processes for making alcoholic beverages, food products, and bioethanol.
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Affiliation(s)
- Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
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Murakami N, Kotaka A, Isogai S, Ashida K, Nishimura A, Matsumura K, Hata Y, Ishida H, Takagi H. Effects of a novel variant of the yeast γ-glutamyl kinase Pro1 on its enzymatic activity and sake brewing. J Ind Microbiol Biotechnol 2020; 47:715-723. [PMID: 32748014 PMCID: PMC7658068 DOI: 10.1007/s10295-020-02297-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/23/2020] [Indexed: 01/04/2023]
Abstract
Sake is a traditional Japanese alcoholic beverage brewed with the yeast Saccharomyces cerevisiae. Sake taste is affected by sugars, organic acids, and amino acids. We previously isolated mutants resistant to the proline analogue azetidine-2-carboxylate derived from a diploid sake yeast strain. Some of the mutants produced a greater amount of proline in the brewed sake. One of them (strain K-9-AZC) carried a novel mutation in the PRO1 gene encoding the Gln79His variant of the γ-glutamyl kinase Pro1, a key enzyme in proline biosynthesis in S. cerevisiae. This mutation resulted in extreme desensitization to feedback inhibition by proline, leading to proline overproduction. Interestingly, sake brewed with K-9-AZC contained 3.7-fold more proline, but only 25% less succinate than sake brewed with the parent strain. Metabolome analysis suggests that the decrease in succinate was attributable to a lower level of 2-oxoglutarate, which is converted into glutamate. The approach here could be a practical method for breeding of yeast strains involved in the diversity of sake taste.
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Affiliation(s)
- Naoyuki Murakami
- 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
| | - Shota Isogai
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Keiko Ashida
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Akira Nishimura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Kengo Matsumura
- Research Institute, Gekkeikan Sake Co. Ltd., 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto, 612-8385, Japan
| | - Yoji Hata
- 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
| | - Hiroshi Takagi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan.
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Mukai Y, Kamei Y, Liu X, Jiang S, Sugimoto Y, Mat Nanyan NSB, Watanabe D, Takagi H. Proline metabolism regulates replicative lifespan in the yeast Saccharomyces cerevisiae. MICROBIAL CELL 2019; 6:482-490. [PMID: 31646149 PMCID: PMC6780008 DOI: 10.15698/mic2019.10.694] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In many plants and microorganisms, intracellular proline has a protective role against various stresses, including heat-shock, oxidation and osmolarity. Environmental stresses induce cellular senescence in a variety of eukaryotes. Here we showed that intracellular proline regulates the replicative lifespan in the budding yeast Saccharomyces cerevisiae. Deletion of the proline oxidase gene PUT1 and expression of the γ-glutamate kinase mutant gene PRO1-I150T that is less sensitive to feedback inhibition accumulated proline and extended the replicative lifespan of yeast cells. Inversely, disruption of the proline biosynthetic genes PRO1, PRO2, and CAR2 decreased stationary proline level and shortened the lifespan of yeast cells. Quadruple disruption of the proline transporter genes unexpectedly did not change intracellular proline levels and replicative lifespan. Overexpression of the stress-responsive transcription activator gene MSN2 reduced intracellular proline levels by inducing the expression of PUT1, resulting in a short lifespan. Thus, the intracellular proline levels at stationary phase was positively correlated with the replicative lifespan. Furthermore, multivariate analysis of amino acids in yeast mutants deficient in proline metabolism showed characteristic metabolic profiles coincident with longevity: acidic and basic amino acids and branched-chain amino acids positively contributed to the replicative lifespan. These results allude to proline metabolism having a physiological role in maintaining the lifespan of yeast cells.
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Affiliation(s)
- Yukio Mukai
- Department of Frontier Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Yuka Kamei
- Department of Frontier Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Xu Liu
- Department of Frontier Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Shan Jiang
- Department of Frontier Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Yukiko Sugimoto
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Noreen Suliani Binti Mat Nanyan
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Daisuke Watanabe
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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Makafe GG, Hussain M, Surineni G, Tan Y, Wong NK, Julius M, Liu L, Gift C, Jiang H, Tang Y, Liu J, Tan S, Yu Z, Liu Z, Lu Z, Fang C, Zhou Y, Zhang J, Zhu Q, Liu J, Zhang T. Quinoline Derivatives Kill Mycobacterium tuberculosis by Activating Glutamate Kinase. Cell Chem Biol 2019; 26:1187-1194.e5. [PMID: 31204286 DOI: 10.1016/j.chembiol.2019.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/24/2019] [Accepted: 05/13/2019] [Indexed: 10/26/2022]
Abstract
There is a great need for identification and development of new anti-tuberculosis drugs with novel targets. Recent drug-discovery efforts typically focus on identifying inhibitors but not activators that perturb metabolic enzymes' functions as a means to kill Mycobacterium tuberculosis (Mtb). Here, we describe a class of quinoline compounds, Z0933/Z0930, which kill Mtb by acting as activators of glutamate kinase (GK), a previously untargeted enzyme catalyzing the first step of proline biosynthesis. We further show that Z0933/Z0930 augment proline production and induce Mtb killing via proline-derived redox imbalance and production of reactive oxygen species. This work highlights the effectiveness of gain-of-function probes against Mtb and provides a framework for the discovery of next-generation allosteric activators of GK.
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Affiliation(s)
- Gaelle G Makafe
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Muzammal Hussain
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; Guangdong Provincial Key Laboratory of Biocomputing, Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Goverdhan Surineni
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, 62 Hengzhigang Road, Yuexiu District, Guangzhou 510095, China
| | - Nai-Kei Wong
- Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, 29 Bulan Road, Longgang District, Shenzhen 518112, China
| | - Mugweru Julius
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; Department of Biological Sciences, University of Embu, Embu 6-60100, Kenya
| | - Lanying Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Chiwala Gift
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Huofeng Jiang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, China
| | - Yunxiang Tang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Shushan District, Hefei 230009, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, 62 Hengzhigang Road, Yuexiu District, Guangzhou 510095, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, 62 Hengzhigang Road, Yuexiu District, Guangzhou 510095, China
| | - Zhijun Yu
- Guangdong Provincial Key Laboratory of Biocomputing, Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Zhiyong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China
| | - Zhili Lu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China
| | - Cuiting Fang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yang Zhou
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm 10691, Sweden
| | - Jiancun Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; Guangdong Provincial Key Laboratory of Biocomputing, Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Qiang Zhu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Jinsong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; Guangdong Provincial Key Laboratory of Biocomputing, Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China.
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), 190 Kaiyuan Avenue, Science Park, Huangpu District, Guangzhou 510530, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China.
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9
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Takagi H. Metabolic regulatory mechanisms and physiological roles of functional amino acids and their applications in yeast. Biosci Biotechnol Biochem 2019; 83:1449-1462. [PMID: 30712454 DOI: 10.1080/09168451.2019.1576500] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In yeast, amino acid metabolism and its regulatory mechanisms vary under different growth environments by regulating anabolic and catabolic processes, including uptake and export, and the metabolic styles form a complicated but robust network. There is also crosstalk with various metabolic pathways, products and signal molecules. The elucidation of metabolic regulatory mechanisms and physiological roles is important fundamental research for understanding life phenomenon. In terms of industrial application, the control of amino acid composition and content is expected to contribute to an improvement in productivity, and to add to the value of fermented foods, alcoholic beverages, bioethanol, and other valuable compounds (proteins and amino acids, etc.). This review article mainly describes our research in constructing yeast strains with high functionality, focused on the metabolic regulatory mechanisms and physiological roles of "functional amino acids", such as l-proline, l-arginine, l-leucine, l-valine, l-cysteine, and l-methionine, found in yeast.
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Affiliation(s)
- Hiroshi Takagi
- a Division of Biological Science, Graduate School of Science and Technology , Nara Institute of Science and Technology , Nara , Japan
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10
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Omedi JO, Huang W, Zhang B, Li Z, Zheng J. Advances in present-day frozen dough technology and its improver and novel biotech ingredients development trends-A review. Cereal Chem 2019. [DOI: 10.1002/cche.10122] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Jacob O. Omedi
- State Key Laboratory of Food Science and Technology, Laboratory of Baking and Fermentation Science, Cereal/Sourdough and Ingredient Functionality Research, School of Food Science and Technology; Jiangnan University; Wuxi China
| | - Weining Huang
- State Key Laboratory of Food Science and Technology, Laboratory of Baking and Fermentation Science, Cereal/Sourdough and Ingredient Functionality Research, School of Food Science and Technology; Jiangnan University; Wuxi China
| | - Binle Zhang
- State Key Laboratory of Food Science and Technology, Laboratory of Baking and Fermentation Science, Cereal/Sourdough and Ingredient Functionality Research, School of Food Science and Technology; Jiangnan University; Wuxi China
- MagiBake GS International; Jinjiang; Quanzhou China
| | - Zhibin Li
- MagiBake GS International; Jinjiang; Quanzhou China
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11
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Miller KJ, Box WG, Jenkins DM, Boulton CA, Linforth R, Smart KA. Does Generation Number Matter? The Impact of Repitching on Wort Utilization. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-2013-1003-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Katherine J. Miller
- Division of Food Sciences, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Wendy G. Box
- Division of Food Sciences, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough, LE12 5RD, UK
| | - David M. Jenkins
- Division of Food Sciences, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Christopher A. Boulton
- Division of Food Sciences, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Robert Linforth
- Division of Food Sciences, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Katherine A. Smart
- Division of Food Sciences, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough, LE12 5RD, UK
- SABMiller plc, SABMiller House, Woking, Surrey GU21 6HS, UK
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12
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Gibson BR, Boulton CA, Box WG, Graham NS, Lawrence SJ, Linforth RST, Smart KA. Amino Acid Uptake and Yeast Gene Transcription during Industrial Brewery Fermentation. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-2009-0720-01] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Brian R. Gibson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Chris A. Boulton
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Wendy G. Box
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Neil S. Graham
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Stephen J. Lawrence
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Robert S. T. Linforth
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Katherine A. Smart
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
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13
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Oshoma CE, Phister TG, Powell CD, Smart KA, Du C. Proline as a Formic Acid Stress Protectant During Fermentation of Glucose to Ethanol bySaccharomycesspp. Ind Biotechnol (New Rochelle N Y) 2017. [DOI: 10.1089/ind.2017.0017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Cyprian E. Oshoma
- Department of Microbiology, University of Benin, Benin City, Nigeria
- Bioenergy and Brewing Science Building School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | | | - Chris D. Powell
- Bioenergy and Brewing Science Building School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | | | - Chenyu Du
- Bioenergy and Brewing Science Building School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
- School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
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14
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Li H, Zhang Z, He C, Qin G, Tian S. Comparative Proteomics Reveals the Potential Targets of BcNoxR, a Putative Regulatory Subunit of NADPH Oxidase of Botrytis cinerea. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:990-1003. [PMID: 27898285 DOI: 10.1094/mpmi-11-16-0227-r] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The NADPH oxidase (NOX) complex has been shown to play a crucial role in stress response and in the virulence of various fungal pathogens. The underlying molecular mechanisms of NOX, however, remain largely unknown. In the present study, a comparative proteomic analysis compared changes in protein abundance in wild-type Botrytis cinerea and ΔbcnoxR mutants in which the regulatory subunit of NOX was deleted. The ΔbcnoxR mutants exhibited reduced growth, sporulation, and impaired virulence. A total of 60 proteins, representing 49 individual genes, were identified in ΔbcnoxR mutants that exhibited significant differences in abundance relative to wild-type. Reverse transcription-quantitative polymerase chain reaction analysis demonstrated that the differences in transcript levels for 36 of the genes encoding the identified proteins were in agreement with the proteomic analysis, while the remainder exhibited reverse levels. Functional analysis of four proteins that decreased abundance in the ΔbcnoxR mutants indicated that 6-phosphogluconate dehydrogenase (BcPGD) played a role in the growth and sporulation of B. cinerea. The Δbcpgd mutants also displayed impaired virulence on various hosts, such as apple, strawberry, and tomato fruit. These results suggest that NOX can influence the expression of BcPGD, which has an impact on growth, sporulation, and virulence of B. cinerea.
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Affiliation(s)
- Hua Li
- 1 Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; and
- 2 University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhanquan Zhang
- 1 Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; and
| | - Chang He
- 1 Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; and
- 2 University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guozheng Qin
- 1 Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; and
| | - Shiping Tian
- 1 Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; and
- 2 University of Chinese Academy of Sciences, Beijing 100049, China
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15
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Nugroho RH, Yoshikawa K, Matsuda F, Shimizu H. Positive effects of proline addition on the central metabolism of wild-type and lactic acid-producing Saccharomyces cerevisiae strains. Bioprocess Biosyst Eng 2016; 39:1711-6. [PMID: 27350544 DOI: 10.1007/s00449-016-1646-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 06/20/2016] [Indexed: 01/10/2023]
Abstract
In Saccharomyces cerevisiae, proline is a stress protectant interacting with other substrate uptake systems against oxidative stress under low pH conditions. In this study, we performed metabolomics analysis to investigate the response associated with an increase in cell growth rates and maximum densities when cells were treated with proline under normal and acid stress conditions. Metabolome data show that concentrations of components of central metabolism are increased in proline-treated S. cerevisiae. No consumption of proline was observed, suggesting that proline does not act as a nutrient but regulates metabolic state and growth of cells. Treatment of lactic acid-producing yeast with proline during lactic acid bio-production improved growth rate and increased the final concentration of lactic acid.
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Affiliation(s)
- Riyanto Heru Nugroho
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Katsunori Yoshikawa
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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16
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Takagi H, Taguchi J, Kaino T. Proline accumulation protects Saccharomyces cerevisiae cells in stationary phase from ethanol stress by reducing reactive oxygen species levels. Yeast 2016; 33:355-63. [PMID: 26833688 DOI: 10.1002/yea.3154] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 01/22/2016] [Accepted: 01/23/2016] [Indexed: 11/12/2022] Open
Abstract
During fermentation processes, Saccharomyces cerevisiae cells are exposed to multiple stresses, including a high concentration of ethanol that represents toxicity through intracellular reactive oxygen species (ROS) generation. We previously reported that proline protected yeast cells from damage caused by various stresses, such as freezing and ethanol. As an anti-oxidant, proline is suggested to scavenge intracellular ROS. In this study, we examined the role of intracellular proline during ethanol treatment in S. cerevisiae strains that accumulate different concentrations of proline. When cultured in YPD medium, there was a significant accumulation of proline in the put1 mutant strain, which is deficient in proline oxidase, in the stationary phase. Expression of the mutant PRO1 gene, which encodes the γ-glutamyl kinase variant (Asp154Asn or Ile150Thr) with desensitization to feedback inhibition by proline in the put1 mutant strain, showed a prominent increase in proline content as compared with that of the wild-type strain. The oxidation level was clearly increased in wild-type cells after exposure to ethanol, indicating that the generation of ROS occurred. Interestingly, proline accumulation significantly reduces the ROS level and increases the survival rate of yeast cells in the stationary phase under ethanol stress conditions. However, there was not a clear correlation between proline content and survival rate in yeast cells. An appropriate level of intracellular proline in yeast might be important for its stress-protective effect. Hence, the engineering of proline metabolism could be promising for breeding stress-tolerant industrial yeast strains. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Hiroshi Takagi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Junpei Taguchi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Tomohiro Kaino
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, 1060 Nishikawatsu, Matsue, Shimane, 690-8504, Japan
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17
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Ren X, Ma S, Wang J, Tian S, Fu X, Liu X, Li Z, Zhao B, Wang X. Comparative effects of dexamethasone and bergenin on chronic bronchitis and their anti-inflammatory mechanisms based on NMR metabolomics. MOLECULAR BIOSYSTEMS 2016; 12:1938-47. [DOI: 10.1039/c6mb00041j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
NMR metabolomics was applied to study the anti-inflammation mechanism of dexamethasone and bergenin on chronic bronchitis.
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Affiliation(s)
- Xiaolei Ren
- School of Chinese Materia Medica
- Beijing University of Chinese Medicine
- Beijing 100102
- China
| | - Shuangshuang Ma
- School of Chinese Materia Medica
- Beijing University of Chinese Medicine
- Beijing 100102
- China
| | - Juan Wang
- School of Chinese Materia Medica
- Beijing University of Chinese Medicine
- Beijing 100102
- China
| | - Simin Tian
- School of Chinese Materia Medica
- Beijing University of Chinese Medicine
- Beijing 100102
- China
| | - Xiaorui Fu
- School of Chinese Materia Medica
- Beijing University of Chinese Medicine
- Beijing 100102
- China
| | - Xinfeng Liu
- Department of Chemistry
- Capital Normal University
- Beijing 100048
- China
| | - Zhongfeng Li
- School of Basic Medical Sciences
- Beijing University of Chinese Medicine
- Beijing 100029
- China
| | - Baosheng Zhao
- Center of Scientific Experiment
- Beijing University of Chinese Medicine
- Beijing 100029
- China
| | - Xueyong Wang
- School of Chinese Materia Medica
- Beijing University of Chinese Medicine
- Beijing 100102
- China
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18
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Nugroho RH, Yoshikawa K, Shimizu H. Metabolomic analysis of acid stress response in Saccharomyces cerevisiae. J Biosci Bioeng 2015; 120:396-404. [PMID: 25795572 DOI: 10.1016/j.jbiosc.2015.02.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 02/17/2015] [Accepted: 02/19/2015] [Indexed: 12/24/2022]
Abstract
Acid stress has been reported to inhibit cell growth and decrease productivity during bio-production processes. In this study, a metabolomics approach was conducted to understand the effect of lactic acid induced stress on metabolite pools in Saccharomyces cerevisiae. Cells were cultured with lactic acid as the acidulant, with or without initial pH control, i.e., at pH 6 or pH 2.5, respectively. Under conditions of low pH, lactic acid led to a decrease in the intracellular pH and specific growth rate; however, these parameters remained unaltered in the cultures with pH control. Capillary electrophoresis-mass spectrometry followed by a statistical principal component analysis was used to identify the metabolites and measure the increased concentrations of ATP, glutathione and proline during severe acid stress. Addition of proline to the acidified cultures improved the specific growth rates. We hypothesized that addition of proline protected the cells from acid stress by combating acid-induced oxidative stress. Lactic acid diffusion into the cell resulted in intracellular acidification, which elicited an oxidative stress response and resulted in increased glutathione levels.
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Affiliation(s)
- Riyanto Heru Nugroho
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Katsunori Yoshikawa
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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19
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Fichman Y, Gerdes SY, Kovács H, Szabados L, Zilberstein A, Csonka LN. Evolution of proline biosynthesis: enzymology, bioinformatics, genetics, and transcriptional regulation. Biol Rev Camb Philos Soc 2014; 90:1065-99. [PMID: 25367752 DOI: 10.1111/brv.12146] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 08/27/2014] [Accepted: 09/02/2014] [Indexed: 12/17/2022]
Abstract
Proline is not only an essential component of proteins but it also has important roles in adaptation to osmotic and dehydration stresses, redox control, and apoptosis. Here, we review pathways of proline biosynthesis in the three domains of life. Pathway reconstruction from genome data for hundreds of eubacterial and dozens of archaeal and eukaryotic organisms revealed evolutionary conservation and variations of this pathway across different taxa. In the most prevalent pathway of proline synthesis, glutamate is phosphorylated to γ-glutamyl phosphate by γ-glutamyl kinase, reduced to γ-glutamyl semialdehyde by γ-glutamyl phosphate reductase, cyclized spontaneously to Δ(1)-pyrroline-5-carboxylate and reduced to proline by Δ(1)-pyrroline-5-carboxylate reductase. In higher plants and animals the first two steps are catalysed by a bi-functional Δ(1) -pyrroline-5-carboxylate synthase. Alternative pathways of proline formation use the initial steps of the arginine biosynthetic pathway to ornithine, which can be converted to Δ(1)-pyrroline-5-carboxylate by ornithine aminotransferase and then reduced to proline or converted directly to proline by ornithine cyclodeaminase. In some organisms, the latter pathways contribute to or could be fully responsible for the synthesis of proline. The conservation of proline biosynthetic enzymes and significance of specific residues for catalytic activity and allosteric regulation are analysed on the basis of protein structural data, multiple sequence alignments, and mutant studies, providing novel insights into proline biosynthesis in organisms. We also discuss the transcriptional control of the proline biosynthetic genes in bacteria and plants.
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Affiliation(s)
- Yosef Fichman
- Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, Tel-Aviv 6997803, Israel
| | - Svetlana Y Gerdes
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, U.S.A
| | - Hajnalka Kovács
- Institute of Plant Biology, Biological Research Centre, 6726 Szeged, Hungary
| | - László Szabados
- Institute of Plant Biology, Biological Research Centre, 6726 Szeged, Hungary
| | - Aviah Zilberstein
- Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, Tel-Aviv 6997803, Israel
| | - Laszlo N Csonka
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, U.S.A
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20
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Tan H, Dong J, Wang G, Xu H, Zhang C, Xiao D. Enhanced freeze tolerance of baker’s yeast by overexpressed trehalose-6-phosphate synthase gene (TPS1) and deleted trehalase genes in frozen dough. ACTA ACUST UNITED AC 2014; 41:1275-85. [DOI: 10.1007/s10295-014-1467-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 05/22/2014] [Indexed: 11/30/2022]
Abstract
Abstract
Several recombinant strains with overexpressed trehalose-6-phosphate synthase gene (TPS1) and/or deleted trehalase genes were obtained to elucidate the relationships between TPS1, trehalase genes, content of intracellular trehalose and freeze tolerance of baker’s yeast, as well as improve the fermentation properties of lean dough after freezing. In this study, strain TL301TPS1 overexpressing TPS1 showed 62.92 % higher trehalose-6-phosphate synthase (Tps1) activity and enhanced the content of intracellular trehalose than the parental strain. Deleting ATH1 exerted a significant effect on trehalase activities and the degradation amount of intracellular trehalose during the first 30 min of prefermentation. This finding indicates that acid trehalase (Ath1) plays a role in intracellular trehalose degradation. NTH2 encodes a functional neutral trehalase (Nth2) that was significantly involved in intracellular trehalose degradation in the absence of the NTH1 and/or ATH1 gene. The survival ratio, freeze-tolerance ratio and relative fermentation ability of strain TL301TPS1 were approximately twice as high as those of the parental strain (BY6-9α). The increase in freeze tolerance of strain TL301TPS1 was accompanied by relatively low trehalase activity, high Tps1 activity and high residual content of intracellular trehalose. Our results suggest that overexpressing TPS1 and deleting trehalase genes are sufficient to improve the freeze tolerance of baker’s yeast in frozen dough. The present study provides guidance for the commercial baking industry as well as the research on the intracellular trehalose mobilization and freeze tolerance of baker’s yeast.
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Affiliation(s)
- Haigang Tan
- grid.413109.e 0000000097356249 Tianjin Industrial Microbiology Key Laboratory College of Biotechnology, Tianjin University of Science and Technology 300457 Tianjin People’s Republic of China
- grid.419897.a 000000040369313X Key Laboratory of Industrial Fermentation Microbiology Ministry of Education Tianjin People’s Republic of China
- grid.412608.9 0000000095266338 College of Food Science and Engineering Qingdao Agricultural University 266109 Qingdao People’s Republic of China
| | - Jian Dong
- grid.413109.e 0000000097356249 Tianjin Industrial Microbiology Key Laboratory College of Biotechnology, Tianjin University of Science and Technology 300457 Tianjin People’s Republic of China
- grid.419897.a 000000040369313X Key Laboratory of Industrial Fermentation Microbiology Ministry of Education Tianjin People’s Republic of China
| | - Guanglu Wang
- grid.413109.e 0000000097356249 Tianjin Industrial Microbiology Key Laboratory College of Biotechnology, Tianjin University of Science and Technology 300457 Tianjin People’s Republic of China
- grid.419897.a 000000040369313X Key Laboratory of Industrial Fermentation Microbiology Ministry of Education Tianjin People’s Republic of China
| | - Haiyan Xu
- grid.413109.e 0000000097356249 Tianjin Industrial Microbiology Key Laboratory College of Biotechnology, Tianjin University of Science and Technology 300457 Tianjin People’s Republic of China
- grid.419897.a 000000040369313X Key Laboratory of Industrial Fermentation Microbiology Ministry of Education Tianjin People’s Republic of China
| | - Cuiying Zhang
- grid.413109.e 0000000097356249 Tianjin Industrial Microbiology Key Laboratory College of Biotechnology, Tianjin University of Science and Technology 300457 Tianjin People’s Republic of China
- grid.419897.a 000000040369313X Key Laboratory of Industrial Fermentation Microbiology Ministry of Education Tianjin People’s Republic of China
| | - Dongguang Xiao
- grid.413109.e 0000000097356249 Tianjin Industrial Microbiology Key Laboratory College of Biotechnology, Tianjin University of Science and Technology 300457 Tianjin People’s Republic of China
- grid.419897.a 000000040369313X Key Laboratory of Industrial Fermentation Microbiology Ministry of Education Tianjin People’s Republic of China
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21
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Presence of proline has a protective effect on weak acid stressed Saccharomyces cerevisiae. Antonie van Leeuwenhoek 2014; 105:641-52. [DOI: 10.1007/s10482-014-0118-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/17/2014] [Indexed: 11/24/2022]
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22
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Tatehashi Y, Takagi H. Characterization of γ-glutamyl kinase mutants from Saccharomyces cerevisiae. J Biosci Bioeng 2013; 116:576-9. [DOI: 10.1016/j.jbiosc.2013.05.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 05/09/2013] [Accepted: 05/10/2013] [Indexed: 10/26/2022]
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23
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Singh P, Tiwari A, Singh SP, Asthana RK. Proline biosynthesizing enzymes (glutamate 5-kinase and pyrroline-5-carboxylate reductase) from a model cyanobacterium for desiccation tolerance. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2013; 19:521-528. [PMID: 24431521 PMCID: PMC3781280 DOI: 10.1007/s12298-013-0186-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Drought is the most important abiotic stress, challenging sustainable agriculture globally. For desiccation being the multigenic trait, a combination of identified genes from the appropriate organism may render crop tolerant to the water stress. Among the compatible solutes, proline plays multifaceted role in counteracting such stress. The genes encoding proline biosynthesizing enzymes, glutamate 5-kinase (G5K), and pyrroline-5-carboxylate reductase (P5CR) from the low-desiccation-tolerant cyanobacterium Anabaena sp. PCC 7120, were cloned and overexpressed in Escherichia coli BL21(DE3) individually. The recombinant E. coli cells harboring G5K, failed to exhibit enhanced desiccation tolerance relative to those with P5CR that showed increased growth/survival over the wild type. This may be ascribed to the overexpression of the reductase gene. Multiple sequence alignment showed P5CR to be conserved in all the organisms. We hypothesize that P5CR gene from high-desiccation-tolerant cyanobacteria may be adopted as the candidate for making transgenic N2-fixing cyanobacterium for paddy fields and/or crop development in future.
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Affiliation(s)
- Priyanka Singh
- />Centre of Advanced study in Botany, Banaras Hindu University, Varanasi, 221005 India
| | - Anupam Tiwari
- />Centre of Advanced study in Botany, Banaras Hindu University, Varanasi, 221005 India
| | | | - Ravi Kumar Asthana
- />Centre of Advanced study in Botany, Banaras Hindu University, Varanasi, 221005 India
- />Department of Botany, Banaras Hindu University, Varanasi, 221005 India
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24
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Bach TMH, Takagi H. Properties, metabolisms, and applications of l-proline analogues. Appl Microbiol Biotechnol 2013; 97:6623-34. [DOI: 10.1007/s00253-013-5022-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 05/24/2013] [Accepted: 05/26/2013] [Indexed: 12/26/2022]
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25
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Randez-Gil F, Córcoles-Sáez I, Prieto JA. Genetic and Phenotypic Characteristics of Baker's Yeast: Relevance to Baking. Annu Rev Food Sci Technol 2013; 4:191-214. [DOI: 10.1146/annurev-food-030212-182609] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Francisca Randez-Gil
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, 46980 Paterna, Valencia, Spain;
| | - Isaac Córcoles-Sáez
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, 46980 Paterna, Valencia, Spain;
| | - José A. Prieto
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, 46980 Paterna, Valencia, Spain;
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26
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Simultaneous accumulation of proline and trehalose in industrial baker's yeast enhances fermentation ability in frozen dough. J Biosci Bioeng 2012; 113:592-5. [DOI: 10.1016/j.jbiosc.2011.12.018] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 12/26/2011] [Indexed: 11/22/2022]
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27
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Sasano Y, Haitani Y, Hashida K, Ohtsu I, Shima J, Takagi H. Enhancement of the proline and nitric oxide synthetic pathway improves fermentation ability under multiple baking-associated stress conditions in industrial baker's yeast. Microb Cell Fact 2012; 11:40. [PMID: 22462683 PMCID: PMC3359278 DOI: 10.1186/1475-2859-11-40] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Accepted: 04/01/2012] [Indexed: 11/21/2022] Open
Abstract
Background During the bread-making process, industrial baker's yeast, mostly Saccharomyces cerevisiae, is exposed to baking-associated stresses, such as air-drying and freeze-thaw stress. These baking-associated stresses exert severe injury to yeast cells, mainly due to the generation of reactive oxygen species (ROS), leading to cell death and reduced fermentation ability. Thus, there is a great need for a baker's yeast strain with higher tolerance to baking-associated stresses. Recently, we revealed a novel antioxidative mechanism in a laboratory yeast strain that is involved in stress-induced nitric oxide (NO) synthesis from proline via proline oxidase Put1 and N-acetyltransferase Mpr1. We also found that expression of the proline-feedback inhibition-less sensitive mutant γ-glutamyl kinase (Pro1-I150T) and the thermostable mutant Mpr1-F65L resulted in an enhanced fermentation ability of baker's yeast in bread dough after freeze-thaw stress and air-drying stress, respectively. However, baker's yeast strains with high fermentation ability under multiple baking-associated stresses have not yet been developed. Results We constructed a self-cloned diploid baker's yeast strain with enhanced proline and NO synthesis by expressing Pro1-I150T and Mpr1-F65L in the presence of functional Put1. The engineered strain increased the intracellular NO level in response to air-drying stress, and the strain was tolerant not only to oxidative stress but also to both air-drying and freeze-thaw stresses probably due to the reduced intracellular ROS level. We also showed that the resultant strain retained higher leavening activity in bread dough after air-drying and freeze-thaw stress than that of the wild-type strain. On the other hand, enhanced stress tolerance and fermentation ability did not occur in the put1-deficient strain. This result suggests that NO is synthesized in baker's yeast from proline in response to oxidative stresses that induce ROS generation and that increased NO plays an important role in baking-associated stress tolerance. Conclusions In this work, we clarified the importance of Put1- and Mpr1-mediated NO generation from proline to the baking-associated stress tolerance in industrial baker's yeast. We also demonstrated that baker's yeast that enhances the proline and NO synthetic pathway by expressing the Pro1-I150T and Mpr1-F65L variants showed improved fermentation ability under multiple baking-associated stress conditions. From a biotechnological perspective, the enhancement of proline and NO synthesis could be promising for breeding novel baker's yeast strains.
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Affiliation(s)
- Yu Sasano
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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Sasano Y, Haitani Y, Ohtsu I, Shima J, Takagi H. Proline accumulation in baker's yeast enhances high-sucrose stress tolerance and fermentation ability in sweet dough. Int J Food Microbiol 2012; 152:40-3. [DOI: 10.1016/j.ijfoodmicro.2011.10.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2011] [Revised: 10/03/2011] [Accepted: 10/09/2011] [Indexed: 10/16/2022]
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Poole K, E Walker M, Warren T, Gardner J, McBryde C, de Barros Lopes M, Jiranek V. Proline transport and stress tolerance of ammonia-insensitive mutants of the PUT4-encoded proline-specific permease in yeast. J GEN APPL MICROBIOL 2010; 55:427-39. [PMID: 20118607 DOI: 10.2323/jgam.55.427] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The imino amino acid, proline, has roles in both cellular nutrition and response to stress. Proline uptake in Saccharomyces cerevisiae is largely mediated by a high affinity, specific permease, Put4p, and a low affinity general amino acid permease, Gap1p. Both are subject to nitrogen catabolite repression (NCR) and nitrogen catabolite inactivation (NCI). In order for proline to be fully exploited, its transport must be derepressed, as occurs upon depletion of preferred nitrogen sources, and molecular oxygen must be present to allow the first step of catabolism via proline oxidase. This study focuses on the isolation of variants of Put4p, which are insensitive to repression by a preferred nitrogen source (ammonia) and their subsequent effect on proline transport and stress tolerance. Specific amino acid residues in the carboxy-terminal region of Put4p were targeted by site-directed mutagenesis. Substitution at Serine(605), a potential phosphorylation target, led to the amelioration of ammonia-induced down-regulation of Put4p. When combined with a promoter mutation (-160), the S(605)A mutation resulted in increased proline uptake and accumulation. This increase in proline accumulation was associated with increased cell viability in conditions of high temperature and osmotic stress raising possible benefits in industrial fermentation applications.
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Affiliation(s)
- Kate Poole
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, Australia
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Antioxidant N-acetyltransferase Mpr1/2 of industrial baker's yeast enhances fermentation ability after air-drying stress in bread dough. Int J Food Microbiol 2010; 138:181-5. [DOI: 10.1016/j.ijfoodmicro.2010.01.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2009] [Revised: 12/10/2009] [Accepted: 01/01/2010] [Indexed: 11/21/2022]
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31
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Abstract
Accumulation of proline in higher plants is an indication of disturbed physiological condition, triggered by biotic or abiotic stress condition. Free proline content can increase upon exposure of plants to drought, salinity, cold, heavy metals, or certain pathogens. Determination of free proline levels is a useful assay to monitor physiological status and to assess stress tolerance of higher plants. Here we describe three methods suitable for determination of free proline content. The isatin paper assay is simple and is suitable to assay proline content in large number of samples. The colorimetric measurement is quantitative and provides reliable data about proline content. The HPLC-based amino acid analysis can be employed when concentration of all amino acids has to be compared.
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Todorova TT, Petrova VY, Vuilleumier S, Kujumdzieva AV. Response to different oxidants of Saccharomyces cerevisiae ure2Delta mutant. Arch Microbiol 2009; 191:837-45. [PMID: 19777209 DOI: 10.1007/s00203-009-0512-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Revised: 07/09/2009] [Accepted: 09/07/2009] [Indexed: 01/18/2023]
Abstract
Growth of Saccharomyces cerevisiae ure2Delta mutant strain was investigated in the presence of diverse oxidant compounds. The inability of the strain to grow on a medium supplemented with H(2)O(2) was confirmed and a relationship between diminishing levels of glutathione (GSH) and peroxide sensitivity was established. Data for the lack of significant effect of URE2 disruption on the cellular growth in the presence of paraquat and menadione were obtained. The possible role of Ure2p in acquiring sensitivity to oxidative stress by means of its regulatory role in the GATA signal transduction pathway was discussed. It was suggested that the susceptibility of ure2Delta mutant to the exogenous hydrogen peroxide can result from increased GSH degradation due to the deregulated localization of the gamma-glutamyl transpeptidase activating factors Gln3/Gat1. The important role of Ure2p in in vivo glutathione-mediated reactive oxygen species (ROS) scavenging was shown by measuring the activity of antioxidant enzymes glutathione peroxidase, superoxide dismutase (SOD) and catalase in an URE2 disrupted strain. A time-dependent increase in SOD and catalase activity was observed. More importantly, it was shown that the ure2 mutation could cause significant disturbance in cellular oxidant balance and increased ROS level.
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Affiliation(s)
- Tatina T Todorova
- University of Strasbourg UMR 7156 CNRS, 28 rue Goethe, 67083 Strasbourg Cedex, France
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Ding J, Huang X, Zhang L, Zhao N, Yang D, Zhang K. Tolerance and stress response to ethanol in the yeast Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2009; 85:253-63. [PMID: 19756577 DOI: 10.1007/s00253-009-2223-1] [Citation(s) in RCA: 209] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Revised: 08/23/2009] [Accepted: 08/24/2009] [Indexed: 11/30/2022]
Abstract
Eukaryotic cells have developed diverse strategies to combat the harmful effects of a variety of stress conditions. In the model yeast Saccharomyces cerevisiae, the increased concentration of ethanol, as the primary fermentation product, will influence the membrane fluidity and be toxic to membrane proteins, leading to cell growth inhibition and even death. Though little is known about the complex signal network responsible for alcohol stress responses in yeast cells, several mechanisms have been reported to be associated with this process, including changes in gene expression, in membrane composition, and increases in chaperone proteins that help stabilize other denatured proteins. Here, we review the recent progresses in our understanding of ethanol resistance and stress responses in yeast.
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Affiliation(s)
- Junmei Ding
- Laboratory for Conservation and Utilization of Bio-resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan 650091, China
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Insufficiency of copper ion homeostasis causes freeze-thaw injury of yeast cells as revealed by indirect gene expression analysis. Appl Environ Microbiol 2009; 75:6706-11. [PMID: 19749072 DOI: 10.1128/aem.00905-09] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Saccharomyces cerevisiae is exposed to freeze-thaw stress in commercial processes, including frozen dough baking. Cell viability and fermentation activity after a freeze-thaw cycle were dramatically decreased due to freeze-thaw injury. Because this type of injury involves complex phenomena, the injury mechanisms are not fully understood. We examined freeze-thaw injury by indirect gene expression analysis during postthaw incubation after freeze-thaw treatment using DNA microarray profiling. The results showed that genes involved in the homeostasis of metal ions were frequently contained in genes that were upregulated, depending on the freezing period. We assessed the phenotype of deletion mutants of the metal ion homeostasis genes that exhibited freezing period-dependent upregulation and found that the strains with deletion of the MAC1 and CTR1 genes involved in copper ion homeostasis exhibited freeze-thaw sensitivity, suggesting that copper ion homeostasis is required for freeze-thaw tolerance. We found that supplementation with copper ions during postthaw incubation increased intracellular superoxide dismutase activity and intracellular levels of reactive oxygen species were decreased. Moreover, cell viability was increased by supplementation with copper ions. These results suggest that insufficiency of copper ion homeostasis may be one of the causes of freeze-thaw injury.
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Stress-tolerance of baker's-yeast (Saccharomyces cerevisiae) cells: stress-protective molecules and genes involved in stress tolerance. Biotechnol Appl Biochem 2009; 53:155-64. [DOI: 10.1042/ba20090029] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Abstract
The traditional use of the yeast Saccharomyces cerevisiae in alcoholic fermentation has, over time, resulted in substantial accumulated knowledge concerning genetics, physiology, and biochemistry as well as genetic engineering and fermentation technologies. S. cerevisiae has become a platform organism for developing metabolic engineering strategies, methods, and tools. The current review discusses the relevance of several engineering strategies, such as rational and inverse metabolic engineering, evolutionary engineering, and global transcription machinery engineering, in yeast strain improvement. It also summarizes existing tools for fine-tuning and regulating enzyme activities and thus metabolic pathways. Recent examples of yeast metabolic engineering for food, beverage, and industrial biotechnology (bioethanol and bulk and fine chemicals) follow. S. cerevisiae currently enjoys increasing popularity as a production organism in industrial ("white") biotechnology due to its inherent tolerance of low pH values and high ethanol and inhibitor concentrations and its ability to grow anaerobically. Attention is paid to utilizing lignocellulosic biomass as a potential substrate.
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Proline as a stress protectant in yeast: physiological functions, metabolic regulations, and biotechnological applications. Appl Microbiol Biotechnol 2008; 81:211-23. [DOI: 10.1007/s00253-008-1698-5] [Citation(s) in RCA: 152] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Revised: 08/29/2008] [Accepted: 09/01/2008] [Indexed: 10/21/2022]
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38
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Self-cloning baker's yeasts that accumulate proline enhance freeze tolerance in doughs. Appl Environ Microbiol 2008; 74:5845-9. [PMID: 18641164 DOI: 10.1128/aem.00998-08] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We constructed self-cloning diploid baker's yeast strains by disrupting PUT1, encoding proline oxidase, and replacing the wild-type PRO1, encoding gamma-glutamyl kinase, with a pro1(D154N) or pro1(I150T) allele. The resultant strains accumulated intracellular proline and retained higher-level fermentation abilities in the frozen doughs than the wild-type strain. These results suggest that proline-accumulating baker's yeast is suitable for frozen-dough baking.
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39
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Donalies UEB, Nguyen HTT, Stahl U, Nevoigt E. Improvement of Saccharomyces yeast strains used in brewing, wine making and baking. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2008; 111:67-98. [PMID: 18463806 DOI: 10.1007/10_2008_099] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Yeast was the first microorganism domesticated by mankind. Indeed, the production of bread and alcoholic beverages such as beer and wine dates from antiquity, even though the fact that the origin of alcoholic fermentation is a microorganism was not known until the nineteenth century. The use of starter cultures in yeast industries became a common practice after methods for the isolation of pure yeast strains were developed. Moreover, effort has been undertaken to improve these strains, first by classical genetic methods and later by genetic engineering. In general, yeast strain development has aimed at improving the velocity and efficiency of the respective production process and the quality of the final products. This review highlights the achievements in genetic engineering of Saccharomyces yeast strains applied in food and beverage industry.
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Affiliation(s)
- Ute E B Donalies
- Department of Microbiology and Genetics, Berlin University of Technology, Seestr. 13, 13353, Berlin, Germany
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40
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Kaino T, Takagi H. Gene expression profiles and intracellular contents of stress protectants in Saccharomyces cerevisiae under ethanol and sorbitol stresses. Appl Microbiol Biotechnol 2008; 79:273-83. [DOI: 10.1007/s00253-008-1431-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Revised: 02/23/2008] [Accepted: 02/24/2008] [Indexed: 11/28/2022]
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41
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Krishnan N, Dickman MB, Becker DF. Proline modulates the intracellular redox environment and protects mammalian cells against oxidative stress. Free Radic Biol Med 2008; 44:671-81. [PMID: 18036351 PMCID: PMC2268104 DOI: 10.1016/j.freeradbiomed.2007.10.054] [Citation(s) in RCA: 251] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2007] [Revised: 10/25/2007] [Accepted: 10/30/2007] [Indexed: 10/22/2022]
Abstract
The potential of proline to suppress reactive oxygen species (ROS) and apoptosis in mammalian cells was tested by manipulating intracellular proline levels exogenously and endogenously by overexpression of proline metabolic enzymes. Proline was observed to protect cells against H(2)O(2), tert-butyl hydroperoxide, and a carcinogenic oxidative stress inducer but was not effective against superoxide generators such as menadione. Oxidative stress protection by proline requires the secondary amine of the pyrrolidine ring and involves preservation of the glutathione redox environment. Overexpression of proline dehydrogenase (PRODH), a mitochondrial flavoenzyme that oxidizes proline, resulted in 6-fold lower intracellular proline content and decreased cell survival relative to control cells. Cells overexpressing PRODH were rescued by pipecolate, an analog that mimics the antioxidant properties of proline, and by tetrahydro-2-furoic acid, a specific inhibitor of PRODH. In contrast, overexpression of the proline biosynthetic enzymes Delta(1)-pyrroline-5-carboxylate (P5C) synthetase (P5CS) and P5C reductase (P5CR) resulted in 2-fold higher proline content, significantly lower ROS levels, and increased cell survival relative to control cells. In different mammalian cell lines exposed to physiological H(2)O(2) levels, increased endogenous P5CS and P5CR expression was observed, indicating that upregulation of proline biosynthesis is an oxidative stress response.
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Affiliation(s)
- Navasona Krishnan
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588
| | - Martin B. Dickman
- Institute for Plant Genomics and Biotechnology, Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843
| | - Donald F. Becker
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588
- Corresponding Author: Department of Biochemistry, University of Nebraska, N258 Beadle Center, Lincoln, NE 68588, Tel. 402-472-9652; Fax. 402-472-7842;
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42
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Rosell CM, Gómez M. Frozen Dough and Partially Baked Bread: An Update. FOOD REVIEWS INTERNATIONAL 2007. [DOI: 10.1080/87559120701418368] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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43
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Takagi H, Matsui F, Kawaguchi A, Wu H, Shimoi H, Kubo Y. Construction and analysis of self-cloning sake yeasts that accumulate proline. J Biosci Bioeng 2007; 103:377-80. [PMID: 17502281 DOI: 10.1263/jbb.103.377] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2006] [Accepted: 01/13/2007] [Indexed: 11/17/2022]
Abstract
We constructed self-cloning diploid sake yeast strains that accumulate proline. The appropriate proline level is important for its protective effect against ethanol stress in yeast cells. Sake brewed with the proline-accumulating strains contained two- to threefold more proline than the sake brewed with the parent strain. It was also suggested that intracellular proline does not affect overall fermentation profiles, but reduces fermentation time in terms of ethanol production rate.
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Affiliation(s)
- Hiroshi Takagi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
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44
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Sekine T, Kawaguchi A, Hamano Y, Takagi H. Desensitization of feedback inhibition of the Saccharomyces cerevisiae gamma-glutamyl kinase enhances proline accumulation and freezing tolerance. Appl Environ Microbiol 2007; 73:4011-9. [PMID: 17449694 PMCID: PMC1932739 DOI: 10.1128/aem.00730-07] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In response to osmotic stress, proline is accumulated in many bacterial and plant cells as an osmoprotectant. The yeast Saccharomyces cerevisiae induces trehalose or glycerol synthesis but does not increase intracellular proline levels during various stresses. Using a proline-accumulating mutant, we previously found that proline protects yeast cells from damage by freezing, oxidative, or ethanol stress. This mutant was recently shown to carry an allele of PRO1 which encodes the Asp154Asn mutant gamma-glutamyl kinase (GK), the first enzyme of the proline biosynthetic pathway. Here, enzymatic analysis of recombinant proteins revealed that the GK activity of S. cerevisiae is subject to feedback inhibition by proline. The Asp154Asn mutant was less sensitive to feedback inhibition than wild-type GK, leading to proline accumulation. To improve the enzymatic properties of GK, PCR random mutagenesis in PRO1 was employed. The mutagenized plasmid library was introduced into an S. cerevisiae non-proline-utilizing strain, and proline-overproducing mutants were selected on minimal medium containing the toxic proline analogue azetidine-2-carboxylic acid. We successfully isolated several mutant GKs that, due to extreme desensitization to inhibition, enhanced the ability to synthesize proline better than the Asp154Asn mutant. The amino acid changes were localized at the region between positions 142 and 154, probably on the molecular surface, suggesting that this region is involved in allosteric regulation. Furthermore, we found that yeast cells expressing Ile150Thr and Asn142Asp/Ile166Val mutant GKs were more tolerant to freezing stress than cells expressing the Asp154Asn mutant.
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Affiliation(s)
- Tomoko Sekine
- Department of Bioscience, Fukui Prefectural University, Japan
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45
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Ando A, Nakamura T, Murata Y, Takagi H, Shima J. Identification and classification of genes required for tolerance to freezeâthaw stress revealed by genome-wide screening ofSaccharomyces cerevisiaedeletion strains. FEMS Yeast Res 2007; 7:244-53. [PMID: 16989656 DOI: 10.1111/j.1567-1364.2006.00162.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Yeasts used in bread making are exposed to freeze-thaw stress during frozen-dough baking. To clarify the genes required for freeze-thaw tolerance, genome-wide screening was performed using the complete deletion strain collection of diploid Saccharomyces cerevisiae. The screening identified 58 gene deletions that conferred freeze-thaw sensitivity. These genes were then classified based on their cellular function and on the localization of their products. The results showed that the genes required for freeze-thaw tolerance were frequently involved in vacuole functions and cell wall biogenesis. The highest numbers of gene products were components of vacuolar H(+)-ATPase. Next, the cross-sensitivity of the freeze-thaw-sensitive mutants to oxidative stress and to cell wall stress was studied; both of these are environmental stresses closely related to freeze-thaw stress. The results showed that defects in the functions of vacuolar H(+)-ATPase conferred sensitivity to oxidative stress and to cell wall stress. In contrast, defects in gene products involved in cell wall assembly conferred sensitivity to cell wall stress but not to oxidative stress. Our results suggest the presence of at least two different mechanisms of freeze-thaw injury: oxidative stress generated during the freeze-thaw process, and defects in cell wall assembly.
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Affiliation(s)
- Akira Ando
- National Food Research Institute, Tsukuba, Ibaraki, Japan
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HONJOH KI, MACHIDA T, NISHI K, MATSUURA K, SOLI KW, SAKAI T, ISHIKAWA H, MATSUMOTO K, MIYAMOTO T, IIO M. Improvement of Freezing and Oxidative Stress Tolerance in Saccharomyces cerevisiae by Taurine. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2007. [DOI: 10.3136/fstr.13.145] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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47
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Chen C, Wanduragala S, Becker DF, Dickman MB. Tomato QM-like protein protects Saccharomyces cerevisiae cells against oxidative stress by regulating intracellular proline levels. Appl Environ Microbiol 2006; 72:4001-6. [PMID: 16751508 PMCID: PMC1489650 DOI: 10.1128/aem.02428-05] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Exogenous proline can protect cells of Saccharomyces cerevisiae from oxidative stress. We altered intracellular proline levels by overexpressing the proline dehydrogenase gene (PUT1) of S. cerevisiae. Put1p performs the first enzymatic step of proline degradation in S. cerevisiae. Overexpression of Put1p results in low proline levels and hypersensitivity to oxidants, such as hydrogen peroxide and paraquat. A put1-disrupted yeast mutant deficient in Put1p activity has increased protection from oxidative stress and increased proline levels. Following a conditional life/death screen in yeast, we identified a tomato (Lycopersicon esculentum) gene encoding a QM-like protein (tQM) and found that stable expression of tQM in the Put1p-overexpressing strain conferred protection against oxidative damage from H2O2, paraquat, and heat. This protection was correlated with reactive oxygen species (ROS) reduction and increased proline accumulation. A yeast two-hybrid system assay was used to show that tQM physically interacts with Put1p in yeast, suggesting that tQM is directly involved in modulating proline levels. tQM also can rescue yeast from the lethality mediated by the mammalian proapoptotic protein Bax, through the inhibition of ROS generation. Our results suggest that tQM is a component of various stress response pathways and may function in proline-mediated stress tolerance in plants.
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Affiliation(s)
- Changbin Chen
- Institute for Plant Genomics and Biotechnology, Department of Plant Pathology and Microbiology, Texas A&M University, 2123 TAMU, College Station, TX 77843, USA
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48
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Krishnan N, Becker DF. Oxygen reactivity of PutA from Helicobacter species and proline-linked oxidative stress. J Bacteriol 2006; 188:1227-35. [PMID: 16452403 PMCID: PMC1367249 DOI: 10.1128/jb.188.4.1227-1235.2006] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Proline is converted to glutamate in two successive steps by the proline utilization A (PutA) flavoenzyme in gram-negative bacteria. PutA contains a proline dehydrogenase domain that catalyzes the flavin adenine dinucleotide (FAD)-dependent oxidation of proline to delta1-pyrroline-5-carboxylate (P5C) and a P5C dehydrogenase domain that catalyzes the NAD+-dependent oxidation of P5C to glutamate. Here, we characterize PutA from Helicobacter hepaticus (PutA(Hh)) and Helicobacter pylori (PutA(Hp)) to provide new insights into proline metabolism in these gastrointestinal pathogens. Both PutA(Hh) and PutA(Hp) lack DNA binding activity, in contrast to PutA from Escherichia coli (PutA(Ec)), which both regulates and catalyzes proline utilization. PutA(Hh) and PutA(Hp) display catalytic activities similar to that of PutA(Ec) but have higher oxygen reactivity. PutA(Hh) and PutA(Hp) exhibit 100-fold-higher turnover numbers (approximately 30 min(-1)) than PutA(Ec) (<0. 3 min(-1)) using oxygen as an electron acceptor during catalytic turnover with proline. Consistent with increased oxygen reactivity, PutA(Hh) forms a reversible FAD-sulfite adduct. The significance of increased oxygen reactivity in PutA(Hh) and PutA(Hp) was probed by oxidative stress studies in E. coli. Expression of PutA(Ec) and PutA from Bradyrhizobium japonicum, which exhibit low oxygen reactivity, does not diminish stress survival rates of E. coli cell cultures. In contrast, PutA(Hp) and PutA(Hh) expression dramatically reduces E. coli cell survival and is correlated with relatively lower proline levels and increased hydrogen peroxide formation. The discovery of reduced oxygen species formation by PutA suggests that proline catabolism may influence redox homeostasis in the ecological niches of these Helicobacter species.
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Affiliation(s)
- Navasona Krishnan
- Department of Biochemistry, University of Nebraska, N258 Beadle Center, Lincoln, Nebraska 68588, USA
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Matsuura K, Takagi H. Vacuolar functions are involved in stress-protective effect of intracellular proline in Saccharomyces cerevisiae. J Biosci Bioeng 2006; 100:538-44. [PMID: 16384793 DOI: 10.1263/jbb.100.538] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2005] [Accepted: 07/29/2005] [Indexed: 11/17/2022]
Abstract
Proline protects yeast cells from damage caused by various stresses. A yeast Saccharomyces cerevisiae mutant with high levels of intracellular proline grown in a minimal medium accumulated proline in its vacuole, but when grown in a nutrient medium, accumulated proline mainly in the cytosol. To understand the role of the proline pool in the vacuole, we examined the stress-protective effect of proline in proline-accumulating yeast cells deficient in vacuolar functions. The disruption of PEP3 encoding a vacuolar membrane protein required for vacuolar biogenesis caused hypersensitivity to heat shock and ethanol stresses, probably due to disappearance of normal vacuoles. The vph1-disrupted cells lacking vacuolar-ATPase activity showed resistance to heat shock without any change in proline localization, but showed severe growth defects in an ethanol-containing medium. These results indicate that vacuolar functions are involved in the stress-protective effect of proline in S. cerevisiae. Also, it appears that excess proline is transported to the vacuole in an ATP-independent manner.
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Affiliation(s)
- Keisuke Matsuura
- Department of Bioscience, Fukui Prefectural University, 4-1-1 Kenjojima, Fukui 910-1195, Japan
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Takagi H, Takaoka M, Kawaguchi A, Kubo Y. Effect of L-proline on sake brewing and ethanol stress in Saccharomyces cerevisiae. Appl Environ Microbiol 2006; 71:8656-62. [PMID: 16332860 PMCID: PMC1317411 DOI: 10.1128/aem.71.12.8656-8662.2005] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During the fermentation of sake, cells of Saccharomyces cerevisiae are exposed to high concentrations of ethanol, thereby damaging the cell membrane and functional proteins. L-proline protects yeast cells from damage caused by freezing or oxidative stress. In this study, we evaluated the role of intracellular L-proline in cells of S. cerevisiae grown under ethanol stress. An L-proline-accumulating laboratory strain carries a mutant allele of PRO1, pro1(D154N), which encodes the Asp154Asn mutant gamma-glutamyl kinase. This mutation increases the activity of gamma-glutamyl kinase and gamma-glutamyl phosphate reductase, which catalyze the first two steps of L-proline synthesis and which together may form a complex in vivo. When cultured in liquid medium in the presence of 9% and 18% ethanol under static conditions, the cell viability of the L-proline-accumulating laboratory strain is greater than the cell viability of the parent strain. This result suggests that intracellular accumulation of L-proline may confer tolerance to ethanol stress. We constructed a novel sake yeast strain by disrupting the PUT1 gene, which is required for L-proline utilization, and replacing the wild-type PRO1 allele with the pro1(D154N) allele. The resultant strain accumulated L-proline and was more tolerant to ethanol stress than was the control strain. We used the strain that could accumulate L-proline to brew sake containing five times more L-proline than what is found in sake brewed with the control strain, without affecting the fermentation profiles.
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Affiliation(s)
- Hiroshi Takagi
- Department of Bioscience, Fukui Prefectural University, 4-1-1 Kenjojima, Matsuoka-cho, Fukui 910-1195, Japan.
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