61 results on '"Tian, Qiong"'
Search Results
2. High-Level Production of Patchoulol in Yarrowia lipolytica via Systematic Engineering Strategies
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Qian-Qian Peng, Qi Guo, Cheng Chen, Ping Song, Yue-Tong Wang, Xiao-Jun Ji, Chao Ye, and Tian-Qiong Shi
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General Chemistry ,General Agricultural and Biological Sciences - Published
- 2023
3. Advances in the metabolic engineering of Saccharomyces cerevisiae and Yarrowia lipolytica for the production of β-carotene
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Qi Guo, Qian-Qian Peng, Ya-Wen Li, Fang Yan, Yue-Tong Wang, Chao Ye, and Tian-Qiong Shi
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General Medicine ,Applied Microbiology and Biotechnology ,Biotechnology - Published
- 2023
4. Synthesis, characterization and uranium (VI) adsorption mechanism of novel adsorption material poly(tetraethylenepentamine–trimesoyl chloride)
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Tian-qiong Peng, Yan-fei Wang, Yu-fen Xu, and Zheng-chen Liu
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Nuclear Energy and Engineering ,Health, Toxicology and Mutagenesis ,Public Health, Environmental and Occupational Health ,Radiology, Nuclear Medicine and imaging ,Pollution ,Spectroscopy ,Analytical Chemistry - Published
- 2023
5. Engineering Yarrowia lipolytica to produce nutritional fatty acids: Current status and future perspectives
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Lizhen Cao, Mingxue Yin, Tian-Qiong Shi, Lu Lin, Rodrigo Ledesma-Amaro, and Xiao-Jun Ji
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Yarrowia lipolytica ,Conjugated fatty acids ,Structural Biology ,Genetics ,Biomedical Engineering ,Polyunsaturated fatty acids ,Nutritional fatty acids ,Metabolic engineering ,Applied Microbiology and Biotechnology - Abstract
Due to their vital physiological functions, nutritional fatty acids have great potential as nutraceutical food supplements for preventing an array of diseases such as inflammation, depression, arthritis, osteoporosis, diabetes and cancer. Microbial biosynthesis of fatty acids follows the trend of sustainable development, as it enables green, environmentally friendly and efficient production. As a natural oleaginous yeast, Yarrowia lipolytica is especially well-suited for the production of fatty acids. Moreover, it has a variety of genetic engineering tools and novel metabolic engineering strategies that make it a robust workhorse for the production of an array of value-added products. In this review, we summarize recent advances in metabolic engineering strategies for accumulating nutritional fatty acids in Y. lipolytica, including conjugated fatty acids and polyunsaturated fatty acids. In addition, the future prospects of nutritional fatty acid production using the Y. lipolytica platform are discussed in light of the current progress, challenges, and trends in this field. Finally, guidelines for future studies are also emphasized.
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- 2022
6. Dual cytoplasmic‐peroxisomal engineering for high‐yield production of sesquiterpene α‐humulene in Yarrowia lipolytica
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Qi Guo, Ya‐Wen Li, Fang Yan, Ke Li, Yue‐Tong Wang, Chao Ye, Tian‐Qiong Shi, and He Huang
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Monocyclic Sesquiterpenes ,Cytosol ,Metabolic Engineering ,Yarrowia ,Bioengineering ,Sesquiterpenes ,Applied Microbiology and Biotechnology ,Biotechnology - Abstract
The sesquiterpene α-humulene is an important plant natural product, which has been used in the pharmaceutical industry due to its anti-inflammatory and anticancer activities. Although phytoextraction and chemical synthesis have previously been applied in α-humulene production, the low efficiency and high costs limit the development. In this study, Yarrowia lipolytica was engineered as the robust cell factory for sustainable α-humulene production. First, a chassis with high α-humulene output in the cytoplasm was constructed by integrating α-humulene synthases with high catalytic activity, optimizing the flux of mevalonate and acetyl-CoA pathways. Subsequently, the strategy of dual cytoplasmic-peroxisomal engineering was adopted in Y. lipolytica; the best strain GQ3006 generated by introducing 31 copies of 12 different genes could produce 2280.3± 38.2 mg/l (98.7 ± 4.2 mg/g dry cell weight) α-humulene, a 100-fold improvement relative to the baseline strain. To further improve the titer, a novel strategy for downregulation of squalene biosynthesis based on Cu
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- 2022
7. Advances in Metabolic Engineering Paving the Way for the Efficient Biosynthesis of Terpenes in Yeasts
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Wenjuan Li, Liuwei Cui, Jie Mai, Tian-Qiong Shi, Lu Lin, Zhi-Gang Zhang, Rodrigo Ledesma-Amaro, Weiliang Dong, and Xiao-Jun Ji
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Metabolic Engineering ,Terpenes ,Yarrowia ,Synthetic Biology ,Saccharomyces cerevisiae ,General Chemistry ,General Agricultural and Biological Sciences - Abstract
Terpenes are a large class of secondary metabolites with diverse structures and functions that are commonly used as valuable raw materials in food, cosmetics, and medicine. With the development of metabolic engineering and emerging synthetic biology tools, these important terpene compounds can be sustainably produced using different microbial chassis. Currently, yeasts such as
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- 2022
8. A novel control strategy in mitigating bus bunching: Utilizing real-time information
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Zhou, Chang, Tian, Qiong, Wang, David Zhi Wei, and School of Civil and Environmental Engineering
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Civil engineering [Engineering] ,Congestion Information ,Geography, Planning and Development ,Information Provision ,Transportation - Abstract
A variety of control mechanisms have been recommended to concentrate on the issue of bus bunching. However, the majority of existing measures focus on controlling the bus operation directly from the operator's perspective. This study, nevertheless, presents a novel control technique by providing passengers with real-time wait time information and degrees of in-vehicle congestion. Specifically, passengers are expected to use the given information to calculate the overall travel cost and, therefore, make decisions on whether boarding on the arriving bus or waiting for the next buses. In this way, bus service operators would reduce bus bunching by adjusting passengers' boarding choice behavior rather than controlling the bus vehicles directly. We propose a bus traffic propagation model to simulate the bus movements, through which several system performance metrics, such as the shortest vehicle spacing distribution and the average ridership per bus vehicle at each stop, can be evaluated for different bus bunching control measures. The numerical results show that providing in-vehicle congestion information is as effective as the schedule-based and headway-based control methods in achieving mitigation of bus bunching. Passengers on long trips are more inclined to wait for a few more shifts for a bus that is not very crowded. This study proposes a novel control strategy by offering passengers real-time information to serve as a supplement, never a substitute, to the existing control measures in mitigating bus bunching problems. Ministry of Education (MOE) The study was funded by the National Natural Science Foundation of China (No. 72071013, 71890971/71890970) and the Singapore Ministry of Education (MOE) AcRF Tier 1 Grant MOE2021-T1-002-062.
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- 2022
9. Editorial: Design and construction of microbial cell factories for the production of fuels and chemicals
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Tian-Qiong Shi, Farshad Darvishi, Mingfeng Cao, Boyang Ji, and Xiao-Jun Ji
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Histology ,Biomedical Engineering ,Bioengineering ,Biotechnology - Published
- 2023
10. Retraction Note: Mutagenesis combined with fermentation optimization to enhance gibberellic acid GA3 yield in Fusarium fujikuroi
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Ya-Wen Li, Cai-Ling Yang, Hui Peng, Zhi-Kui Nie, Tian-Qiong Shi, and He Huang
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Renewable Energy, Sustainability and the Environment ,Biomedical Engineering ,Food Science ,Biotechnology - Published
- 2023
11. Bone age recognition based on mask R-CNN using xception regression model
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Zhi-Qiang Liu, Zi-Jian Hu, Tian-Qiong Wu, Geng-Xin Ye, Yu-Liang Tang, Zi-Hua Zeng, Zhong-Min Ouyang, and Yuan-Zhe Li
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Physiology ,Physiology (medical) - Abstract
Background and Objective: Bone age detection plays an important role in medical care, sports, judicial expertise and other fields. Traditional bone age identification and detection is according to manual interpretation of X-ray images of hand bone by doctors. This method is subjective and requires experience, and has certain errors. Computer-aided detection can effectually enhance the validity of medical diagnosis, especially with the fast development of machine learning and neural network, the method of bone age recognition using machine learning has gradually become the focus of research, which has the advantages of simple data pretreatment, good robustness and high recognition accuracy.Methods: In this paper, the hand bone segmentation network based on Mask R-CNN was proposed to segment the hand bone area, and the segmented hand bone region was directly input into the regression network for bone age evaluation. The regression network is using an enhancd network Xception of InceptionV3. After the output of Xception, the convolutional block attention module is connected to refine the feature mapping from channel and space to obtain more effective features.Results: According to the experimental results, the hand bone segmentation network model based on Mask R-CNN can segment the hand bone region and eliminate the interference of redundant background information. The average Dice coefficient on the verification set is 0.976. The mean absolute error of predicting bone age on our data set was only 4.97 months, which exceeded the accuracy of most other bone age assessment methods.Conclusion: Experiments show that the accuracy of bone age assessment can be enhancd by using the Mask R-CNN-based hand bone segmentation network and the Xception bone age regression network to form a model, which can be well applied to actual clinical bone age assessment.
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- 2023
12. Additional file 1 of High-yield α-humulene production in Yarrowia lipolytica from waste cooking oil based on transcriptome analysis and metabolic engineering
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Guo, Qi, Peng, Qian-Qian, Chen, Ying-Ying, Song, Ping, Ji, Xiao-Jun, Huang, He, and Shi, Tian-Qiong
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Additional file 1: Fig. S1. Influence of WCO from different canteens on α-humulene production. Fig. S2. Influence of differential genes regulation on α-humulene production (DCW). (A) Overexpression of genes with significantly up-regulated transcript levels. (B) down-regulation of gene with significantly down-regulated transcript levels. The data represent the means ± standard deviations (n = 3). Fig. S3. Rational metabolic engineering to improve α-humulene production (DCW). YALI0_B21780g and YALI0_B21142g were down-regulated. YALI0_E32835g was overexpressed. The data represent the means ± standard deviations (n = 3).
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- 2023
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13. CRISPR-Based Construction of a BL21 (DE3)-Derived Variant Strain Library to Rapidly Improve Recombinant Protein Production
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Zi-Jia Li, Zi-Xu Zhang, Yan Xu, Tian-Qiong Shi, Chao Ye, Xiao-Man Sun, and He Huang
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Escherichia coli ,Biomedical Engineering ,Membrane Proteins ,Clustered Regularly Interspaced Short Palindromic Repeats ,General Medicine ,CRISPR-Cas Systems ,Protein Engineering ,Biochemistry, Genetics and Molecular Biology (miscellaneous) ,Recombinant Proteins - Published
- 2021
14. Harnessing Yarrowia lipolytica Peroxisomes as a Subcellular Factory for α-Humulene Overproduction
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Xiao-Jun Ji, Tian-Qiong Shi, He Huang, Xiao-Man Sun, Qian-Qian Peng, and Guo Qi
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chemistry.chemical_classification ,Humulene ,biology ,Chemistry ,Yarrowia ,General Chemistry ,Peroxisome ,Sesquiterpene ,biology.organism_classification ,chemistry.chemical_compound ,Enzyme ,Biochemistry ,Biosynthesis ,Bioreactor ,General Agricultural and Biological Sciences ,Overproduction - Abstract
The sesquiterpene α-humulene has been shown to have anti-inflammatory and anticancer activities, which has led to its vast application potential in medicine. However, α-humulene production methods including phytoextraction and chemical synthesis currently were limited to low yield, high costs, and expensive catalysts, which cannot meet the increasing market demand. In this study, Yarrowia lipolytica was developed as a robust cell factory for α-humulene production. The peroxisome in Y. lipolytica was first engineered to boost the synthesis of the sesquiterpene α-humulene. By compartmentalization of the α-humulene biosynthesis pathway, improving ATP and acetyl-CoA supply, and optimizing the gene copy numbers of rate-limiting enzymes, the engineered strain GQ2012 could produce 3.2 g/L α-humulene in a 5 L bioreactor, the highest α-humulene titer reported so far. Our study provides a valuable reference for highly sustainable production of terpenoids by peroxisome engineering in Y. lipolytica.
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- 2021
15. High-yield α-humulene production in Yarrowia lipolytica from waste cooking oil based on transcriptome analysis and metabolic engineering
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Qi Guo, Qian-Qian Peng, Ying-Ying Chen, Ping Song, Xiao-Jun Ji, He Huang, and Tian-Qiong Shi
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Bioengineering ,Applied Microbiology and Biotechnology ,Biotechnology - Abstract
Background α-Humulene is an important biologically active sesquiterpene, whose heterologous production in microorganisms is a promising alternative biotechnological process to plant extraction and chemical synthesis. In addition, the reduction of production expenses is also an extremely critical factor in the sustainable and industrial production of α-humulene. In order to meet the requirements of industrialization, finding renewable substitute feedstocks such as low cost or waste substrates for terpenoids production remains an area of active research. Results In this study, we investigated the feasibility of peroxisome-engineering strain to utilize waste cooking oil (WCO) for high production of α-humulene while reducing the cost. Subsequently, transcriptome analysis revealed differences in gene expression levels with different carbon sources. The results showed that single or combination regulations of target genes identified by transcriptome were effective to enhance the α-humulene titer. Finally, the engineered strain could produce 5.9 g/L α‐humulene in a 5‐L bioreactor. Conclusion To the best of our knowledge, this is the first report that converted WCO to α-humulene in peroxisome-engineering strain. These findings provide valuable insights into the high-level production of α-humulene in Y. lipolytica and its utilization in WCO bioconversion. Graphical Abstract
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- 2022
16. Recent Development of Advanced Biotechnology in the Oleaginous Fungi for Arachidonic Acid Production
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Ya-Wen Li, Qi Guo, Qian-Qian Peng, Qi Shen, Zhi-Kui Nie, Chao Ye, and Tian-Qiong Shi
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Arachidonic Acid ,Fish Oils ,Metabolic Engineering ,Biomedical Engineering ,Fungi ,General Medicine ,Biochemistry, Genetics and Molecular Biology (miscellaneous) ,Biotechnology - Abstract
Arachidonic acid is an essential ω-6 polyunsaturated fatty acid, which plays a significant role in cardiovascular health and neurological development, leading to its wide use in the food and pharmaceutical industries. Traditionally, ARA is obtained from deep-sea fish oil. However, this source is limited by season and is depleting the already threatened global fish stocks. With the rapid development of synthetic biology in recent years, oleaginous fungi have gradually attracted increasing attention as promising microbial sources for large-scale ARA production. Numerous advanced technologies including metabolic engineering, dynamic regulation of fermentation conditions, and multiomics analysis were successfully adapted to increase ARA synthesis. This review summarizes recent advances in the bioengineering of oleaginous fungi for ARA production. Finally, perspectives for future engineering approaches are proposed to further improve the titer yield and productivity of ARA.
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- 2022
17. RETRACTED ARTICLE: Mutagenesis combined with fermentation optimization to enhance gibberellic acid GA3 yield in Fusarium fujikuroi
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Ya-Wen Li, Cai-Ling Yang, Hui Peng, Zhi-Kui Nie, Tian-Qiong Shi, and He Huang
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Renewable Energy, Sustainability and the Environment ,Biomedical Engineering ,Food Science ,Biotechnology - Abstract
Gibberellic acid (GA3) is a plant growth hormone that plays an important role in the production of crops, fruits, and vegetables with a wide market share. Due to intrinsic advantages, liquid fermentation of Fusarium fujikuroi has become the sole method for industrial GA3 production, but the broader application of GA3 is hindered by low titer. In this study, we combined atmospheric and room-temperature plasma (ARTP) with ketoconazole-based screening to obtain the mutant strain 3-6-1 with high yield of GA3. Subsequently, the medium composition and fermentation parameters were systematically optimized to increase the titer of GA3, resulting in a 2.5-fold increase compared with the titer obtained under the initial conditions. Finally, considering that the strain is prone to substrate inhibition and glucose repression, a new strategy of fed-batch fermentation was adopted to increase the titer of GA3 to 575.13 mg/L, which was 13.86% higher than the control. The strategy of random mutagenesis combined with selection and fermentation optimization developed in this study provides a basis for subsequent research on the industrial production of GA3. Graphical Abstract
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- 2022
18. Cover Image, Volume 119, Number 10, October 2022
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Qi Guo, Ya‐Wen Li, Fang Yan, Ke Li, Yue‐Tong Wang, Chao Ye, Tian‐Qiong Shi, and He Huang
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Bioengineering ,Applied Microbiology and Biotechnology ,Biotechnology - Published
- 2022
19. Engineering
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Kaifeng, Wang, Tian-Qiong, Shi, Lu, Lin, Ping, Wei, Rodrigo, Ledesma-Amaro, and Xiao-Jun, Ji
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Metabolic Engineering ,Fatty Acids ,Animals ,Yarrowia - Abstract
Microbial production of value-added chemicals derived from fatty acids is a sustainable alternative to petroleum-derived chemicals and unsustainable lipids from animals and plants. Fatty acids with different carbon chain lengths including short- (C6), medium- (C6-C12), long- (C14-C20), and very-long- (C20), with either even or odd number of carbons, have significantly different characteristics and wide applications in energy, material, medicine, and nutrition. Tailoring chain-length specificity of these compounds using metabolic engineering would be of high interest.
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- 2022
20. Engineering Yarrowia lipolytica to produce tailored chain-length fatty acids and their derivatives
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Kaifeng Wang, Tian-Qiong Shi, Lu Lin, Ping Wei, Rodrigo Ledesma-Amaro, and Xiao-Jun Ji
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Biomedical Engineering ,General Medicine ,Biochemistry, Genetics and Molecular Biology (miscellaneous) - Abstract
Microbial production of value-added chemicals derived from fatty acids is a sustainable alternative to petroleum-derived chemicals and unsustainable lipids from animals and plants. Fatty acids with different carbon chain lengths including short- (C20), with either even or odd number of carbons, have significantly different characteristics and wide applications in energy, material, medicine, and nutrition. Tailoring chain-length specificity of these compounds using metabolic engineering would be of high interest. Yarrowia lipolytica, as an oleaginous yeast, is a superior industrial chassis for the production of tailored chain-length fatty acids and their derivatives due to its hyper-oil-producing capability. In this Review, we cover metabolic engineering approaches that can lead to fatty acid chain length control in this microorganism. These approaches involve the manipulation of the fatty acid synthase, the thioesterase, the β-oxidation pathway, the elongation and desaturation pathway, the polyketide synthase-like polyunsaturated fatty acid synthase pathway, and the odd-chain fatty acids synthesis pathway. Finally, we also discuss alternative strategies that can be used in the future to tailored chain-length control.
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- 2022
21. Engineering
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Lizhen, Cao, Mingxue, Yin, Tian-Qiong, Shi, Lu, Lin, Rodrigo, Ledesma-Amaro, and Xiao-Jun, Ji
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Due to their vital physiological functions, nutritional fatty acids have great potential as nutraceutical food supplements for preventing an array of diseases such as inflammation, depression, arthritis, osteoporosis, diabetes and cancer. Microbial biosynthesis of fatty acids follows the trend of sustainable development, as it enables green, environmentally friendly and efficient production. As a natural oleaginous yeast
- Published
- 2022
22. Advanced Strategies for the Synthesis of Terpenoids in Yarrowia lipolytica
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Xiao-Man Sun, He Huang, Tian-Qiong Shi, Ling-Ru Wang, Yu-Zhou Wang, and Zi-Jia Li
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0106 biological sciences ,biology ,Chemistry ,fungi ,010401 analytical chemistry ,Acetyl-CoA ,Yarrowia ,General Chemistry ,Mevalonic acid ,biology.organism_classification ,01 natural sciences ,Terpenoid ,Yeast ,0104 chemical sciences ,Metabolic engineering ,chemistry.chemical_compound ,Biochemistry ,Biosynthesis ,Lipid biosynthesis ,General Agricultural and Biological Sciences ,010606 plant biology & botany - Abstract
Terpenoids are an important class of secondary metabolites that play an important role in food, agriculture, and other fields. Microorganisms are rapidly emerging as a promising source for the production of terpenoids. As an oleaginous yeast, Yarrowia lipolytica contains a high lipid content which indicates that it must produce high amounts of acetyl-CoA, a necessary precursor for the biosynthesis of terpenoids. Y. lipolytica has a complete eukaryotic mevalonic acid (MVA) pathway but it has not yet seen commercial use due to its low productivity. Several metabolic engineering strategies have been developed to improve the terpenoids production of Y. lipolytica, including developing the orthogonal pathway for terpenoid synthesis, increasing the catalytic efficiency of terpenoids synthases, enhancing the supply of acetyl-CoA and NADPH, expressing rate-limiting genes, and modifying the branched pathway. Moreover, most of the acetyl-CoA is used to produce lipid, so it is an effective strategy to strike a balance of precursor distribution by rewiring the lipid biosynthesis pathway. Lastly, the latest developed non-homologous end-joining strategy for improving terpenoid production is introduced. This review summarizes the status and metabolic engineering strategies of terpenoids biosynthesis in Y. lipolytica and proposes new insights to move the field forward.
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- 2021
23. Engineering the Lipid and Fatty Acid Metabolism in
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Kaifeng, Wang, Tian-Qiong, Shi, Jinpeng, Wang, Ping, Wei, Rodrigo, Ledesma-Amaro, and Xiao-Jun, Ji
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Metabolic Engineering ,Fatty Acids ,Plant Oils ,Yarrowia ,Oleic Acid - Abstract
Oleic acid is widely applied in the chemical, material, nutritional, and pharmaceutical industries. However, the current production of oleic acid via high oleic plant oils is limited by the long growth cycle and climatic constraints. Moreover, the global demand for high oleic plant oils, especially the palm oil, has emerged as the driver of tropical deforestation causing tropical rainforest destruction, climate change, and biodiversity loss. In the present study, an alternative and sustainable strategy for high oleic oil production was established by reprogramming the metabolism of the oleaginous yeast
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- 2022
24. YALIcloneNHEJ: An Efficient Modular Cloning Toolkit for NHEJ Integration of Multigene Pathway and Terpenoid Production in Yarrowia lipolytica
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Ya-Wen Li, Cai-Ling Yang, Qi Shen, Qian-Qian Peng, Qi Guo, Zhi-Kui Nie, Xiao-Man Sun, Tian-Qiong Shi, Xiao-Jun Ji, and He Huang
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Histology ,Biomedical Engineering ,Bioengineering ,Biotechnology - Abstract
Non-homologous end-joining (NHEJ)-mediated random integration in Yarrowia lipolytica has been demonstrated to be an effective strategy for screening hyperproducer strains. However, there was no multigene assembly method applied for NHEJ integration, which made it challenging to construct and integrate metabolic pathways. In this study, a Golden Gate modular cloning system (YALIcloneNHEJ) was established to develop a robust DNA assembly platform in Y. lipolytica. By optimizing key factors, including the amounts of ligase and the reaction cycles, the assembly efficiency of 4, 7, and 10 fragments reached up to 90, 75, and 50%, respectively. This YALIcloneNHEJ system was subsequently applied for the overproduction of the sesquiterpene (-)-α-bisabolol by constructing a biosynthesis route and enhancing the flux in the mevalonate pathway. The resulting strain produced 4.4 g/L (-)-α-bisabolol, the highest titer reported in yeast to date. Our study expands the toolbox of metabolic engineering and is expected to enable a highly efficient production of various terpenoids.
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- 2022
25. Engineering the lipid and fatty acid metabolism in Yarrowia lipolytica for sustainable production of high oleic oils
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Kaifeng Wang, Tian-Qiong Shi, Jinpeng Wang, Ping Wei, Rodrigo Ledesma-Amaro, Xiao-Jun Ji, and The Royal Society
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Yarrowia lipolytica ,0304 Medicinal and Biomolecular Chemistry ,monounsaturated fatty acids ,Fatty Acids ,Biomedical Engineering ,Yarrowia ,General Medicine ,triacylglycerides ,0601 Biochemistry and Cell Biology ,Biochemistry, Genetics and Molecular Biology (miscellaneous) ,oleic acid ,Metabolic Engineering ,0903 Biomedical Engineering ,Plant Oils ,lipids (amino acids, peptides, and proteins) ,push-pull-block strategy - Abstract
Oleic acid is widely applied in the chemical, material, nutritional, and pharmaceutical industries. However, the current production of oleic acid via high oleic plant oils is limited by the long growth cycle and climatic constraints. Moreover, the global demand for high oleic plant oils, especially the palm oil, has emerged as the driver of tropical deforestation causing tropical rainforest destruction, climate change, and biodiversity loss. In the present study, an alternative and sustainable strategy for high oleic oil production was established by reprogramming the metabolism of the oleaginous yeast Yarrowia lipolytica using a two-layer "push-pull-block" strategy. Specifically, the fatty acid synthesis pathway was first engineered to increase oleic acid proportion by altering the fatty acid profiles. Then, the content of storage oils containing oleic acid was boosted by engineering the synthesis and degradation pathways of triacylglycerides. The strain resulting from this two-layer engineering strategy produced the highest titer of high oleic microbial oil reaching 56 g/L with 84% oleic acid in fed-batch fermentation, representing a remarkable improvement of a 110-fold oil titer and 2.24-fold oleic acid proportion compared with the starting strain. This alternative and sustainable method for high oleic oil production shows the potential of substitute planting.
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- 2022
26. Concentration difference of auxin involved in stem development in soybean
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Zhen-feng Jiang, Li Wenbin, Yu-hai Cui, Tian-qiong Wang, Xi-long Liang, Zhi-hua Liu, and Dan-dan Liu
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0106 biological sciences ,Tryptamine ,Cell division ,Agriculture (General) ,Flavonoid ,concentration difference of auxin ,Plant Science ,stem development ,01 natural sciences ,Biochemistry ,S1-972 ,chemistry.chemical_compound ,Food Animals ,Auxin ,heterocyclic compounds ,soybean ,metabolites ,chemistry.chemical_classification ,Ecology ,Auxin homeostasis ,fungi ,Tryptophan ,food and beverages ,04 agricultural and veterinary sciences ,Cell biology ,chemistry ,Shoot ,040103 agronomy & agriculture ,0401 agriculture, forestry, and fisheries ,Animal Science and Zoology ,Elongation ,Agronomy and Crop Science ,010606 plant biology & botany ,Food Science - Abstract
Auxin regulates cell division and elongation of the primordial cells through its concentration and then shaped the plant architecture. Cell division and elongation form the internode of soybean and result in different plant heights and lodging resistance. Yet the mechanisms behind are unclear in soybean. To elucidate the mechanism of the concentration difference of auxin related to stem development in soybean, samples of apical shoot, elongation zone, and mature zone from the developing stems of soybean seedlings, Charleston, were harvested and measured for auxin concentration distributions and metabolites to identify the common underlying mechanisms responsible for concentration difference of auxin. Distribution of indole-3-acetic acid (IAA), indole-3-butyric acid (IBA), and methylindole-3-acetic acid (Me-IAA) were determined and auxin concentration distributions were found to have a complex regulation mechanism. The concentrations of IAA and Me-IAA in apical shoot were significantly different between elongation zone and mature zone resulting in an IAA gradient. Tryptophan dependent pathway from tryptamine directly to IAA or through indole-3-acetonitrile to IAA and from indole-3-propionic acid (IPA) to IAA were three primary IAA synthesis pathways. Moreover, some plant metabolites from flavonoid and phenylpropanoid synthesis pathways showed similar or reverse gradient and should involve in auxin homeostasis and concentration difference. All the data give the first insight in the concentration difference and homeostasis of auxin in soybean seedlings and facilitate a deeper understanding of the molecular mechanism of stem development and growth. The gathered information also helps to elucidate how plant height is formed in soybean and what strategy should be adopted to regulate the lodging resistance in soybean.
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- 2020
27. Advancing Yarrowia lipolytica as a superior biomanufacturing platform by tuning gene expression using promoter engineering
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Mei-Li Sun, Tian-Qiong Shi, Lu Lin, Rodrigo Ledesma-Amaro, Xiao-Jun Ji, Biotechnology and Biological Sciences Research Council (BBSRC), The Royal Society, and British Council (UK)
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Gene Editing ,Yarrowia lipolytica ,Environmental Engineering ,Renewable Energy, Sustainability and the Environment ,Yarrowia ,Bioengineering ,General Medicine ,Gene expression ,CRISPR-Cas Systems ,Promoter engineering ,Waste Management and Disposal ,Metabolic engineering ,Biotechnology - Abstract
Yarrowia lipolytica is recognized as an excellent non-conventional yeast in the field of biomanufacturing, where it is used as a host to produce oleochemicals, terpenes, organic acids, polyols and recombinant proteins. Consequently, metabolic engineering of this yeast is becoming increasingly popular to advance it as a superior biomanufacturing platform, of which promoters are the most basic elements for tuning gene expression. Endogenous promoters of Yarrowia lipolytica were reviewed, which are the basis for promoter engineering. The engineering strategies, such as hybrid promoter engineering, intron enhancement promoter engineering, and transcription factor-based inducible promoter engineering are described. Additionally, the applications of Yarrowia lipolytica promoter engineering to rationally reconstruct biosynthetic gene clusters and improve the genome-editing efficiency of the CRISPR-Cas systems were reviewed. Finally, research needs and future directions for promoter engineering are also discussed in this review.
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- 2022
28. Development of an Efficient Gene Editing Tool in Schizochytrium sp. and Improving Its Lipid and Terpenoid Biosynthesis
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Peng-Wei Huang, Ying-Shuang Xu, Xiao-Man Sun, Tian-Qiong Shi, Yang Gu, Chao Ye, and He Huang
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Nutrition and Dietetics ,Agrobacterium tumefaciens ,terpenoids ,lipid ,Nutrition. Foods and food supply ,Endocrinology, Diabetes and Metabolism ,Schizochytrium sp ,TX341-641 ,genetic manipulation ,Nutrition ,Original Research ,Food Science - Abstract
Schizochytrium sp. HX-308 is a marine microalga with fast growth and high lipid content, which has potential as microbial cell factories for lipid compound biosynthesis. It is significant to develop efficient genetic editing tool and discover molecular target in Schizochytrium sp. HX-308 for lipid compound biosynthesis. In this study, we developed an efficient gene editing tool in HX-308 which was mediated by Agrobacterium tumefaciens AGL-1. Results showed that the random integration efficiency reached 100%, and the homologous recombination efficiency reached about 30%. Furthermore, the metabolic pathway of lipid and terpenoid biosynthesis were engineered. Firstly, the acetyl-CoA c-acetyltransferase was overexpressed in HX-308 with a strong constitutive promoter. With the overexpression of acetyl-CoA c-acetyltransferase, more acetyl-CoA was used to synthesize terpenoids, and the production of squalene, β-carotene and astaxanthin was increased 5.4, 1.8, and 2.4 times, respectively. Interestingly, the production of saturated fatty acids and polyunsaturated fatty acids also changed. Moreover, three Acyl-CoA oxidase genes which catalyze the first step of β-oxidation were knocked out using homologous recombination. Results showed that the production of lipids increased in the three knock-out strains. Our results demonstrated that the A. tumefaciens-mediated transformation method will be of great use for the study of function genes, as well as developing Schizochytrium sp. as a strong cell factory for producing high value products.
- Published
- 2021
29. YALIcloneNHEJ: An Efficient Modular Cloning Toolkit for NHEJ Integration of Multigene Pathway and Terpenoid Production in
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Ya-Wen, Li, Cai-Ling, Yang, Qi, Shen, Qian-Qian, Peng, Qi, Guo, Zhi-Kui, Nie, Xiao-Man, Sun, Tian-Qiong, Shi, Xiao-Jun, Ji, and He, Huang
- Abstract
Non-homologous end-joining (NHEJ)-mediated random integration in
- Published
- 2021
30. Harnessing
- Author
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Qi, Guo, Tian-Qiong, Shi, Qian-Qian, Peng, Xiao-Man, Sun, Xiao-Jun, Ji, and He, Huang
- Subjects
Monocyclic Sesquiterpenes ,Metabolic Engineering ,Peroxisomes ,Yarrowia - Abstract
The sesquiterpene α-humulene has been shown to have anti-inflammatory and anticancer activities, which has led to its vast application potential in medicine. However, α-humulene production methods including phytoextraction and chemical synthesis currently were limited to low yield, high costs, and expensive catalysts, which cannot meet the increasing market demand. In this study
- Published
- 2021
31. Advances in the metabolic engineering of Yarrowia lipolytica for the production of terpenoids
- Author
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He Huang, Xiao-Jun Ji, Wei-Jian Wang, Tian-Qiong Shi, Ying Ding, Kai-Feng Wang, and Yi-Rong Ma
- Subjects
0106 biological sciences ,Large class ,Environmental Engineering ,Yarrowia ,Bioengineering ,Computational biology ,010501 environmental sciences ,Biology ,01 natural sciences ,Metabolic engineering ,chemistry.chemical_compound ,010608 biotechnology ,Waste Management and Disposal ,0105 earth and related environmental sciences ,Biological Products ,Natural product ,Terpenes ,Renewable Energy, Sustainability and the Environment ,fungi ,General Medicine ,biology.organism_classification ,Yeast ,Terpenoid ,Metabolic Engineering ,chemistry ,Oil production ,Mevalonate pathway - Abstract
Terpenoids are a large class of natural compounds based on the C5 isoprene unit, with many biological effects such activity against cancer and allergies, while some also have an agreeable aroma. Consequently, they have received extensive attention in the food, pharmaceutical and cosmetic fields. With the identification and analysis of the underlying natural product synthesis pathways, current microbial-based metabolic engineering approaches have yielded new strategies for the production of highly valuable terpenoids. Yarrowia lipolytica is a non-conventional oleaginous yeast that is rapidly emerging as a valuable host for the production of terpenoids due to its own endogenous mevalonate pathway and high oil production capacity. This review aims to summarize the status and strategies of metabolic engineering for the heterologous synthesis of terpenoids in Y. lipolytica in recent years and proposes new methods aiming towards further improvement of terpenoid production.
- Published
- 2019
32. CRISPR/Cas9-Based Genome Editing in the Filamentous Fungus Fusarium fujikuroi and Its Application in Strain Engineering for Gibberellic Acid Production
- Author
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Jian Gao, He Huang, Kai-Feng Wang, Guo-Qin Xu, Wei-Jian Wang, Tian-Qiong Shi, and Xiao-Jun Ji
- Subjects
0106 biological sciences ,Plant growth ,Biomedical Engineering ,Biology ,01 natural sciences ,Biochemistry, Genetics and Molecular Biology (miscellaneous) ,03 medical and health sciences ,chemistry.chemical_compound ,Fusarium ,Genome editing ,010608 biotechnology ,Botany ,CRISPR ,Gibberellic acid ,030304 developmental biology ,Gene Editing ,0303 health sciences ,fungi ,Fungi ,Fusarium fujikuroi ,food and beverages ,General Medicine ,Gibberellins ,Filamentous fungus ,Metabolic pathway ,chemistry ,CRISPR-Cas Systems ,Genome, Fungal - Abstract
The filamentous fungus Fusarium fujikuroi is well-known for its production of natural plant growth hormones: a series of gibberellic acids (GAs). Some GAs, including GA1, GA3, GA4, and GA7, are biologically active and have been widely applied in agriculture. However, the low efficiency of traditional genetic tools limits the further research toward making this fungus more efficient and able to produce tailor-made GAs. Here, we established an efficient CRISPR/Cas9-based genome editing tool for F. fujikuroi. First, we compared three different nuclear localization signals (NLS) and selected an efficient NLS from histone H2B (HTB
- Published
- 2019
33. Advanced Strategies for the Synthesis of Terpenoids in
- Author
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Zi-Jia, Li, Yu-Zhou, Wang, Ling-Ru, Wang, Tian-Qiong, Shi, Xiao-Man, Sun, and He, Huang
- Subjects
Metabolic Engineering ,Acetyl Coenzyme A ,Terpenes ,Mevalonic Acid ,Yarrowia - Abstract
Terpenoids are an important class of secondary metabolites that play an important role in food, agriculture, and other fields. Microorganisms are rapidly emerging as a promising source for the production of terpenoids. As an oleaginous yeast
- Published
- 2021
34. Recent advances in the application of multiplex genome editing in Saccharomyces cerevisiae
- Author
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Tian-Qiong Shi, Ling-Ru Wang, Xiao-Man Sun, Ying-Shuang Xu, Wan-Ting Jiang, He Huang, and Zi-Xu Zhang
- Subjects
Gene Editing ,0303 health sciences ,Transcription activator-like effector nuclease ,Key genes ,biology ,030306 microbiology ,Computer science ,Saccharomyces cerevisiae ,Repetitive Sequences ,General Medicine ,Computational biology ,biology.organism_classification ,Applied Microbiology and Biotechnology ,03 medical and health sciences ,ComputingMethodologies_PATTERNRECOGNITION ,Genome editing ,CRISPR ,Multiplex ,CRISPR-Cas Systems ,Gene ,030304 developmental biology ,Biotechnology - Abstract
Saccharomyces cerevisiae is a widely used microorganism and a greatly popular cell factory for the production of various chemicals. In order to improve the yield of target chemicals, it is often necessary to increase the copy numbers of key genes or engineer the related metabolic pathways, which traditionally required time-consuming repetitive rounds of gene editing. With the development of gene-editing technologies such as meganucleases, TALENs, and the CRISPR/Cas system, multiplex genome editing has entered a period of rapid development to speed up cell factory optimization. Multi-copy insertion and removing bottlenecks in biosynthetic pathways can be achieved through gene integration and knockout, for which multiplexing can be accomplished by targeting repetitive sequences and multiple sites, respectively. Importantly, the development of the CRISPR/Cas system has greatly increased the speed and efficiency of multiplex editing. In this review, the various multiplex genome editing technologies in S. cerevisiae were summarized, and the principles, advantages, and the disadvantages were analyzed and discussed. Finally, the practical applications and future prospects of multiplex genome editing were discussed. KEY POINTS: • The development of multiplex genome editing in S. cerevisiae was summarized. • The pros and cons of various multiplex genome editing technologies are discussed. • Further prospects on the improvement of multiplex genome editing are proposed.
- Published
- 2021
35. Additional file 4 of UBTF facilitates melanoma progression via modulating MEK1/2-ERK1/2 signalling pathways by promoting GIT1 transcription
- Author
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Zhang, Jian, Zhang, Jiaojiao, Liu, Wenli, Ge, Rui, Gao, Tianyuan, Tian, Qiong, Mu, Xin, Zhao, Lingyu, and Li, Xu
- Abstract
Additional file 4: Table S1. Sequences of siRNA. Table S2. Sequencesof recombinant plasmids. Table S3. Primer sequence used for qRT-PCR or ChIP-qRT-PCR.Table S4. Information on antibodies used for the correlationanalysis. TableS5. Association between UBTF mRNA expression and clinical pathological featuresof melanoma (n = 66). Table S6. Relationshipbetween GIT1 mRNA expression and clinical pathological characteristics ofmelanoma (n = 66).
- Published
- 2021
- Full Text
- View/download PDF
36. Three new 3-formyl-2-arylbenzofurans from
- Author
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Tian-Qiong, Lang, Guo-Yong, Luo, Wen-Chen, Pu, Zhi-Wei, Wang, Jian, Wang, Xiao-Long, Tian, Pan, Zhang, Neng-Wu, Zhao, Wu-De, Yang, and Hui-Fang, Chai
- Subjects
Carcinoma, Hepatocellular ,MAP Kinase Signaling System ,Cell Line, Tumor ,Liver Neoplasms ,Humans ,Apoptosis ,Cell Proliferation ,Signal Transduction - Abstract
Five 3-formyl-2-arylbenzofuran derivatives, including three new compounds (
- Published
- 2020
37. Stresses as First-Line Tools for Enhancing Lipid and Carotenoid Production in Microalgae
- Author
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Tian-Qiong Shi, Ling-Ru Wang, He Huang, Xiao-Man Sun, and Zi-Xu Zhang
- Subjects
0301 basic medicine ,Histology ,Mini Review ,First line ,lcsh:Biotechnology ,Biomedical Engineering ,Biomass ,Bioengineering ,02 engineering and technology ,Oxidative damage ,lipids ,03 medical and health sciences ,stresses ,lcsh:TP248.13-248.65 ,Carotenoid ,chemistry.chemical_classification ,omics technologies ,Chemistry ,Mechanism (biology) ,microalgae ,carotenoids ,Bioengineering and Biotechnology ,food and beverages ,021001 nanoscience & nanotechnology ,Carbon storage ,030104 developmental biology ,Biophysics ,Stress conditions ,0210 nano-technology ,Biotechnology ,Omics technologies - Abstract
Microalgae can produce high-value-added products such as lipids and carotenoids using light or sugars, and their biosynthesis mechanism can be triggered by various stress conditions. Under nutrient deprivation or environmental stresses, microalgal cells accumulate lipids as an energy-rich carbon storage battery and generate additional amounts of carotenoids to alleviate the oxidative damage induced by stress conditions. Though stressful conditions are unfavorable for biomass accumulation and can induce oxidative damage, stress-based strategies are widely used in this field due to their effectiveness and economy. For the overproduction of different target products, it is required and meaningful to deeply understand the effects and mechanisms of various stress conditions so as to provide guidance on choosing the appropriate stress conditions. Moreover, the underlying molecular mechanisms under stress conditions can be clarified by omics technologies, which exhibit enormous potential in guiding rational genetic engineering for improving lipid and carotenoid biosynthesis., Graphical Abstract Development of new production microalgae strains with high lipid production capacity and cell growth with the aids of gene editing tools for selecting key genes under stress conditions.
- Published
- 2020
38. Characterization of chemical components with diuretic potential from
- Author
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Tian-Qiong, Lang, Yan, Zhang, Fei, Chen, Guo-Yong, Luo, and Wu-De, Yang
- Subjects
Molecular Structure ,Polypodiaceae ,Plant Extracts ,Diuretics - Abstract
Three compounds with diuretic potential were identified from the 95% ethanol extract of
- Published
- 2020
39. Advancing metabolic engineering of Yarrowia lipolytica using the CRISPR/Cas system
- Author
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Eduard J. Kerkhoven, He Huang, Xiao-Jun Ji, and Tian-Qiong Shi
- Subjects
0301 basic medicine ,Yarrowia lipolytica ,Yarrowia ,Computational biology ,Biology ,Applied Microbiology and Biotechnology ,Metabolic engineering ,03 medical and health sciences ,CRISPR/Cas ,Genome editing ,Bacterial Proteins ,CRISPR ,Clustered Regularly Interspaced Short Palindromic Repeats ,Transcription activator-like effector nuclease ,Cas9 ,Effector ,General Medicine ,Mini-Review ,biology.organism_classification ,Yeast ,030104 developmental biology ,Metabolic Engineering ,CRISPR-Cas Systems ,Biotechnology - Abstract
The oleaginous yeast Yarrowia lipolytica is widely used for the production of both bulk and fine chemicals, including organic acids, fatty acid-derived biofuels and chemicals, polyunsaturated fatty acids, single-cell proteins, terpenoids, and other valuable products. Consequently, it is becoming increasingly popular for metabolic engineering applications. Multiple gene manipulation tools including URA blast, Cre/LoxP, and transcription activator-like effector nucleases (TALENs) have been developed for metabolic engineering in Y. lipolytica. However, the low efficiency and time-consuming procedures involved in these methods hamper further research. The emergence of the CRISPR/Cas system offers a potential solution for these problems due to its high efficiency, ease of operation, and time savings, which can significantly accelerate the genomic engineering of Y. lipolytica. In this review, we summarize the research progress on the development of CRISPR/Cas systems for Y. lipolytica, including Cas9 proteins and sgRNA expression strategies, as well as gene knock-out/knock-in and repression/activation applications. Finally, the most promising and tantalizing future prospects in this area are highlighted.
- Published
- 2018
40. Biotechnological production of lipid and terpenoid from thraustochytrids
- Author
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Wen-Zheng Liu, Fei Du, Xiao-Man Sun, Yu-Zhou Wang, He Huang, Tian-Qiong Shi, and Ying-Shuang Xu
- Subjects
0106 biological sciences ,0303 health sciences ,Downstream processing ,Docosahexaenoic Acids ,Terpenes ,Biomass ,Bioengineering ,Schizochytrium ,Biology ,biology.organism_classification ,01 natural sciences ,Applied Microbiology and Biotechnology ,Terpenoid ,Metabolic engineering ,03 medical and health sciences ,Metabolic pathway ,Bioreactors ,010608 biotechnology ,Bioreactor ,Production (economics) ,Food science ,Stramenopiles ,030304 developmental biology ,Biotechnology - Abstract
As fungus-like protists, thraustochytrids have been increasingly studied for their faster growth rates and high lipid content. In the 1990s, thraustochytrids were used as docosahexaenoic acid (DHA) producers for the first time. Thraustochytrids genera, such as Thraustochytrium, Schizochytrium, and Aurantiochytrium have been developed and patented as industrial strains for DHA production. The high DHA yield is attributed to its unique and efficient polyketide-like synthase (PKS) pathway. Moreover, thraustochytrids possess a completed mevalonate (MVA) pathway, so it can be used as host for terpenoid production. In order to improve strain performance, the metabolic engineering strategies have been applied to promote or disrupt intracellular metabolic pathways, such as genetic engineering and addition of chemical activators. However, it is difficult to realize industrialization only by improving strain performance. Various operation strategies were developed to enlarge the production quantities from the laboratory-scale, including two-stage cultivation strategies, scale-up technologies and bioreactor design. Moreover, an economical and effective downstream process is also an important consideration for the industrial application of thraustochytrids. Downstream costs accounts for 20-60% of the overall process costs, which represents an attractive target for increasing the cost-competitiveness of thraustochytrids, including how to improve the efficiency of lipid extraction and the further application of biomass residues. This review aims to overview the whole lipid biotechnology of thraustochytrids to provide the background information for researchers.
- Published
- 2021
41. CRISPR/Cas9-based genome editing of the filamentous fungi: the state of the art
- Author
-
Ping Song, Kun Shi, He Huang, Rong-Yu Ji, Guan-Nan Liu, Tian-Qiong Shi, Lu-Jing Ren, and Xiao-Jun Ji
- Subjects
Gene Editing ,0301 basic medicine ,Cas9 ,business.industry ,030106 microbiology ,Fungi ,Agriculture ,General Medicine ,Computational biology ,Industrial microbiology ,Biology ,Applied Microbiology and Biotechnology ,Biotechnology ,Industrial Microbiology ,03 medical and health sciences ,030104 developmental biology ,Genome editing ,Fungal Diversity ,Food Industry ,CRISPR ,CRISPR-Cas Systems ,Genome, Fungal ,business ,Functional genomics - Abstract
In recent years, a variety of genetic tools have been developed and applied to various filamentous fungi, which are widely applied in agriculture and the food industry. However, the low efficiency of gene targeting has for many years hampered studies on functional genomics in this important group of microorganisms. The emergence of CRISPR/Cas9 genome-editing technology has sparked a revolution in genetic research due to its high efficiency, versatility, and easy operation and opened the door for the discovery and exploitation of many new natural products. Although the application of the CRISPR/Cas9 system in filamentous fungi is still in its infancy compared to its common use in E. coli, yeasts, and mammals, the deep development of this system will certainly drive the exploitation of fungal diversity. In this review, we summarize the research progress on CRISPR/Cas9 systems in filamentous fungi and finally highlight further prospects in this area.
- Published
- 2017
42. Payment for Rice Growers to Reduce Using N Fertilizer in the GHG Mitigation Program Driven by the Government: Evidence from Shanghai
- Author
-
Hai-Ying Gu, Qing-Mi Hu, and Tian-Qiong Wang
- Subjects
020209 energy ,media_common.quotation_subject ,Shadow price ,Geography, Planning and Development ,TJ807-830 ,Social Welfare ,02 engineering and technology ,010501 environmental sciences ,Management, Monitoring, Policy and Law ,TD194-195 ,01 natural sciences ,Profit (economics) ,Renewable energy sources ,N fertilizer ,prices of the payment ,Agricultural science ,0202 electrical engineering, electronic engineering, information engineering ,particiaption rate ,GE1-350 ,0105 earth and related environmental sciences ,media_common ,Environmental effects of industries and plants ,Renewable Energy, Sustainability and the Environment ,GHG mitigation program ,Payment ,Environmental sciences ,Greenhouse gas ,Sustainability ,Renminbi ,Business ,social welfare - Abstract
The overuse of N fertilizer by rice growers triggers excessive greenhouse gas (GHG) emission, leading to the environmental and climatic problem. However, growers will probably suffer loss in profits if they reduce the use of N fertilizer under the existing technology condition. The payment in market-based or government-driven way may overcome the potential barrier. For the appropriate carbon trading market is absent, the government-driven program will play a role in the payment. Three key issues in the designed program are the price of the payment, the participation rate of rice growers, and the variation of items associated with the social welfare. Due to the difficulty in estimating the economic value, prices of the payment can be set according to shadow prices. This paper applies the parametric directional output distance function to derive shadow prices of CO2 for 308 rice growers in Shanghai from 2008&ndash, 2015. Average shadow prices range from RMB 1130 to 3769 yuan/ton (or US 163 to 618 $/ton). Taking the year of 2015 as sample, this paper predicts the participation rate (97.08%) of rice growers with the aim of 10% N fertilizer reduction and the specific price of the payment (7.47 yuan/kg). Moreover, this paper discusses on the variation of factors linked with the social welfare, and derive two important relationships from it. In detail, the relationship between the yield of the rice and the reduction of the N fertilizer should be balanced, the relationship between the improvement on the profit of rice growers (or the participation rate) in the program and the payment by the government should also be balanced.
- Published
- 2019
43. Increasing the homologous recombination efficiency of eukaryotic microorganisms for enhanced genome engineering
- Author
-
Wei-Jian Wang, He Huang, Xiao-Jun Ji, Ying Ding, Tian-Qiong Shi, Yi-Rong Ma, and Kai-Feng Wang
- Subjects
Gene Editing ,0303 health sciences ,Candidate gene ,030306 microbiology ,Microorganism ,Fungi ,General Medicine ,Computational biology ,Applied Microbiology and Biotechnology ,Genome engineering ,Non-homologous end joining ,03 medical and health sciences ,Genome editing ,Metabolic Engineering ,Basic research ,Yeasts ,Homologous recombination ,Homologous Recombination ,Recombination ,030304 developmental biology ,Biotechnology - Abstract
In recent years, eukaryotic microorganisms have been widely applied to offer many solutions for everyday life and have come to play important roles in agriculture, food, health care, and the fine-chemicals industry. However, the complex genetic background and low homologous recombination efficiency have hampered the implementation of large-scale and high-throughput gene editing in many eukaryotic microorganisms. The low efficiency of homologous recombination (HR) not only makes the modification process labor-intensive but also completely precludes the application of many otherwise very useful genome editing techniques. Thus, increasing the efficiency of HR is clearly an enabling technology for basic research and gene editing in eukaryotic microorganisms. In this review, we summarize the current strategies for enhancing the efficiency of HR in eukaryotic microorganisms (particularly yeasts and filamentous fungi), list some small molecules and candidate genes associated with homologous and non-homologous recombination, and briefly discuss the further development prospects of these strategies.
- Published
- 2019
44. Application of the CRISPR/Cas system for genome editing in microalgae
- Author
-
Jia-Yi Jiang, Yuting Zhang, Quanyu Zhao, Lu-Jing Ren, Xiao-Man Sun, He Huang, and Tian-Qiong Shi
- Subjects
Computational biology ,Biology ,Applied Microbiology and Biotechnology ,03 medical and health sciences ,Transformation, Genetic ,Genome editing ,CRISPR-Associated Protein 9 ,Microalgae ,CRISPR ,Gene ,030304 developmental biology ,Gene Editing ,0303 health sciences ,Transcription activator-like effector nuclease ,CRISPR interference ,030306 microbiology ,Cas9 ,Effector ,General Medicine ,Zinc finger nuclease ,Gene Expression Regulation ,Gene Targeting ,CRISPR-Cas Systems ,Genetic Engineering ,Biotechnology ,RNA, Guide, Kinetoplastida - Abstract
Microalgae are arguably the most abundant single-celled eukaryotes and are widely distributed in oceans and freshwater lakes. Moreover, microalgae are widely used in biotechnology to produce bioenergy and high-value products such as polyunsaturated fatty acids (PUFAs), bioactive peptides, proteins, antioxidants and so on. In general, genetic editing techniques were adapted to increase the production of microalgal metabolites. The main genome editing tools available today include zinc finger nucleases (ZFNs), transcriptional activator-like effector nucleases (TALENs), and the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas nuclease system. Due to its high genome editing efficiency, the CRISPR/Cas system is emerging as the most important genome editing method. In this review, we summarized the available literature on the application of CRISPR/Cas in microalgal genetic engineering, including transformation methods, strategies for the expression of Cas9 and sgRNA, the CRISPR/Cas9-mediated gene knock-in/knock-out strategies, and CRISPR interference expression modification strategies.
- Published
- 2018
45. Charging Method for Power Grid Engineering 3-D Design
- Author
-
Ya-ping Wang, Tian-qiong Chen, Bo-yang Cao, Wei-ning Wen, and Yan Ren
- Subjects
Disk formatting ,Speedup ,Work (electrical) ,Computer science ,Component (UML) ,Control (management) ,Systems engineering ,Technical management ,Power grid - Abstract
In order to speed up the power grid engineering 3-D design, strengthen project costs management and control, it is urgent to carry out the research on charging standard for power grid engineering 3-D design, providing guidance for power grid engineering 3-D design. Based on the pilot project of power grid engineering 3-D design, design work day calculation model was constructed, forming a 3-D design charging method covering power grid engineering projects’ every stage. In the future, the 3-D design fee can be adjusted reasonably according to 3-D design work maturity, to improve engineering technology and technical management work.
- Published
- 2018
46. Morphological and genetic variations of Sophora davidii populations originating from different altitudes in the mountains of southwestern China
- Author
-
Wen Zhang, Yu Zhang, Zhao Lili, Juan Chen, Tian-Qiong Luo, and Pu-Chang Wang
- Subjects
0106 biological sciences ,geography ,Genetic diversity ,geography.geographical_feature_category ,Ecology ,ved/biology ,ved/biology.organism_classification_rank.species ,Plant Science ,Biology ,Karst ,010603 evolutionary biology ,01 natural sciences ,Shrub ,Gene flow ,Sophora davidii ,Botany ,Genetic variation ,Ecosystem ,China ,Ecology, Evolution, Behavior and Systematics ,010606 plant biology & botany - Abstract
Sophora davidii Franch. is a multipurpose shrub with significant economic and ecological importance in karst mountainous regions of southeastern China. These mountainous ecosystems are associated with altitudinal gradients that can lead to major morphological and genetic differences in the species. We examined the morphological and genetic variation of this species at six sites with different altitudes (600 m–1950 m asl). Significant morphological variations (p
- Published
- 2016
47. Microbial production of plant hormones: Opportunities and challenges
- Author
-
Peng Hui, Rong-Yu Ji, Si-Yu Zeng, Tian-Qiong Shi, He Huang, Kun Shi, and Xiao-Jun Ji
- Subjects
0106 biological sciences ,0301 basic medicine ,Bioengineering ,Biology ,01 natural sciences ,Applied Microbiology and Biotechnology ,03 medical and health sciences ,chemistry.chemical_compound ,Plant Growth Regulators ,Auxin ,Commentaries ,Botany ,Brassinosteroid ,Abscisic acid ,chemistry.chemical_classification ,Indoleacetic Acids ,business.industry ,fungi ,Fungi ,food and beverages ,General Medicine ,Ethylenes ,biology.organism_classification ,Gibberellins ,Biotechnology ,030104 developmental biology ,chemistry ,Agriculture ,Gibberellin ,Fermentation ,Plant hormone ,business ,Abscisic Acid ,010606 plant biology & botany ,Hormone - Abstract
Plant hormones are a class of organic substances which are synthesized during the plant metabolism. They have obvious physiological effect on plant growth at very low concentrations. Generally, plant hormones are mainly divided into 5 categories: auxins, cytokinins, ethylene, gibberellins (GAs) and abscisic acid (ABA). With the deepening of research, some novel plant hormones such as brassinosteroid and salicylates have been found and identified. The plant hormone products are mainly obtained through plant extraction, chemical synthesis as well as microbial fermentation. However, the extremely low yield in plants and relatively complex chemical structure limit the development of the former 2 approaches. Therefore, more attention has been paid into the microbial fermentative production. In this commentary, the developments and technological achievements of the 2 important plant hormones (GAs and ABA) have been discussed. The discovery, producing strains, fermentation technologies, and their accumulation mechanisms are first introduced. Furthermore, progresses in the industrial mass scale production are discussed. Finally, guidelines for future studies for GAs and ABA production are proposed in light of the current progress, challenges and trends in the field. With the widespread use of plant hormones in agriculture, we believe that the microbial production of plant hormones will have a bright future.
- Published
- 2016
48. Metabolic Engineering of Yeast for the Production of 3-Hydroxypropionic Acid
- Author
-
Rong-Yu Ji, Ying Ding, Tian-Qiong Shi, Lu Lin, He Huang, Zhen Gao, and Xiao-Jun Ji
- Subjects
0301 basic medicine ,Microbiology (medical) ,β-alanine pathway ,Mini Review ,Saccharomyces cerevisiae ,lcsh:QR1-502 ,yeast ,3-Hydroxypropionic acid ,medicine.disease_cause ,Microbiology ,lcsh:Microbiology ,Metabolic engineering ,03 medical and health sciences ,chemistry.chemical_compound ,Glycerol ,medicine ,Escherichia coli ,biology ,malonyl-CoA reductase pathway ,biology.organism_classification ,Yeast ,030104 developmental biology ,chemistry ,Biochemistry ,Yield (chemistry) ,Fermentation ,metabolic engineering - Abstract
The beta-hydroxy acid 3-hydroxypropionic acid (3-HP) is an attractive platform compound that can be used as a precursor for many commercially interesting compounds. In order to reduce the dependence on petroleum and follow sustainable development, 3-HP has been produced biologically from glucose or glycerol. It is reported that 3-HP synthesis pathways can be constructed in microbes such as Escherichia coli, Klebsiella pneumoniae and the yeast Saccharomyces cerevisiae. Among these host strains, yeast is prominent because of its strong acid tolerance which can simplify the fermentation process. Currently, the malonyl-CoA reductase pathway and the β-alanine pathway have been successfully constructed in yeast. This review presents the current developments in 3-HP production using yeast as an industrial host. By combining genome-scale engineering tools, malonyl-CoA biosensors and optimization of downstream fermentation, the production of 3-HP in yeast has the potential to reach or even exceed the yield of chemical production in the future.
- Published
- 2018
49. Competitiveness Ability Evaluation Model of Electrical Equipment Enterprise in China’s New Development Period
- Author
-
Tian-Qiong Chen
- Subjects
Service (systems architecture) ,Index (economics) ,Scale (social sciences) ,Electrical equipment ,Siemens ,Key (cryptography) ,Differential (mechanical device) ,Business ,China ,Industrial organization - Abstract
Constructing competitive ability evaluation model of electrical equipment enterprise is significance for enterprises to find their own advantages and disadvantages, and adopt differential improvement strategy to improve competitiveness. Evaluation index system of competitive ability of electrical equipment enterprises in china is puts forward creatively in this paper, which covering scale and performance, customer and service, brand and image, strategy and culture, operation and management, innovation and growth these second level indicators, whose index weight were determined by Key Successful Factors method. Through the case study, it is found that SGCC's electrical equipment business is at the leading level in China, but there is still a gap compared with the ABB and SIEMENS such international first-class enterprises.
- Published
- 2018
50. Reactive Oxygen Species-Mediated Cellular Stress Response and Lipid Accumulation in Oleaginous Microorganisms: The State of the Art and Future Perspectives
- Author
-
Xiao-Jun Ji, Kun Shi, Zhen Gao, Tian-Qiong Shi, Ping Song, Lu-Jing Ren, and He Huang
- Subjects
0106 biological sciences ,0301 basic medicine ,Microbiology (medical) ,Cell signaling ,Mini Review ,lcsh:QR1-502 ,Biology ,01 natural sciences ,Microbiology ,lcsh:Microbiology ,Transcriptome ,03 medical and health sciences ,010608 biotechnology ,Cellular stress response ,Lipid biosynthesis ,Metabolome ,chemistry.chemical_classification ,reactive oxygen species ,oleaginous microorganisms ,Reactive oxygen species ,lipid accumulation ,Lipid metabolism ,stress response ,030104 developmental biology ,chemistry ,Biochemistry ,Second messenger system ,signaling molecules - Abstract
Microbial oils, which are mainly extracted from yeasts, molds, and algae, have been of considerable interest as food additives and biofuel resources due to their high lipid content. While these oleaginous microorganisms generally produce only small amounts of lipids under optimal growth conditions, their lipid accumulation machinery can be induced by environmental stresses, such as nutrient limitation and an inhospitable physical environmental. As common second messengers of many stress factors, reactive oxygen species (ROS) may act as a regulator of cellular responses to extracellular environmental signaling. Furthermore, increasing evidence indicates that ROS may act as a mediator of lipid accumulation, which is associated with dramatic changes in the transcriptome, proteome, and metabolome. However, the specific mechanisms of ROS involvement in the crosstalk between extracellular stress signaling and intracellular lipid synthesis require further investigation. Here, we summarize current knowledge on stress-induced lipid biosynthesis and the putative role of ROS in the control of lipid accumulation in oleaginous microorganisms. Understanding such links may provide guidance for the development of stress-based strategies to enhance microbial lipid production.
- Published
- 2017
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