Article
Agriculture, Multidisciplinary
Xiao Kong, Yaokang Wu, Wenwen Yu, Yanfeng Liu, Jianghua Li, Guocheng Du, Xueqin Lv, Long Liu
Summary: In this study, efficient biosynthesis of limonene in Saccharomyces cerevisiae was achieved through metabolic engineering strategies. The metabolic flow was directed towards limonene synthesis, and the titer reached 2.63 g/L, the highest reported in S. cerevisiae.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Agriculture, Multidisciplinary
Qingxuan Mu, Ya'nan Shi, Rongshan Li, Chao Ma, Yong Tao, Bo Yu
Summary: This study presents a novel approach to efficiently and purely produce propionic acid from L-threonine. By optimizing the expression of key enzymes and using engineered strains, high yield and high purity propionate production has been achieved, along with demonstrating an efficient sequential fermentation-biotransformation process.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Biotechnology & Applied Microbiology
Sae-Byuk Lee, Mary Tremaine, Michael Place, Lisa Liu, Austin Pier, David J. Krause, Dan Xie, Yaoping Zhang, Robert Landick, Audrey P. Gasch, Chris Todd Hittinger, Trey K. Sato
Summary: The efficient conversion of xylose into biofuels has been limited by bottlenecks, but a new method involving engineered yeast strains has shown promise in aerobically fermenting xylose to ethanol. Through gene duplications and deletions, the rates and yields of xylose fermentation were increased, potentially enabling sustainable production of industrial biofuels. This research offers insights into how key regulatory mutations can prime yeast for aerobic xylose fermentation, leading to increased xylose flux and redirection into fermentation products.
METABOLIC ENGINEERING
(2021)
Article
Agriculture, Multidisciplinary
Jiaxuan Guo, Xixi Sun, Yujie Yuan, Qitong Chen, Zutian Ou, Zixin Deng, Tian Ma, Tiangang Liu
Summary: Vitamin B5, or D-pantothenic acid, is an essential vitamin widely used in various industries. However, microbial production of D-pantothenic acid, particularly in Saccharomyces cerevisiae, has been poorly studied. This study successfully constructed an efficient pathway for D-pantothenic acid production in S. cerevisiae by optimizing key genes and fermentation conditions. The resulting strain, DPA171, achieved the highest titer of D-pantothenic acid in S. cerevisiae to date. This research provides valuable guidance for the development of microbial cell factories for vitamin B5 production.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Microbiology
Pan Zhu, Rui Luo, Yize Li, Xiulai Chen
Summary: This study successfully improved the production efficiency and acid tolerance of L-lactic acid by pathway and transporter engineering in Saccharomyces cerevisiae. The engineered strain achieved high levels of L-lactic acid production through adaptive evolution.
MICROBIOLOGY SPECTRUM
(2022)
Article
Agriculture, Multidisciplinary
Ya-Ping Wang, Zhong-guan Sun, Xiao-Qing Wei, Xue-Wu Guo, Dong-Guang Xiao
Summary: This study identified key genes and pathways for the production of n-propanol by S. cerevisiae by deleting n-propanol metabolism-related genes. It revealed that glycine and threonine transformation and the formation of propanal from 2-ketobutyrate were core pathways for n-propanol synthesis, with YML082W playing an important role in directly producing 2-ketobutyric acid. The findings provide valuable insights for future optimization of yeast strains in Baijiu making.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Biotechnology & Applied Microbiology
Renam Luis Acorsi, Matheus Yuri Gritzenco De Giovanni, Jose Eduardo Olivo, Cid Marcos Goncalves Andrade
Summary: This study developed two models to simulate the fermentation process of ethanol production using the glycolytic Embden-Meyerhof-Parnas route in Saccharomyces cerevisiae. The addition of branches to the metabolic network improved the prediction of ethanol production, bringing it closer to experimental results.
FERMENTATION-BASEL
(2022)
Article
Agricultural Engineering
Tiantian Liu, Li Sun, Cheng Zhang, Yanfeng Liu, Jianghua Li, Guocheng Du, Xueqin Lv, Long Liu
Summary: This study presents an efficient bioproduction method for L-lactic acid (L-LA) using a modified Saccharomyces cerevisiae strain. By optimizing metabolic pathways and fermentation conditions, high titers of L-LA were achieved.
BIORESOURCE TECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Zhan-Tao Zhu, Meng-Meng Du, Bei Gao, Xin-Yi Tao, Ming Zhao, Yu-Hong Ren, Feng-Qing Wang, Dong-Zhi Wei
Summary: Harnessing mitochondria for terpene biosynthesis is promising but can lead to metabolic burden and poor cell growth. Analysis shows toxicity from MVA pathway phosphorylated intermediates within mitochondria inhibits cellular functions. Combining cytoplasmic and mitochondrial engineering strategies can alleviate metabolic burden and enhance terpene production.
METABOLIC ENGINEERING
(2021)
Article
Biotechnology & Applied Microbiology
Guokun Wang, Aline Tavares, Simone Schmitz, Lucas Franca, Hugo Almeida, Joao Cavalheiro, Ana Carolas, Suleyman Ozmerih, Lars M. Blank, Bruno S. Ferreira, Irina Borodina
Summary: This study developed an integrated process for manufacturing CCM from glucose by yeast fermentation, achieving high CCM yield and purity. The engineered strain ST10209 produced 1.4 g/L CCM in microplate assay and 22.5 g/L CCM in a 2 L fermenter, outperforming the previous strain ST8943. The CCM recovery yield reached 66.3% with 95.4% purity using a recovery and purification process involving activated carbon treatment.
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Review
Agriculture, Multidisciplinary
Wenjuan Li, Liuwei Cui, Jie Mai, Tian-Qiong Shi, Lu Lin, Zhi-Gang Zhang, Rodrigo Ledesma-Amaro, Weiliang Dong, Xiao-Jun Ji
Summary: This review summarizes the important roles and engineering strategies of Saccharomyces cerevisiae and Yarrowia lipolytica in terpene production, discusses the future prospects and challenges, and emphasizes guidelines for future studies.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Review
Biotechnology & Applied Microbiology
Mingkai Li, Mengyu Ma, Zhenke Wu, Xiqin Liang, Qiusheng Zheng, Defang Li, Tianyue An, Guoli Wang
Summary: Rare ginsenosides, which are deglycosylated derivatives of major ginsenosides, have better absorption and biological activity. Traditional preparation methods hindered their potential applications. Recent advances in understanding ginsenoside biosynthetic pathways and the use of synthetic biology techniques have allowed for large-scale production of rare ginsenosides. This review summarizes the identification of key enzymes involved in their biosynthesis and the construction of microbial chassis for their production, highlighting the importance of discovering more enzymes and improving their catalytic efficiencies for metabolic engineering of rare ginsenosides.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Food Science & Technology
Pieter W. J. Labuschagne, Steohanie Rollero, Benoit Divol
Summary: The study found that B-complex vitamins significantly impact the fermentation performance of Kluyveromyces marxianus IWBT Y885, especially thiamine, which is crucial for ensuring optimal fermentation rate and sugar utilization. Higher concentrations of thiamine may lead to delayed uptake in K. marxianus Y885, and the different metabolites produced in wine fermentations between this yeast and others suggest that thiamine concentration affects the carbon metabolic flux differently in these yeasts, potentially influencing final wine properties.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2021)
Article
Agriculture, Multidisciplinary
Shengli Wang, Chuanling Zhan, Shengxin Nie, Daoguang Tian, Juane Lu, Mingzhang Wen, Jianjun Qiao, Hongji Zhu, Qinggele Caiyin
Summary: In this study, a highly efficient a-farnesene-producing yeast cell factory was constructed through enzyme and metabolic engineering strategies. The most active a-farnesene synthase (AFS) from Camellia sinensis (CsAFS) was introduced into Saccharomyces cerevisiae, resulting in the highest a-farnesene production. The supply of the precursor farnesyl pyrophosphate was improved by increasing the metabolic flux of the mevalonate pathway. Site-directed mutagenesis in CsAFS and the introduction of a SKIK tag further increased a-farnesene production. The final a-farnesene titer of 28.3 g/L was obtained in a 5 L bioreactor through fed-batch fermentation.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Biochemical Research Methods
Young-Oh Lee, Sang-Hun Do, Jae Yoon Won, Young-Wook Chin, Legesse S. S. Chewaka, Bo-Ram Park, Soo-Jung Kim, Sun-Ki Kim
Summary: Production of Saccharomyces cerevisiae-based single cell protein (SCP) has been of great interest due to population growth and environmental concerns. This study utilized an inverse metabolic engineering approach to enhance yeast SCP production. Mutants with increased protein content and/or concentration were isolated from a UV-random mutagenesis-generated S. cerevisiae mutant library through three rounds of screening. The #1021 mutant strain exhibited significant improvements in amino acid content and concentration. The PAN2* strain, with a single nucleotide polymorphism in the PAN2 gene, produced virtually identical amino acids as the #1021 mutant strain. Glucose-limited fed-batch fermentation showed the PAN2* strain produced 16% more amino acids than the parental strain.
BIOTECHNOLOGY JOURNAL
(2023)
Review
Biotechnology & Applied Microbiology
Jinyu Fu, Junjie Li, Jing Chen, Yabei Li, Jiajia Liu, Xin Su, Shuobo Shi
Summary: Detection of nucleic acids is crucial for clinical diagnostics and biotechnological applications, but the low concentration of targets in real samples often requires amplification steps. While amplification increases sensitivity, the lack of highly accurate precise strategies leads to significant false positives and false negatives. Nucleases with high catalytic activity have been explored for more specific and sensitive nucleic acid testing tools.
CRITICAL REVIEWS IN BIOTECHNOLOGY
(2022)
Review
Biochemical Research Methods
Shuobo Shi, Nailing Qi, Jens Nielsen
Summary: Microorganisms have become an attractive option for producing various chemicals from renewable resources. The CRISPR-Cas system has emerged as a powerful tool for manipulating nucleic acids and generating cell factories with desired properties. This review highlights recent advances in using CRISPR-Cas systems to develop microbial cell factories for chemical production, including identifying better biocatalysts, fine-tuning metabolic flux, utilizing inexpensive substrates, and improving metabolic robustness. The potential applications and further development of CRISPR-Cas systems for strain improvement are also discussed.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Article
Chemistry, Analytical
Liyang Wang, Jinyu Fu, Guang Cai, Xiyu Cheng, Di Zhang, Shuobo Shi, Yueping Zhang
Summary: Dermatophytosis, a globally significant infectious disease, can affect the hair, nails, and superficial layers of the skin. Traditional clinical diagnostic methods include Wood's lamp examination, microscopic identification, and fungal culture, but they cannot be used for point-of-care testing. The recent development of a CRISPR-based diagnostic platform provides a rapid, accurate, and portable diagnostic tool.
Review
Biotechnology & Applied Microbiology
Weibo Qiao, Genlai Dong, Shijie Xu, Lingyun Li, Shuobo Shi
Summary: This review discusses the latest advances in microbial metabolism engineering towards producing propionyl-CoA and considers future research directions and challenges towards optimized production of Odd-chain fatty acids (OcFAs).
CRITICAL REVIEWS IN BIOTECHNOLOGY
(2023)
Review
Biotechnology & Applied Microbiology
Ning Qin, Lingyun Li, Zheng Wang, Shuobo Shi
Summary: Odd-chain fatty acids (OcFAs) and their derivatives have potential as alternatives to advanced fuels due to their beneficial physiological effects. However, cells naturally produce mainly even-chain fatty acids (EcFAs) and lack sufficient precursor for OcFA production. Synthetic biology strategies have been used to engineer microorganisms to increase precursor production and enable efficient biosynthesis of OcFAs. This review discusses metabolic pathways for precursor biosynthesis and advances in engineering cell factories for OcFA production, as well as the trends and challenges in synthetic biology-driven OcFA production.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Nailing Qi, Wentao Ding, Genlai Dong, Zhihui Wang, Shuobo Shi
Summary: A novel pathway for de novo synthesis of odd-chain fatty acids (OCFAs) via 3-hydroxypropionic acid (3-HP) was designed and established in Saccharomyces cerevisiae. Through optimization of the precursor 3-HP and combination with other strategies, a de novo production of OCFAs with high yield and percentage was achieved.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Review
Agriculture, Multidisciplinary
Yi Yu, Shuobo Shi
Summary: Rhodotorula toruloides has attracted significant attention as a potential low-cost producer for various fuels and chemicals due to its fast growth, high lipid and carotenoid production, and ability to utilize a wide range of substrates. However, the lack of understanding and genetic engineering tools has hindered its metabolic engineering applications. This review focuses on recent advancements in genetic engineering tools, systems biology, and engineered strains for metabolic engineering applications of R. toruloides. Future trends and challenges in developing R. toruloides as a cell factory are also discussed.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Biochemical Research Methods
Faying Zhang, Xian Fan, Ke Xu, Shihui Wang, Shuobo Shi, Li Yi, Guimin Zhang
Summary: Developing effective bacterial autolytic systems could simplify purification procedures and help with high throughput screening of mutant libraries in protein engineering.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Juan Octavio Valle-Rodriguez, Verena Siewers, Jens Nielsen, Shuobo Shi
Summary: A random mutagenesis approach was used to enhance the catalytic efficiency of a wax ester synthase (WS) from Marinobacter hydrocarbonoclasticus, resulting in improved selectivity towards ethanol and shorter alcohols. This work also introduced a new high-throughput selection system for isolating WSs with desired selectivity.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Jie Meng, Yue Qiu, Yueping Zhang, Huimin Zhao, Shuobo Shi
Summary: This study presents a CRISPR/Cas9 based multiplexed integration (CMI) system in Saccharomyces cerevisiae, which enables quadruple integration at an individual locus without pre-engineering the host. The use of a fused protein, Cas9-Brex27, attracts Rad51 recombinase to the double-strand breaks induced by the CRISPR/Cas9 system. The efficiency of quadruple integration was significantly improved to 53.9% with 40 bp homology arms and 78% with 100 bp homology arms.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Xiao Guo, Zhenzhen Bai, Yang Zhang, Huimin Zhao, Shuobo Shi
Summary: This study identified a set of constitutive promoters with varying strengths in Rhodosporidium toruloides through transcriptome analysis. These promoters were further characterized and used to optimize the linoleic acid biosynthetic pathway, resulting in significantly increased production of linoleic acid. The findings contribute to the development of R. toruloides as a platform organism for applications in biomanufacturing and synthetic biology.
Article
Biotechnology & Applied Microbiology
Shijie Xu, Weibo Qiao, Zuanwen Wang, Xiaoying Fu, Zihe Liu, Shuobo Shi
Summary: The 3-HP pathway is a natural carbon fixation pathway that utilizes bicarbonate as the carbon source. It has been regarded as the most suitable pathway for aerobic CO2 fixation among the six natural carbon fixation pathways. Mesaconate, a valuable derivative in the 3-HP pathway, can be used for the production of fire-retardant materials and hydrogels. This study optimized the sub-part of the 3-HP pathway in Saccharomyces cerevisiae using mesaconate as a reporting compound. By fine-tuning the expression level of malonyl-CoA reductase and optimizing 3-Hydroxypropionyl-CoA synthase, the 3-HP sub-pathway achieved mesaconate productions of 90.78 mg/L and 61.2 mg/L using glucose and ethanol as substrates, respectively.
BIORESOURCES AND BIOPROCESSING
(2023)
Article
Chemistry, Analytical
Jinyu Fu, Linghao Zhang, Yanlin Long, Zihe Liu, Geng Meng, Huimin Zhao, Xin Su, Shuobo Shi
Summary: In this study, a multiplexed CRISPR-based nucleic acid detection system with single-nucleotide resolution using a single Cas protein was developed. This system, called CRISPR-TMSD, integrated the toehold-mediated strand displacement reaction and the cis-cleavage activity of the Cas protein. By utilizing target-specific reporters, multiplexed detection was achieved using just one Cas protein. The combination with recombinase polymerase amplification allowed for extremely sensitive detection, with a detection limit as low as 1 copy/μL. This work presents a new strategy for designing CRISPR-based diagnostic systems and has the potential to expand the applications of CRISPR-based diagnostics.
ANALYTICAL CHEMISTRY
(2023)
Article
Agriculture, Multidisciplinary
Genlai Dong, Shijie Xu, Shuobo Shi
Summary: This study developed a novel method to produce high levels of C18:1ω-7 fatty acids in Saccharomyces cerevisiae while reducing the content of C18:1ω-9. By optimizing enzyme expression and the source of cytochrome b5, the production of C18:1ω-7 was significantly increased, while the content of C18:1ω-9 was greatly reduced in the yeast.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)