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Zhang P, Li B, Wen P, Wang P, Yang Y, Chen Q, Chang Y, Hu X. Metabolic Engineering of Four GATA Factors to Reduce Urea and Ethyl Carbamate Formation in a Model Rice Wine System. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:10881-10889. [PMID: 30246534 DOI: 10.1021/acs.jafc.8b04370] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Urea is the most important precursor of ethyl carbamate (EC), a harmful carcinogenic product, in fermented wines. In this study, the effects of four GATA transcriptional factors (Gln3p, Gat1p, Dal80p ,and Gzf3p) on extracellular urea and EC formation and transcriptional changes in urea degradation related genes ( DUR1,2 and DUR3) were examined. Compared to the WT strain, the Δ gzf3 mutant showed 18.7% urea reduction and exhibited synergistic effects with overexpressed Gln3p1-653 and Gat1p1-375 on extracellular urea reduction. Moreover, Δ gzf3+Gln3p1-653 and Δ gzf3+Gat1p1-375 showed significant 38.7% and 43.7% decreases in urea concentration and 41.7% and 48.5% decreases in EC concentration, respectively, in a model rice wine system. These results provide a promising way to reduce urea and EC formation during wine fermentation and raise some cues for the regulations of the four GATA transcriptional factors on the expression of individual nitrogen catabolite repression sensitive genes and their related metabolism pathway.
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Affiliation(s)
- Peng Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology , Nanchang University , Nanchang 330047 , China
| | - Bang Li
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology , Nanchang University , Nanchang 330047 , China
| | - Peng Wen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology , Nanchang University , Nanchang 330047 , China
| | - Peilin Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology , Nanchang University , Nanchang 330047 , China
| | - Yu Yang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology , Nanchang University , Nanchang 330047 , China
| | - Qian Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology , Nanchang University , Nanchang 330047 , China
| | - Yuxin Chang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology , Nanchang University , Nanchang 330047 , China
| | - Xing Hu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology , Nanchang University , Nanchang 330047 , China
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Yang F, Lu X, Zong H, Ji H, Zhuge B. Gene expression profiles of Candida glycerinogenes under combined heat and high-glucose stresses. J Biosci Bioeng 2018; 126:464-469. [PMID: 29724569 DOI: 10.1016/j.jbiosc.2018.04.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 04/05/2018] [Accepted: 04/06/2018] [Indexed: 10/17/2022]
Abstract
Low cell tolerance is a basic issue in high-glucose fermentation under high temperature to economically obtain high product titer. Candida glycerinogenes, an industrial yeast, has excellent tolerance to the combined heat and high-glucose stress than Saccharomycescerevisiae. The potential mechanism responsible for the high tolerance was illustrated here. The transcription of the potential stress-responsive genes in two strains were varied under single stress (heat or high-glucose), especially the ribosome-related genes. Unlike S. cerevisiae, C. glycerinogenes up-regulated 17 genes, including most of the single stress responsive genes, and genes Avt1 and Pfk1 under the combined stress, indicating a more systematic stress-responsive system in C. glycerinogenes. Further down-regulating the 17 potential key responsive genes indicated that genes Dip5, Gpd1, Pfk1, Hxt4, Hxt6, and Ino4 are important for cell tolerance to the combined stress. Furthermore, most of the ribosomal function related genes, such as Mrt4, Nug1, Nop53, Rpa190, Rex4, and Nsr1, play important role in cell tolerance. Therefore, the wider responsive gene spectrum and the activated expression of ribosomal function related genes might be key and prerequisite factors for the excellent tolerance to the combined stress of C. glycerinogenes.
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Affiliation(s)
- Fei Yang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Xinyao Lu
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Hong Zong
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Hao Ji
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Bin Zhuge
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
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3
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Zhang P, Hu X. Metabolic engineering of arginine permeases to reduce the formation of urea in Saccharomyces cerevisiae. World J Microbiol Biotechnol 2018. [DOI: 10.1007/s11274-018-2430-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Ethyl carbamate: An emerging food and environmental toxicant. Food Chem 2017; 248:312-321. [PMID: 29329860 DOI: 10.1016/j.foodchem.2017.12.072] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 11/28/2017] [Accepted: 12/20/2017] [Indexed: 11/21/2022]
Abstract
Ethyl carbamate (EC), a chemical substance widely present in fermented food products and alcoholic beverages, has been classified as a Group 2A carcinogen by the International Agency for Research on Cancer (IARC). New evidence indicates that long-term exposure to EC may cause neurological disorders. Formation of EC in food and its metabolism have therefore been studied extensively and analytical methods for EC in various food matrices have been established. Due to the potential threat of EC to human health, mitigation strategies for EC in food products by physical, chemical, enzymatic, and genetic engineering methods have been developed. Natural products are suggested to provide protection against EC-induced toxicity through the modulation of oxidative stress. This review summarizes knowledge on the formation and metabolism of EC, detection of EC in food products, toxic effects of EC on various organs, and mitigation strategies including prevention of EC-induced tumorigenesis and genotoxicity by natural products.
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Zhang P, Du G, Zou H, Xie G, Chen J, Shi Z, Zhou J. Mutant Potential Ubiquitination Sites in Dur3p Enhance the Urea and Ethyl Carbamate Reduction in a Model Rice Wine System. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:1641-1648. [PMID: 28185458 DOI: 10.1021/acs.jafc.6b05348] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Ubiquitination can significantly affect the endocytosis and degradation of plasma membrane proteins. Here, the ubiquitination of a Saccharomyces cerevisiae urea plasma membrane transporter (Dur3p) was altered. Two potential ubiquitination sites, lysine residues K556 and K571, of Dur3p were predicted and replaced by arginine, and the effects of these mutations on urea utilization and formation under different nitrogen conditions were investigated. Compared with Dur3p, the Dur3pK556R mutant showed a 20.1% decrease in ubiquitination level in yeast nitrogen base medium containing urea and glutamine. It also exhibited a >75.8% decrease in urea formation in yeast extract-peptone-dextrose medium and 41.3 and 55.4% decreases in urea and ethyl carbamate formation (a known carcinogen), respectively, in a model rice wine system. The results presented here show that the mutation of Dur3p ubiquitination sites could significantly affect urea utilization and formation. Modifying the ubiquitination of specific transporters might have promising applications in rationally engineering S. cerevisiae strains to efficiently use specific nitrogen sources.
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Affiliation(s)
- Peng Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University , 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University , 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Huijun Zou
- Zhejiang Guyuelongshan Shaoxing Wine Company , 13 Yangjiang Road, Shaoxing, Zhejiang 312099, China
| | - Guangfa Xie
- Zhejiang Guyuelongshan Shaoxing Wine Company , 13 Yangjiang Road, Shaoxing, Zhejiang 312099, China
| | - Jian Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University , 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Zhongping Shi
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University , 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University , 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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Chin YW, Kang WK, Jang HW, Turner TL, Kim HJ. CAR1 deletion by CRISPR/Cas9 reduces formation of ethyl carbamate from ethanol fermentation by Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2016; 43:1517-1525. [PMID: 27573438 DOI: 10.1007/s10295-016-1831-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/15/2016] [Indexed: 12/22/2022]
Abstract
Enormous advances in genome editing technology have been achieved in recent decades. Among newly born genome editing technologies, CRISPR/Cas9 is considered revolutionary because it is easy to use and highly precise for editing genes in target organisms. CRISPR/Cas9 technology has also been applied for removing unfavorable target genes. In this study, we used CRISPR/Cas9 technology to reduce ethyl carbamate (EC), a potential carcinogen, which was formed during the ethanol fermentation process by yeast. Because the yeast CAR1 gene encoding arginase is the key gene to form ethyl carbamate, we inactivated the yeast CAR1 gene by the complete deletion of the gene or the introduction of a nonsense mutation in the CAR1 locus using CRISPR/Cas9 technology. The engineered yeast strain showed a 98 % decrease in specific activity of arginase while displaying a comparable ethanol fermentation performance. In addition, the CAR1-inactivated mutants showed reduced formation of EC and urea, as compared to the parental yeast strain. Importantly, CRISPR/Cas9 technology enabled generation of a CAR1-inactivated yeast strains without leaving remnants of heterologous genes from a vector, suggesting that the engineered yeast by CRISPR/Cas9 technology might sidestep GMO regulation.
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Affiliation(s)
- Young-Wook Chin
- Division of Nutrition and Metabolism Research, Korea Food Research Institute, Seongnam, 13539, Republic of Korea
| | - Woo-Kyung Kang
- Division of Nutrition and Metabolism Research, Korea Food Research Institute, Seongnam, 13539, Republic of Korea.,Department of Food Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Hae Won Jang
- Division of Strategic Food Research, Korea Food Research Institute, Seongnam, 13539, Republic of Korea
| | - Timothy L Turner
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, 260 Bevier Hall, Urbana, IL, 61801, USA
| | - Hyo Jin Kim
- Division of Nutrition and Metabolism Research, Korea Food Research Institute, Seongnam, 13539, Republic of Korea. .,Department of Food Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea.
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Fang RS, Dong YC, Chen F, Chen QH. Bacterial Diversity Analysis during the Fermentation Processing of Traditional Chinese Yellow Rice Wine Revealed by 16S rDNA 454 Pyrosequencing. J Food Sci 2015; 80:M2265-71. [PMID: 26409170 DOI: 10.1111/1750-3841.13018] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/04/2015] [Indexed: 01/08/2023]
Abstract
Rice wine is a traditional Chinese fermented alcohol drink. Spontaneous fermentation with the use of the Chinese starter and wheat Qu lead to the growth of various microorganisms during the complete brewing process. It's of great importance to fully understand the composition of bacteria diversity in rice wine in order to improve the quality and solve safety problems. In this study, a more comprehensive bacterial description was shown with the use of bacteria diversity analysis, which enabled us to have a better understanding. Rarefaction, rank abundance, alpha Diversity, beta diversity and principal coordinates analysis simplified their complex bacteria components and provide us theoretical foundation for further investigation. It has been found bacteria diversity is more abundant at mid-term and later stage of brewing process. Bacteria community analysis reveals there is a potential safety hazard existing in the fermentation, since most of the sequence reads are assigned to Enterobacter (7900 at most) and Pantoea (7336 at most), followed by Staphylococcus (2796 at most) and Pseudomonas (1681 at most). Lactic acid bacteria are rare throughout the fermentation process which is not in accordance with other reports. This work may offer us an opportunity to investigate micro ecological fermentation system in food industry.
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Affiliation(s)
- Ruo-si Fang
- Dept. of Food Science and Nutrition, Zhejiang Univ, Hangzhou, 310058, China
| | - Ya-chen Dong
- Dept. of Food Science and Nutrition, Zhejiang Univ, Hangzhou, 310058, China
| | - Feng Chen
- Dept. of Food Science and Nutrition, Zhejiang Univ, Hangzhou, 310058, China
| | - Qi-he Chen
- Food Science and Human Nutrition, Clemson Univ, S.C, 29634, U.S.A
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8
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Zhang X, Chen Z, Chen F. Construction of car1 Deletion Mutant fromSaccharomyces cerevisiaeand Evaluation of Its Fermentation Ability. FOOD BIOTECHNOL 2015. [DOI: 10.1080/08905436.2015.1059765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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9
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Li X, Shen C, Wu D, Lu J, Chen J, Xie G. Enhancement of urea uptake in Chinese rice wine yeast strain N85 by the constitutive expression ofDUR3for ethyl carbamate elimination. JOURNAL OF THE INSTITUTE OF BREWING 2015. [DOI: 10.1002/jib.208] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Xiaomin Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- School of Biotechnology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
| | - Chao Shen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- School of Biotechnology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
| | - Dianhui Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- School of Biotechnology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
| | - Jian Lu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- School of Biotechnology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- Industrial Technology Research Institute of Jiangnan University in Suqian; 888 Renmin Road Suqian 223800 China
| | - Jian Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- School of Biotechnology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
| | - Guangfa Xie
- School of Biotechnology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- National Engineering Research Centre for Chinese Rice Wine; China Shaoxing Rice Wine Group Co., Ltd; Shaoxing 312000 People's Republic of China
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10
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Fang RS, Dong YC, Li HJ, Chen QH. Ethyl carbamate formation regulated bySaccharomyces cerevisiaeZJU in the processing of Chinese yellow rice wine. Int J Food Sci Technol 2014. [DOI: 10.1111/ijfs.12665] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Ruo-Si Fang
- Department of Food Science and Nutrition; Zhejiang University; Yuhangtang Rd.866 Hangzhou 310058 China
- Food Microbiology Research Key Laboratory of Zhejiang Province; Hangzhou 310058 China
| | - Ya-Chen Dong
- Department of Food Science and Nutrition; Zhejiang University; Yuhangtang Rd.866 Hangzhou 310058 China
- Food Microbiology Research Key Laboratory of Zhejiang Province; Hangzhou 310058 China
| | - Hong-Ji Li
- Department of Food Science and Nutrition; Zhejiang University; Yuhangtang Rd.866 Hangzhou 310058 China
- Food Microbiology Research Key Laboratory of Zhejiang Province; Hangzhou 310058 China
| | - Qi-He Chen
- Department of Food Science and Nutrition; Zhejiang University; Yuhangtang Rd.866 Hangzhou 310058 China
- Food Microbiology Research Key Laboratory of Zhejiang Province; Hangzhou 310058 China
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11
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Jiao Z, Dong Y, Chen Q. Ethyl Carbamate in Fermented Beverages: Presence, Analytical Chemistry, Formation Mechanism, and Mitigation Proposals. Compr Rev Food Sci Food Saf 2014; 13:611-626. [DOI: 10.1111/1541-4337.12084] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 03/26/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Zhihua Jiao
- Dept. of Food Science and Nutrition; Zhejiang Univ; Nr. 866, Yuhangtang Road Xihu District Hangzhou 310058 China
| | - Yachen Dong
- Dept. of Food Science and Nutrition; Zhejiang Univ; Nr. 866, Yuhangtang Road Xihu District Hangzhou 310058 China
| | - Qihe Chen
- Dept. of Food Science and Nutrition; Zhejiang Univ; Nr. 866, Yuhangtang Road Xihu District Hangzhou 310058 China
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Zhao X, Zou H, Fu J, Chen J, Zhou J, Du G. Nitrogen regulation involved in the accumulation of urea in Saccharomyces cerevisiae. Yeast 2013; 30:437-47. [PMID: 23996237 DOI: 10.1002/yea.2980] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 08/19/2013] [Accepted: 08/23/2013] [Indexed: 11/07/2022] Open
Abstract
Rice wine is a popular traditional alcoholic drink with a long history in China. However, the presence of the potential carcinogen ethyl carbamate (EC) raises a series of food safety concerns. Although the metabolic pathway of urea (the major precusor of EC) has been characterized in Saccharomyces cerevisiae, the regulation of urea accumulation remains unclear, making the efficient elimination of urea difficult. To demonstrate the regulatory mechanisms governing urea accumulation, three key nitrogen sources that can inhibit urea utilization for a commercial S. cerevisiae strain were identified. In addition, regulators of nitrogen catabolite repression (NCR) and target of rapamycin (TOR) pathways were identified as being involved in urea accumulation by real-time quantitative PCR. Based on these results, preferred nitrogen sources were found to repress urea utilization by converting them to glutamine or glutamate. Moreover, the results indicated that the manner of urea metabolism regulation was different for two positive regulators involved in NCR; Gln3p can be retained in the cytoplasm by glutamine, while Gat1p can be retained by glutamine and glutamate. Furthermore, this was confirmed by fluorescence location detection. These new findings provide new targets for eliminating EC and other harmful nitrogen-containing compounds in fermented foods.
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Affiliation(s)
- Xinrui Zhao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, People's Republic of China
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Zhao X, Du G, Zou H, Fu J, Zhou J, Chen J. Progress in preventing the accumulation of ethyl carbamate in alcoholic beverages. Trends Food Sci Technol 2013. [DOI: 10.1016/j.tifs.2013.05.009] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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14
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Dahabieh M, Husnik J, Van Vuuren H. Functional enhancement of Sake yeast strains to minimize the production of ethyl carbamate in Sake wine. J Appl Microbiol 2010; 109:963-73. [DOI: 10.1111/j.1365-2672.2010.04723.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Iron-dependent remodeling of fungal metabolic pathways associated with ferrichrome biosynthesis. Appl Environ Microbiol 2010; 76:3806-17. [PMID: 20435771 DOI: 10.1128/aem.00659-10] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The fission yeast Schizosaccharomyces pombe excretes and accumulates the hydroxamate-type siderophore ferrichrome. The sib1(+) and sib2(+) genes encode, respectively, a siderophore synthetase and an l-ornithine N(5)-oxygenase that participate in ferrichrome biosynthesis. In the present report, we demonstrate that sib1(+) and sib2(+) are repressed by the GATA-type transcriptional repressor Fep1 in response to high levels of iron. We further found that the loss of Fep1 results in increased ferrichrome production. We showed that a sib1Delta sib2Delta mutant strain exhibits a severe growth defect on iron-poor media. We determined that two metabolic pathways are involved in biosynthesis of ornithine, an obligatory precursor of ferrichrome. Ornithine is produced by hydrolysis of arginine by the Car1 and Car3 proteins. Although car3(+) was constitutively expressed, car1(+) transcription levels were repressed upon exposure to iron, with a concomitant decrease of Car1 arginase activity. Ornithine is also generated by transformation of glutamate, which itself is produced by two separate biosynthetic pathways which are transcriptionally regulated by iron in an opposite fashion. In one pathway, the glutamate dehydrogenase Gdh1, which produces glutamate from 2-ketoglutarate, was repressed under iron-replete conditions in a Fep1-dependent manner. The other pathway involves two coupled enzymes, glutamine synthetase Gln1 and Fe-S cluster-containing glutamate synthase Glt1, which were both repressed under iron-limiting conditions but were expressed under iron-replete conditions. Collectively, these results indicate that under conditions of iron deprivation, yeast remodels metabolic pathways linked to ferrichrome synthesis in order to limit iron utilization without compromising siderophore production and its ability to sequester iron from the environment.
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Jung YJ, Park HD. Antisense-mediated inhibition of acid trehalase (ATH1) gene expression promotes ethanol fermentation and tolerance in Saccharomyces cerevisiae. Biotechnol Lett 2006; 27:1855-9. [PMID: 16328979 DOI: 10.1007/s10529-005-3910-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2005] [Revised: 08/02/2005] [Accepted: 09/23/2005] [Indexed: 10/25/2022]
Abstract
Acid trehalase gene (ATH1) expression was decreased using the antisense-RNA technique in Saccharomyces cerevisiae. The 500 bp DNA fragments containing anti-ATH1 gene between +1 and +500 were amplified using PCR and fused to yeast ADH1, CYC1 and ATH1 promoters. Yeast cells harboring the recombinant plasmids had a low activity of acid trehalase and promoted ethanol fermentation compared to the control yeast cells harboring the vector plasmid only. The recombinant yeast had a high viability with 8% (v/v) ethanol.
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Affiliation(s)
- Young-Ji Jung
- Department of Life and Food Sciences, Kyungpook National University, 1370 Sangkyuk, 702-701 Daegu, Korea
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David L, Huber W, Granovskaia M, Toedling J, Palm CJ, Bofkin L, Jones T, Davis RW, Steinmetz LM. A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci U S A 2006; 103:5320-5. [PMID: 16569694 PMCID: PMC1414796 DOI: 10.1073/pnas.0601091103] [Citation(s) in RCA: 508] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
There is abundant transcription from eukaryotic genomes unaccounted for by protein coding genes. A high-resolution genome-wide survey of transcription in a well annotated genome will help relate transcriptional complexity to function. By quantifying RNA expression on both strands of the complete genome of Saccharomyces cerevisiae using a high-density oligonucleotide tiling array, this study identifies the boundary, structure, and level of coding and noncoding transcripts. A total of 85% of the genome is expressed in rich media. Apart from expected transcripts, we found operon-like transcripts, transcripts from neighboring genes not separated by intergenic regions, and genes with complex transcriptional architecture where different parts of the same gene are expressed at different levels. We mapped the positions of 3' and 5' UTRs of coding genes and identified hundreds of RNA transcripts distinct from annotated genes. These nonannotated transcripts, on average, have lower sequence conservation and lower rates of deletion phenotype than protein coding genes. Many other transcripts overlap known genes in antisense orientation, and for these pairs global correlations were discovered: UTR lengths correlated with gene function, localization, and requirements for regulation; antisense transcripts overlapped 3' UTRs more than 5' UTRs; UTRs with overlapping antisense tended to be longer; and the presence of antisense associated with gene function. These findings may suggest a regulatory role of antisense transcription in S. cerevisiae. Moreover, the data show that even this well studied genome has transcriptional complexity far beyond current annotation.
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Affiliation(s)
- Lior David
- *Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304
| | - Wolfgang Huber
- European Bioinformatics Institute, European Molecular Biology Laboratory, Cambridge CB10 1SD, United Kingdom; and
| | | | - Joern Toedling
- European Bioinformatics Institute, European Molecular Biology Laboratory, Cambridge CB10 1SD, United Kingdom; and
| | - Curtis J. Palm
- *Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304
| | - Lee Bofkin
- European Bioinformatics Institute, European Molecular Biology Laboratory, Cambridge CB10 1SD, United Kingdom; and
| | - Ted Jones
- *Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304
| | - Ronald W. Davis
- *Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304
- To whom correspondence may be addressed. E-mail:
or
| | - Lars M. Steinmetz
- *Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- To whom correspondence may be addressed. E-mail:
or
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