Article
Engineering, Chemical
Shifan He, Zhanwei Zhang, Chuanbo Zhang, Wenyu Lu
Summary: In this study, five promoters from Saccharomyces cerevisiae were used to construct Malonyl-CoA sensors. By combining different strategies, a series of sensors with different characteristics were obtained. These sensors can be used for high-throughput screening and fine regulation of metabolism, demonstrating the feasibility of combined application of different promoter engineering strategies.
Review
Biotechnology & Applied Microbiology
Shiyun Li, Qiyue Zhang, Jing Wang, Yingli Liu, Yunying Zhao, Yu Deng
Summary: In order to reduce reliance on petroleum, utilizing industrial microorganisms for the biosynthesis of important chemicals from simple substrates has become a focus of interest. This review explores strategies to increase intracellular malonyl-CoA levels and advances in metabolic engineering for directing malonyl-CoA to desired derivatives, including strengthening supply, reducing consumption, and controlling levels effectively. These strategies offer new insights for enhancing malonyl-CoA derivative synthesis in microorganisms.
JOURNAL OF BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Humberto Pereira, Flavio Azevedo, Lucilia Domingues, Bjorn Johansson
Summary: This study developed a new yeast strain to enhance malonyl-CoA accumulation. Introduction of the heterologous gene Y. lipolytica ACC in S. cerevisiae led to higher accumulation of malonyl-CoA but also decreased growth rate. However, simultaneous expression of both the homologous and heterologous ACC1 genes eliminated the growth defect and slightly reduced malonyl-CoA accumulation.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biotechnology & Applied Microbiology
Qian Zhang, Xinglong Wang, Weizhu Zeng, Sha Xu, Dong Li, Shiqin Yu, Jingwen Zhou
Summary: The biosynthetic pathway of carminic acid was reconstructed in Saccharomyces cerevisiae through systematic pathway engineering. The titer of carminic acid reached 7580.9 μg/L in a 5 L bioreactor, the highest reported for a microorganism. Heterologous reconstruction of the carminic acid biosynthetic pathway in S. cerevisiae has great potential for de novo biosynthesis of anthraquinone dye.
METABOLIC ENGINEERING
(2023)
Article
Microbiology
Chenxi Qiu, Mingtao Huang, Yishan Hou, Huilin Tao, Jianzhi Zhao, Yu Shen, Xiaoming Bao, Qingsheng Qi, Jin Hou
Summary: This study developed a growth-based screening system that linked the availability of malonyl-CoA with cell growth and enabled rapid generation of strains with improved malonyl-CoA synthesis through in vivo continuous mutagenesis. Omics analysis and reverse engineering revealed new processes and regulatory mechanisms that contribute to malonyl-CoA synthesis, providing valuable insights for improving its production.
Article
Biochemical Research Methods
Qian Zhang, Shiqin Yu, Yunbin Lyu, Weizhu Zeng, Jingwen Zhou
Summary: This study successfully increased the production of (2S)-naringenin by regulating the fatty acid beta-oxidation pathway and gene expression in yeast, leading to higher levels of acetyl-CoA in the cytosol. Fed-batch fermentation achieved remarkable levels of (2S)-naringenin production, with the highest reported titer in any microorganism.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biophysics
Bojan Zunar, Christine Mosrin, Helene Benedetti, Beatrice Vallee
Summary: This study presents a promising next-generation eukaryotic whole-cell copper biosensor based on the native copper response of yeast S. cerevisiae. The engineered variant exhibits superior specificity, detection limit, and linear range compared to other reported biosensors. It also serves as a dual-sensing reporter for Cu2+ detection and cell viability, and is relatively independent of the cell's physiological status.
BIOSENSORS & BIOELECTRONICS
(2022)
Article
Biochemistry & Molecular Biology
Takuya Matsumoto, Takashi Otani, Ryosuke Yamada, Hiroyasu Ogino
Summary: This study successfully increased the production of 3-hydroxypropionic acid (3-HP) by utilizing a yeast strain that expressed 3-HP biosynthesis enzymes in the mitochondria. Overexpression of the key enzyme cMCR and the use of the delta-integration strategy further enhanced 3-HP production.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Agriculture, Multidisciplinary
Chenyao Zhou, Mingjie Li, Surui Lu, Yanfei Cheng, Xuena Guo, Xiaoxian He, Zhaoyue Wang, Xiu-Ping He
Summary: This study utilized the Escherichia coli MAR operator cis-element marO to engineer promoters in Saccharomyces cerevisiae for metabolic flux control, resulting in increased production of squalene and lanosterol. The engineered promoters using marO were effective in reducing the accumulation of other metabolites, leading to higher yields of the target products.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Biotechnology & Applied Microbiology
Albert Fina, Gabriela Coelho Breda, Miriam Perez-Trujillo, Denise Maria Guimaraes Freire, Rodrigo Volcan Almeida, Joan Albiol, Pau Ferrer
Summary: This study demonstrated the use of P. pastoris as a cell factory to produce 3-hydroxypropionic acid from glycerol. By introducing the mcr gene from Chloroflexus aurantiacus and optimizing enzyme and metabolic engineering modifications, a significant increase in 3-HP production was achieved. The best strain (PpHP6) showed a high volumetric productivity, indicating the promising potential of P. pastoris for the production of bulk chemicals, especially 3-HP, from crude glycerol.
MICROBIAL BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Albert Fina, Stephanie Heux, Joan Albiol, Pau Ferrer
Summary: This study improves the productivity of Pichia pastoris in producing 3-hydroxypropionic acid by combining different metabolic engineering approaches. The results show that, in combination with using glycerol as a carbon source, the metabolically engineered strains achieved the highest concentration and productivity of 3-hydroxypropionic acid reported so far in yeast.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Yunying Zhao, Fangyu Zuo, Quanxian Shu, Xiaoyan Yang, Yu Deng
Summary: In this study, the fusion of MIOX4 and Udh enzymes with different peptide linkers improved glucaric acid production in yeast cells. A strain with the fusion protein linked by (EA(3)K)(3) showed the highest glucaric acid titer. Further engineering of the strain increased glucaric acid production to 8.49 g/L. Finally, a bioreactor fermentation produced a glucaric acid titer of 15.6 g/L.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Agriculture, Multidisciplinary
Pingping Zhou, Chunlei Yue, Yuchen Zhang, Yan Li, Xinyi Da, Xiuqi Zhou, Lidan Ye
Summary: This study constructed a rosmarinic acid producing Saccharomyces cerevisiae strain and achieved efficient biosynthesis through the removal of metabolic bottlenecks and tuning down gene expression. It provides a promising platform for fermentative production of rosmarinic acid.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Olena P. Ishchuka, Ivan Domenzain, Benjamin J. Sanchez, Facundo Muniz-Paredes, Jose L. Martinez, Jens Nielsen, Dina Petranovic
Summary: Heme synthesis can be increased by modifying certain genes, leading to higher production of heme proteins. This study identified 84 gene targets through computational simulations, of which 40 were confirmed to enhance heme production in experiments. Not only genes directly involved in heme biosynthesis, but also genes related to glycolysis, glycine, and succinyl-coenzyme A metabolism were found to affect heme production.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Agriculture, Multidisciplinary
Junhua Wang, Wei Jiang, Chaojuan Liang, Linghuan Zhu, Youran Li, Qin Mo, Sha Xu, Alex Chu, Liang Zhang, Zhongyang Ding, Guiyang Shi
Summary: This study aimed to maximize the flux of farnesyl diphosphate to farnesene biosynthesis in Saccharomyces cerevisiae. Through screening and genetic engineering, a high alpha-farnesene producing yeast strain was developed, reaching a production level of 10.4 g/L. Various strategies were employed, such as overexpressing key enzymes and optimizing gene expression, to achieve the significant improvement in farnesene production.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Biotechnology & Applied Microbiology
Veronica Gast, Anna Sandegren, Finn Dunas, Siri Ekblad, Rezan Guler, Staffan Thoren, Marta Tous Mohedano, Mikael Molin, Martin K. M. Engqvist, Verena Siewers
Summary: This study evaluated the feasibility of using Saccharomyces cerevisiae as a production host for Affibody molecules. The results showed that the Affibody molecules produced in S. cerevisiae were partially degraded, but their intact secretion was achieved by removing specific proteases. The produced Affibody molecules exhibited the same binding capability as those produced in E. coli. A fed-batch fermentation with engineered S. cerevisiae strain achieved a high titer of Affibody molecules.
MICROBIAL CELL FACTORIES
(2022)
Article
Microbiology
Noemi Montini, Tyler W. Doughty, Ivan Domenzain, Darren A. Fenton, Pavel V. Baranov, Ronan Harrington, Jens Nielsen, Verena Siewers, John P. Morrissey
Summary: Research indicates that under high-temperature growth conditions, the expression of specific genes in Kluyveromyces marxianus increases, suggesting a role in adaptation to harsh environments. One identified gene, KLMX_70384, has been confirmed to be essential for competitive growth at high temperatures.
Article
Biotechnology & Applied Microbiology
Marta Tous Mohedano, Oliver Konzock, Yun Chen
Summary: This review summarizes the trends and recent developments in technologies to improve the stress tolerance of microorganisms. It discusses evolutionary, systems biology, and computational methods, as well as membrane and transcription factor engineering approaches. The challenges and perspectives associated with these different approaches are also discussed.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Ivan Domenzain, Benjamin Sanchez, Mihail Anton, Eduard J. Kerkhoven, Aaron Millan-Oropeza, Celine Henry, Verena Siewers, John P. Morrissey, Nikolaus Sonnenschein, Jens Nielsen
Summary: This study upgrades the GECKO toolbox to enhance models with enzyme and proteomics constraints for any organism with a compatible GEM reconstruction. Enzyme-constrained models for three different yeasts were generated and used to study their long-term adaptation to stress factors. Predictions suggest the importance of metabolic robustness in microbial growth under stress and nutrient-limited conditions.
NATURE COMMUNICATIONS
(2022)
Article
Plant Sciences
Junling Bu, Xiuhua Zhang, Qishuang Li, Ying Ma, Zhimin Hu, Jian Yang, Xiuyu Liu, Ruishan Wang, Xiang Jiao, Tong Chen, Changjiangsheng Lai, Guanghong Cui, Jinfu Tang, Yu Kong, Lei Yang, Sheng Lin, Yun Chen, Juan Guo, Luqi Huang
Summary: O-methyltransferases play crucial roles in producing structural diversity and enhancing the biological properties of benzylisoquinoline alkaloids in plants. This study identified several O-methyltransferases in Corydalis yanhusuo with distinct catalytic activities, providing insights into the genetic elements for producing BIAs through metabolic engineering.
HORTICULTURE RESEARCH
(2022)
Article
Multidisciplinary Sciences
Jan Zrimec, Xiaozhi Fu, Azam Sheikh Muhammad, Christos Skrekas, Vykintas Jauniskis, Nora K. Speicher, Christoph S. Boerlin, Vilhelm Verendel, Morteza Haghir Chehreghani, Devdatt Dubhashi, Verena Siewers, Florian David, Jens Nielsen, Aleksej Zelezniak
Summary: Designing de novo synthetic regulatory DNA is a promising approach for controlling gene expression in biotechnology and medicine. In this study, the researchers developed ExpressionGAN, a generative adversarial network that uses genomic and transcriptomic data to generate regulatory DNA sequences with predefined target mRNA levels.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Xiuyu Liu, Xiang Jiao, Yatian Cheng, Ying Ma, Junling Bu, Baolong Jin, Qishuang Li, Zhimin Hu, Jinfu Tang, Changjiangsheng Lai, Jian Wang, Guanghong Cui, Yun Chen, Juan Guo, Luqi Huang
Summary: This study identified two CYP719A enzymes capable of catalyzing the important methylenedioxy bridge formation in protoberberine alkaloids. Through cloning and characterization, these two enzymes were found to have high efficiency in catalyzing the bridge formation on the A or D rings. Specific amino acid residues were identified to control the substrate specificity and catalytic activity of the enzymes. Furthermore, the enzymes were successfully introduced into a yeast system to produce (S)-stylopine. These findings provide insights into the structure-function relationship of CYP719A-mediated bridge formation and offer yeast strains for synthetic biology production of alkaloids.
MICROBIAL CELL FACTORIES
(2023)
Article
Agriculture, Multidisciplinary
Juan Liu, Zhiqiang Xiao, Siqi Zhang, Zhen Wang, Yun Chen, Yang Shan
Summary: Enzyme promiscuity is advantageous for plants in adapting to the environment, but it can negatively impact the expression of plant enzymes in microorganisms. We demonstrated that refining the promiscuity of two enzymes, F3'H and F4'OMT, improved the production of (2S)-hesperetin in Escherichia coli. By employing molecular docking and directed evolution, we obtained a highly substrate-specific ThF3'H and a promiscuity-restricted MpOMT mutant, resulting in a 14-fold increase in (2S)-hesperetin production and reduced side products. This study highlights the importance of optimizing plant enzyme promiscuity for improving natural product production in microbial cell factories.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Biotechnology & Applied Microbiology
Musa Tartik, Juan Liu, Marta Tous Mohedano, Jiwei Mao, Yun Chen
Summary: This study successfully engineered Saccharomyces cerevisiae for high production of flavonoids kaempferol and quercetin. Through reconstructing the biosynthetic pathway, optimizing enzyme expression, and increasing precursor availability, the production of kaempferol and quercetin reached 956 mg L-1 and 930 mg L-1 respectively in yeast. This research provides a promising platform for sustainable and scalable production of kaempferol, quercetin, and their derivatives.
MICROBIAL CELL FACTORIES
(2023)
Article
Chemistry, Physical
Chunjun Zhan, Xiaowei Li, Guangxu Lan, Edward E. K. Baidoo, Yankun Yang, Yuzhong Liu, Yang Sun, Shijie Wang, Yanyan Wang, Guokun Wang, Jens Nielsen, Jay D. Keasling, Yun Chen, Zhonghu Bai
Summary: In this study, S. cerevisiae was successfully engineered to use methanol as the sole carbon source using an engineered module circuit strategy and adaptive laboratory evolution. The evolved glyoxylate-based serine pathway was found to play an important role in methanol-dependent growth by promoting formaldehyde assimilation. Additionally, the upregulation of the isoprenoid biosynthetic pathway resulted in increased concentrations of squalene and ergosterol, potentially alleviating cell membrane damage in the presence of methanol. This work lays the groundwork for expanding the potential of S. cerevisiae as an organic one-carbon platform for biochemical or biofuel production.
Correction
Endocrinology & Metabolism
Tao Yu, Quanli Liu, Xiang Wang, Xiangjian Liu, Yun Chen, Jens Nielsen
Article
Biotechnology & Applied Microbiology
Jiwei Mao, Marta Tous Mohedano, Jing Fu, Xiaowei Li, Quanli Liu, Jens Nielsen, Verena Siewers, Yun Chen
Summary: Researchers have optimized the biosynthetic pathway of (2S)-naringenin to improve its production and reduce the accumulation of p-coumaric acid. They established a dynamic control system and identified a suitable transporter to further increase the production of (2S)-naringenin and decrease the accumulation of p-coumaric acid. This study highlights the importance of systematic control of pathway intermediates for efficient microbial production of plant natural products.
METABOLIC ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Oliver Konzock, Marta Tous-Mohedano, Irene Cibin, Yun Chen, Joakim Norbeck
Summary: In this study, it was found that Yarrowia lipolytica can metabolize cinnamic acid and p-coumaric acid through multiple pathways. Cinnamic acid is converted to p-coumaric acid and p-coumaric acid is further converted to 4-hydroxybenzoic acid. The identification of the gene responsible for the conversion of cinnamic acid to p-coumaric acid provides new insight into the metabolic capabilities of Y. lipolytica and has potential for the future development of improved strains for flavonoid production.
Article
Biotechnology & Applied Microbiology
Zhen Yao, Yufeng Guo, Huan Wang, Yun Chen, Qinhong Wang, Jens Nielsen, Zongjie Dai
Summary: The potential of a newly constructed Crabtree negative S. cerevisiae, sZJD-28, as a chassis cell for the biosynthesis of non-ethanol compounds was explored. Compared with the Crabtree positive strain CEN.PK113-11C, sZJD-28 displayed a significantly different transcriptional profile and obvious advantages in carbon metabolism. The findings suggest that a Crabtree negative S. cerevisiae strain could be a promising chassis cell for the biosynthesis of various chemicals.
BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS
(2023)
Article
Endocrinology & Metabolism
Tao Yu, Quanli Liu, Xiang Wang, Xiangjian Liu, Yun Chen, Jens Nielsen
Summary: This study demonstrates the establishment of a synthetic decarboxylation cycle in the yeast cytosol, which enhances the production of reduced chemicals. By implementing rational design, metabolic rewiring, and recombinant expression, the researchers achieved a significant increase in free fatty acid yield.
