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Zeng DW, Yang YQ, Wang Q, Zhang FL, Zhang MD, Liao S, Liu ZQ, Fan YC, Liu CG, Zhang L, Zhao XQ. Transcriptome analysis of Kluyveromyces marxianus under succinic acid stress and development of robust strains. Appl Microbiol Biotechnol 2024; 108:293. [PMID: 38592508 PMCID: PMC11003901 DOI: 10.1007/s00253-024-13097-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 02/22/2024] [Accepted: 02/28/2024] [Indexed: 04/10/2024]
Abstract
Kluyveromyces marxianus has become an attractive non-conventional yeast cell factory due to its advantageous properties such as high thermal tolerance and rapid growth. Succinic acid (SA) is an important platform molecule that has been applied in various industries such as food, material, cosmetics, and pharmaceuticals. SA bioproduction may be compromised by its toxicity. Besides, metabolite-responsive promoters are known to be important for dynamic control of gene transcription. Therefore, studies on global gene transcription under various SA concentrations are of great importance. Here, comparative transcriptome changes of K. marxianus exposed to various concentrations of SA were analyzed. Enrichment and analysis of gene clusters revealed repression of the tricarboxylic acid cycle and glyoxylate cycle, also activation of the glycolysis pathway and genes related to ergosterol synthesis. Based on the analyses, potential SA-responsive promoters were investigated, among which the promoter strength of IMTCP2 and KLMA_50231 increased 43.4% and 154.7% in response to 15 g/L SA. In addition, overexpression of the transcription factors Gcr1, Upc2, and Ndt80 significantly increased growth under SA stress. Our results benefit understanding SA toxicity mechanisms and the development of robust yeast for organic acid production. KEY POINTS: • Global gene transcription of K. marxianus is changed by succinic acid (SA) • Promoter activities of IMTCP2 and KLMA_50123 are regulated by SA • Overexpression of Gcr1, Upc2, and Ndt80 enhanced SA tolerance.
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Affiliation(s)
- Du-Wen Zeng
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yong-Qiang Yang
- School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Qi Wang
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Feng-Li Zhang
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mao-Dong Zhang
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Sha Liao
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd, Dalian, 116045, China
| | - Zhi-Qiang Liu
- School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Ya-Chao Fan
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd, Dalian, 116045, China
| | - Chen-Guang Liu
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lin Zhang
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd, Dalian, 116045, China.
| | - Xin-Qing Zhao
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Wang Y, Xia T, Li C, Zeng D, Xu L, Song L, Yu H, Chen S, Zhao J, Bao X. Promoting Nucleic Acid Synthesis in Saccharomyces cerevisiae through Enhanced Expression of Rrn7p, Rrn11p, IMPDH, and Pho84p. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:15224-15236. [PMID: 37811818 DOI: 10.1021/acs.jafc.3c05035] [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: 10/10/2023]
Abstract
Saccharomyces cerevisiae has emerged as a preferred source for industrial production of ribonucleic acids (RNAs) and their derivatives, which find wide applications in the food and pharmaceutical sectors. In this study, we employed a modified RNA polymerase I-mediated green fluorescent protein expression system, previously developed by our team, to screen and identify an industrial S. cerevisiae strain with an impressive 18.2% increase in the RNA content. Transcriptome analysis revealed heightened activity of genes and pathways associated with rRNA transcription, purine metabolism, and phosphate transport in the high nucleic acid content mutant strains. Our findings highlighted the crucial role of the transcription factor Sfp1p in enhancing the expression of two key components of the transcription initiation factor complex, Rrn7p and Rrn11p, thereby promoting rRNA synthesis. Moreover, elevated expression of 5'-inosine monophosphate dehydrogenases, regardless of the specific isoform (IMD2, 3, or 4), resulted in increased rRNA synthesis through heightened GTP levels. Additionally, exogenous phosphate application, coupled with overexpression of the phosphate transporter PHO84, led to a 61.4% boost in the RNA yield, reaching 2050.4 mg/L. This comprehensive study provides valuable insights into the mechanism of RNA synthesis and serves as a reference for augmenting RNA production in the food industry.
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Affiliation(s)
- Yun Wang
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China
| | - Tianqing Xia
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China
| | - Chenhao Li
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China
| | - Duwen Zeng
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China
| | - Lili Xu
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China
- Shandong Sunkeen Biological Company, 6789 Xingfuhe Road, Jining 273517, China
| | - Liyun Song
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China
| | - Hengsong Yu
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China
| | - Shichao Chen
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China
| | - Jianzhi Zhao
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China
| | - Xiaoming Bao
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China
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Wu Y, Lei S, Lu C, Li J, Du G, Liu Y. Enhanced Ribonucleic Acid Production by High-Throughput Screening Based on Fluorescence Activation and Transcriptomic-Guided Fermentation Optimization in Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:6673-6680. [PMID: 37071119 DOI: 10.1021/acs.jafc.3c01677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Currently, the primary source of ribonucleic acids (RNAs), which is used as a flavor enhancer and nutritional supplement in the food manufacturing and processing industries, for large-scale industrial production is yeast, where the challenge is to optimize the cellular RNA content. Here, we developed and screened yeast strains yielding abundant RNAs via various methods. The novel Saccharomyces cerevisiae strain H1 with a 45.1% higher cellular RNA content than its FX-2 parent was successfully generated. Comparative transcriptomic analysis elucidated the molecular mechanisms underlying RNA accumulation in H1. Upregulation of genes encoding the hexose monophosphate and sulfur-containing amino acid biosynthesis pathways promoted RNA accumulation in the yeast, particularly in the presence of glucose as the sole carbon source. Feeding methionine into the bioreactor resulted in 145.2 mg/g dry cell weight and 9.6 g/L of cellular RNA content, which is the highest volumetric productivity of RNAs achieved in S. cerevisiae. This strategy of breeding S. cerevisiae strain with a higher capacity of accumulating abundant RNAs did not employ any genetic modification and thus will be favored by the food industry.
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Affiliation(s)
- Yexu Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Angel Yeast Co. Ltd., Chengdong Avenue 168, Yichang 443003, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Senlin Lei
- Angel Yeast Co. Ltd., Chengdong Avenue 168, Yichang 443003, China
| | - Chuanchuan Lu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
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Chen H, Wang J, Li Q, Xu X, Niu C, Zheng F, Liu C. Fed-Batch Fermentation of Saccharomyces pastorianus with High Ribonucleic Acid Yield. Foods 2022; 11:foods11182742. [PMID: 36140869 PMCID: PMC9497889 DOI: 10.3390/foods11182742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/05/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
(1) Background: The degradation products of ribonucleic acid (RNA)are widely used in the food and pharmaceutical industry for their flavoring and nutritional enhancement functions. Yeast is the main source for commercial RNA production, and an efficient strain is the key to reducing production costs; (2) Methods: A mutant Saccharomyces pastorianus G03H8 with a high RNA yield was developed via ARTP mutagenesis and fed-batch fermentation was applied to optimize production capacity. Genome sequencing analysis was used to reveal the underlying mechanism of higher RNA production genetic differences in the preferred mutant; (3) Results: Compared with the highest RNA content of the mutant strain, G03H8 increased by 40% compared with the parental strain G03 after response surface model optimization. Meanwhile, in fed-batch fermentation, G03H8′s dry cell weight (DCW) reached 60.58 g/L in 5 L fermenter by molasses flowing and RNA production reached up to 3.58 g/L. Genome sequencing showed that the ribosome biogenesis, yeast meiosis, RNA transport, and longevity regulating pathway were closely related to the metabolism of high RNA production; (4) Conclusion: S. pastorianus G03H8 was developed for RNA production and had the potential to greatly reduce the cost of RNA production and shorten the fermentation cycle. This work lays the foundation for efficient RNA content using S. pastorianus.
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Affiliation(s)
- Hao Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jinjing Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Qi Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Correspondence: ; Tel.: +86-0510-85918176
| | - Xin Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Chengtuo Niu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Feiyun Zheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Chunfeng Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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Guo X, Zhao B, Zhou X, Lu D, Wang Y, Chen Y, Xiao D. Analysis of the molecular basis of Saccharomyces cerevisiae mutant with high nucleic acid content by comparative transcriptomics. Food Res Int 2021; 142:110188. [PMID: 33773664 DOI: 10.1016/j.foodres.2021.110188] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 01/13/2021] [Accepted: 01/24/2021] [Indexed: 10/22/2022]
Abstract
Ribonucleic acid (RNA) and its degradation products are important functional components widely used in the food industry. Transcription analysis was used to explore the genetic mechanism underlying nucleic acid synthesis in the chemical mutant Saccharomyces cerevisiae strain BY23-195 with high nucleic acid content. Results showed that ribosome biogenesis, meiosis, RNA transport, mitogen-activated protein kinase (MAPK) signaling pathway, tryptophan metabolism, carbon metabolism, and longevity regulating pathway are closely related to the high nucleic acid metabolism of S. cerevisiae. Fourteen most promising genes were selected to evaluate the effect of single-gene deletion or overexpression on the RNA synthesis of S. cerevisiae. Compared with the RNA content of the parent strain BY23, that of mutant strains BY23-HXT1, BY23-ΔGSP2 and BY23-ΔCTT1 increased by 8.19%, 11.60% and 14.00%, respectively. The possible reason why HXT1, GSP2, and CTT1 affect RNA content is by regulating cell fitness. This work was the first to report that regulating the transcription of HXT1, GSP2, and CTT1 could increase the RNA content of S. cerevisiae. This work also provides valuable knowledge on the genetic mechanism of high nucleic acid synthesis in S. cerevisiae and new strategies for increasing its RNA content.
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Affiliation(s)
- Xuewu Guo
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin 300547, China; Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, 300457 Tianjin, China; Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, 300457 Tianjin, China.
| | - Bin Zhao
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin 300547, China; Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, 300457 Tianjin, China
| | - Xinran Zhou
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin 300547, China; Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, 300457 Tianjin, China
| | - Dongxia Lu
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin 300547, China; Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, 300457 Tianjin, China
| | - Yaping Wang
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin 300547, China; Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, 300457 Tianjin, China
| | - Yefu Chen
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin 300547, China; Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, 300457 Tianjin, China; Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, 300457 Tianjin, China
| | - Dongguang Xiao
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin 300547, China; Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, 300457 Tianjin, China; Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, 300457 Tianjin, China
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