1
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Yang G, Li B, Chen K, Du M, Zalán Z, Hegyi F, Kan J. Isolation and evaluation of probiotics from traditional Chinese foods for aflatoxin B 1 detoxification: Geotrichum candidum XG1 (yeast) and mechanistic insights. Food Chem 2024; 452:139541. [PMID: 38718457 DOI: 10.1016/j.foodchem.2024.139541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/11/2024] [Accepted: 05/01/2024] [Indexed: 06/01/2024]
Abstract
Identifying aflatoxin-detoxifying probiotics remains a significant challenge in mitigating the risks associated with aflatoxin contamination in crops. Biological detoxification is a popular technique that reduces mycotoxin hazards and garners consumer acceptance. Through multiple rounds of screening and validation tests, Geotrichum candidum XG1 demonstrated the ability to degrade aflatoxin B1 (AFB1) by 99-100%, exceeding the capabilities of mere adsorption mechanisms. Notably, the degradation efficiency was demonstrably influenced by the presence of copper and iron ions in the liquid medium, suggesting a potential role for proteases in the degradation process. Subsequent validation experiments with red pepper revealed an 83% reduction in AFB1 levels following fermentation with G. candidum XG1. Furthermore, mass spectrometry analysis confirmed the disruption of the AFB1 furan ring structure, leading to a subsequent reduction in its toxicity. Collectively, these findings establish G. candidum XG1 as a promising candidate for effective aflatoxin degradation, with potential applications within the food industry.
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Affiliation(s)
- Gang Yang
- College of Food Science, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400715, PR China; Chinese-Hungarian Cooperative Research Centre for Food Science, Chongqing 400715, PR China; Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing 400715, PR China
| | - Bin Li
- College of Food Science, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400715, PR China; Chinese-Hungarian Cooperative Research Centre for Food Science, Chongqing 400715, PR China; Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing 400715, PR China
| | - Kewei Chen
- College of Food Science, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400715, PR China; Chinese-Hungarian Cooperative Research Centre for Food Science, Chongqing 400715, PR China; Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing 400715, PR China; Laboratory of Quality & Safety Risk Assessment for Agro-products on Storage and Preservation (Chongqing), Ministry of Agriculture, Chongqing 400715, PR China
| | - Muying Du
- College of Food Science, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400715, PR China; Chinese-Hungarian Cooperative Research Centre for Food Science, Chongqing 400715, PR China; Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing 400715, PR China; Laboratory of Quality & Safety Risk Assessment for Agro-products on Storage and Preservation (Chongqing), Ministry of Agriculture, Chongqing 400715, PR China
| | - Zsolt Zalán
- Chinese-Hungarian Cooperative Research Centre for Food Science, Chongqing 400715, PR China; Food Science and Technology Institute, Hungarian University of Agriculture and Life Sciences, Buda Campus, Herman Ottó str. 15, Budapest 1022, Hungary.
| | - Ferenc Hegyi
- Chinese-Hungarian Cooperative Research Centre for Food Science, Chongqing 400715, PR China; Food Science and Technology Institute, Hungarian University of Agriculture and Life Sciences, Buda Campus, Herman Ottó str. 15, Budapest 1022, Hungary.
| | - Jianquan Kan
- College of Food Science, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400715, PR China; Chinese-Hungarian Cooperative Research Centre for Food Science, Chongqing 400715, PR China; Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing 400715, PR China; Laboratory of Quality & Safety Risk Assessment for Agro-products on Storage and Preservation (Chongqing), Ministry of Agriculture, Chongqing 400715, PR China.
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2
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Zhou P, Gao C, Song W, Wei W, Wu J, Liu L, Chen X. Engineering status of protein for improving microbial cell factories. Biotechnol Adv 2024; 70:108282. [PMID: 37939975 DOI: 10.1016/j.biotechadv.2023.108282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 10/23/2023] [Accepted: 11/05/2023] [Indexed: 11/10/2023]
Abstract
With the development of metabolic engineering and synthetic biology, microbial cell factories (MCFs) have provided an efficient and sustainable method to synthesize a series of chemicals from renewable feedstocks. However, the efficiency of MCFs is usually limited by the inappropriate status of protein. Thus, engineering status of protein is essential to achieve efficient bioproduction with high titer, yield and productivity. In this review, we summarize the engineering strategies for metabolic protein status, including protein engineering for boosting microbial catalytic efficiency, protein modification for regulating microbial metabolic capacity, and protein assembly for enhancing microbial synthetic capacity. Finally, we highlight future challenges and prospects of improving microbial cell factories by engineering status of protein.
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Affiliation(s)
- Pei Zhou
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Wanqing Wei
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China.
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3
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Ding Q, Ye C. Microbial engineering for shikimate biosynthesis. Enzyme Microb Technol 2023; 170:110306. [PMID: 37598506 DOI: 10.1016/j.enzmictec.2023.110306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/03/2023] [Accepted: 08/14/2023] [Indexed: 08/22/2023]
Abstract
Shikimate, a precursor to the antiviral drug oseltamivir (Tamiflu®), can influence aromatic metabolites and finds extensive use in antimicrobial, antitumor, and cardiovascular applications. Consequently, various strategies have been developed for chemical synthesis and plant extraction to enhance shikimate biosynthesis, potentially impacting environmental conditions, economic sustainability, and separation and purification processes. Microbial engineering has been developed as an environmentally friendly approach for shikimate biosynthesis. In this review, we provide a comprehensive summary of microbial strategies for shikimate biosynthesis. These strategies primarily include chassis construction, biochemical optimization, pathway remodelling, and global regulation. Furthermore, we discuss future perspectives on shikimate biosynthesis and emphasize the importance of utilizing advanced metabolic engineering tools to regulate microbial networks for constructing robust microbial cell factories.
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Affiliation(s)
- Qiang Ding
- School of Life Sciences, Anhui University, Hefei 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China; Anhui Key Laboratory of Modern Biomanufacturing, Hefei 230601, Anhui, China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China.
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4
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Zhang R, Zhu B, Sun C, Li Y, Yang G, Zhao Y, Pan K. UDP-glucose pyrophosphorylase as a target for regulating carbon flux distribution and antioxidant capacity in Phaeodactylum tricornutum. Commun Biol 2023; 6:750. [PMID: 37468748 PMCID: PMC10356853 DOI: 10.1038/s42003-023-05096-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 07/05/2023] [Indexed: 07/21/2023] Open
Abstract
UDP-glucose pyrophosphorylase (UGPase) is a key enzyme for polysaccharide synthesis, and its role in plants and bacteria is well established; however, its functions in unicellular microalgae remain ill-defined. Here, we perform bioinformatics, subcellular localization as well as in vitro and in vivo analyses to elucidate the functions of two UGPs (UGP1 and UGP2) in the model microalga Phaeodactylum tricornutum. Despite differences in amino acid sequence, substrate specificity, and subcellular localization between UGP1 and UGP2, both enzymes can efficiently increase the production of chrysolaminarin (Chrl) or lipids by regulating carbon flux distribution without impairing growth and photosynthesis in transgenic strains. Productivity evaluation indicate that UGP1 play a bigger role in regulating Chrl and lipid production than UGP2. In addition, UGP1 enhance antioxidant capacity, whereas UGP2 is involved in sulfoquinovosyldiacylglycerol (SQDG) synthesis in P. tricornutum. Taken together, the present results suggest that ideal microalgal strains can be developed for the industrial production of Chrl or lipids and lay the foundation for the development of methods to improve oxidative stress tolerance in diatoms.
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Affiliation(s)
- Ruihao Zhang
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Baohua Zhu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266100, China.
| | - Changze Sun
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Yun Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Guanpin Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yan Zhao
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Kehou Pan
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266100, China.
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5
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Wang N, Peng H, Yang C, Guo W, Wang M, Li G, Liu D. Metabolic Engineering of Model Microorganisms for the Production of Xanthophyll. Microorganisms 2023; 11:1252. [PMID: 37317226 DOI: 10.3390/microorganisms11051252] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/19/2023] [Accepted: 05/06/2023] [Indexed: 06/16/2023] Open
Abstract
Xanthophyll is an oxidated version of carotenoid. It presents significant value to the pharmaceutical, food, and cosmetic industries due to its specific antioxidant activity and variety of colors. Chemical processing and conventional extraction from natural organisms are still the main sources of xanthophyll. However, the current industrial production model can no longer meet the demand for human health care, reducing petrochemical energy consumption and green sustainable development. With the swift development of genetic metabolic engineering, xanthophyll synthesis by the metabolic engineering of model microorganisms shows great application potential. At present, compared to carotenes such as lycopene and β-carotene, xanthophyll has a relatively low production in engineering microorganisms due to its stronger inherent antioxidation, relatively high polarity, and longer metabolic pathway. This review comprehensively summarized the progress in xanthophyll synthesis by the metabolic engineering of model microorganisms, described strategies to improve xanthophyll production in detail, and proposed the current challenges and future efforts needed to build commercialized xanthophyll-producing microorganisms.
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Affiliation(s)
- Nan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huakang Peng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Caifeng Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenfang Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mengqi Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Gangqiang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dehu Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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6
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Zhou P, Liu H, Meng X, Zuo H, Qi M, Guo L, Gao C, Song W, Wu J, Chen X, Chen W, Liu L. Engineered Artificial Membraneless Organelles in Saccharomyces cerevisiae To Enhance Chemical Production. Angew Chem Int Ed Engl 2023; 62:e202215778. [PMID: 36762978 DOI: 10.1002/anie.202215778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/11/2023]
Abstract
Microbial cell factories provide a green and sustainable opportunity to produce value-added products from renewable feedstock. However, the leakage of toxic or volatile intermediates decreases the efficiency of microbial cell factories. In this study, membraneless organelles (MLOs) were reconstructed in Saccharomyces cerevisiae by the disordered protein sequence A-IDPs. A regulation system was designed to spatiotemporally regulate the size and rigidity of MLOs. Manipulating the MLO size of strain ZP03-FM, the amounts of assimilated methanol and malate were increased by 162 % and 61 %, respectively. Furthermore, manipulating the MLO rigidity in strain ZP04-RB made acetyl-coA synthesis from oxidative glycolysis change to non-oxidative glycolysis; consequently, CO2 release decreased by 35 % and the n-butanol yield increased by 20 %. This artificial MLO provides a strategy for the co-localization of enzymes to channel C1 starting materials into value-added chemicals.
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Affiliation(s)
- Pei Zhou
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Hui Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Xin Meng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Huiyun Zuo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Mengya Qi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
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7
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Engineering Microorganisms to Produce Bio-Based Monomers: Progress and Challenges. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9020137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Bioplastics are polymers made from sustainable bio-based feedstocks. While the potential of producing bio-based monomers in microbes has been investigated for decades, their economic feasibility is still unsatisfactory compared with petroleum-derived methods. To improve the overall synthetic efficiency of microbial cell factories, three main strategies were summarized in this review: firstly, implementing approaches to improve the microbial utilization ability of cheap and abundant substrates; secondly, developing methods at enzymes, pathway, and cellular levels to enhance microbial production performance; thirdly, building technologies to enhance microbial pH, osmotic, and metabolites stress tolerance. Moreover, the challenges of, and some perspectives on, exploiting microorganisms as efficient cell factories for producing bio-based monomers are also discussed.
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8
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Ding Q, Ye C. Microbial cell factories based on filamentous bacteria, yeasts, and fungi. Microb Cell Fact 2023; 22:20. [PMID: 36717860 PMCID: PMC9885587 DOI: 10.1186/s12934-023-02025-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/20/2023] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Advanced DNA synthesis, biosensor assembly, and genetic circuit development in synthetic biology and metabolic engineering have reinforced the application of filamentous bacteria, yeasts, and fungi as promising chassis cells for chemical production, but their industrial application remains a major challenge that needs to be solved. RESULTS As important chassis strains, filamentous microorganisms can synthesize important enzymes, chemicals, and niche pharmaceutical products through microbial fermentation. With the aid of metabolic engineering and synthetic biology, filamentous bacteria, yeasts, and fungi can be developed into efficient microbial cell factories through genome engineering, pathway engineering, tolerance engineering, and microbial engineering. Mutant screening and metabolic engineering can be used in filamentous bacteria, filamentous yeasts (Candida glabrata, Candida utilis), and filamentous fungi (Aspergillus sp., Rhizopus sp.) to greatly increase their capacity for chemical production. This review highlights the potential of using biotechnology to further develop filamentous bacteria, yeasts, and fungi as alternative chassis strains. CONCLUSIONS In this review, we recapitulate the recent progress in the application of filamentous bacteria, yeasts, and fungi as microbial cell factories. Furthermore, emphasis on metabolic engineering strategies involved in cellular tolerance, metabolic engineering, and screening are discussed. Finally, we offer an outlook on advanced techniques for the engineering of filamentous bacteria, yeasts, and fungi.
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Affiliation(s)
- Qiang Ding
- grid.252245.60000 0001 0085 4987School of Life Sciences, Anhui University, Hefei, 230601 China ,grid.252245.60000 0001 0085 4987Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, 230601 Anhui China ,Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601 Anhui China
| | - Chao Ye
- grid.260474.30000 0001 0089 5711School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023 China
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9
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Yang Y, Mao Y, Wang R, Li H, Liu Y, Cheng H, Shi Z, Wang Y, Wang M, Zheng P, Liao X, Ma H. AutoESD: a web tool for automatic editing sequence design for genetic manipulation of microorganisms. Nucleic Acids Res 2022; 50:W75-W82. [PMID: 35639727 PMCID: PMC9252779 DOI: 10.1093/nar/gkac417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/20/2022] [Accepted: 05/09/2022] [Indexed: 11/30/2022] Open
Abstract
Advances in genetic manipulation and genome engineering techniques have enabled on-demand targeted deletion, insertion, and substitution of DNA sequences. One important step in these techniques is the design of editing sequences (e.g. primers, homologous arms) to precisely target and manipulate DNA sequences of interest. Experimental biologists can employ multiple tools in a stepwise manner to assist editing sequence design (ESD), but this requires various software involving non-standardized data exchange and input/output formats. Moreover, necessary quality control steps might be overlooked by non-expert users. This approach is low-throughput and can be error-prone, which illustrates the need for an automated ESD system. In this paper, we introduce AutoESD (https://autoesd.biodesign.ac.cn/), which designs editing sequences for all steps of genetic manipulation of many common homologous-recombination techniques based on screening-markers. Notably, multiple types of manipulations for different targets (CDS or intergenic region) can be processed in one submission. Moreover, AutoESD has an entirely cloud-based serverless architecture, offering high reliability, robustness and scalability which is capable of parallelly processing hundreds of design tasks each having thousands of targets in minutes. To our knowledge, AutoESD is the first cloud platform enabling precise, automated, and high-throughput ESD across species, at any genomic locus for all manipulation types.
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Affiliation(s)
- Yi Yang
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yufeng Mao
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Ruoyu Wang
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Haoran Li
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Ye Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Haijiao Cheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Zhenkun Shi
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yu Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Meng Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Ping Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xiaoping Liao
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Hongwu Ma
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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10
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Krujatz F, Dani S, Windisch J, Emmermacher J, Hahn F, Mosshammer M, Murthy S, Steingroewer J, Walther T, Kühl M, Gelinsky M, Lode A. Think outside the box: 3D bioprinting concepts for biotechnological applications – recent developments and future perspectives. Biotechnol Adv 2022; 58:107930. [DOI: 10.1016/j.biotechadv.2022.107930] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/17/2022] [Indexed: 12/14/2022]
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11
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Ding Q, Liu Y, Hu G, Guo L, Gao C, Chen X, Chen W, Chen J, Liu L. Engineering Escherichia coli biofilm to increase contact surface for shikimate and L-malate production. BIORESOUR BIOPROCESS 2021; 8:118. [PMID: 38650289 PMCID: PMC10992329 DOI: 10.1186/s40643-021-00470-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 11/22/2021] [Indexed: 11/10/2022] Open
Abstract
Microbial organelles are a promising model to promote cellular functions for the production of high-value chemicals. However, the concentrations of enzymes and nanoparticles are limited by the contact surface in single Escherichia coli cells. Herein, the definition of contact surface is to improve the amylase and CdS nanoparticles concentration for enhancing the substrate starch and cofactor NADH utilization. In this study, two biofilm-based strategies were developed to improve the contact surface for the production of shikimate and L-malate. First, the contact surface of E. coli was improved by amylase self-assembly with a blue light-inducible biofilm-based SpyTag/SpyCatcher system. This system increased the glucose concentration by 20.7% and the starch-based shikimate titer to 50.96 g L-1, which showed the highest titer with starch as substrate. Then, the contact surface of E. coli was improved using a biofilm-based CdS-biohybrid system by light-driven system, which improved the NADH concentration by 83.3% and increased the NADH-dependent L-malate titer to 45.93 g L-1. Thus, the biofilm-based strategies can regulate cellular functions to increase the efficiency of microbial cell factories based on the optogenetics, light-driven, and metabolic engineering.
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Affiliation(s)
- Qiang Ding
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Yadi Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Guipeng Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China.
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12
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Yang Y, Mao Y, Liu Y, Wang R, Lu H, Li H, Luo J, Wang M, Liao X, Ma H. GEDpm-cg: Genome Editing Automated Design Platform for Point Mutation Construction in Corynebacterium glutamicum. Front Bioeng Biotechnol 2021; 9:768289. [PMID: 34722482 PMCID: PMC8554027 DOI: 10.3389/fbioe.2021.768289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/07/2021] [Indexed: 11/13/2022] Open
Abstract
Advances in robotic system-assisted genome editing techniques and computer-aided design tools have significantly facilitated the development of microbial cell factories. Although multiple separate software solutions are available for vector DNA assembly, genome editing, and verification, by far there is still a lack of complete tool which can provide a one-stop service for the entire genome modification process. This makes the design of numerous genetic modifications, especially the construction of mutations that require strictly precise genetic manipulation, a laborious, time-consuming and error-prone process. Here, we developed a free online tool called GEDpm-cg for the design of genomic point mutations in C. glutamicum. The suicide plasmid-mediated counter-selection point mutation editing method and the overlap-based DNA assembly method were selected to ensure the editability of any single nucleotide at any locus in the C. glutamicum chromosome. Primers required for both DNA assembly of the vector for genetic modification and sequencing verification were provided as design results to meet all the experimental needs. An in-silico design task of over 10,000 single point mutations can be completed in 5 min. Finally, three independent point mutations were successfully constructed in C. glutamicum guided by GEDpm-cg, which confirms that the in-silico design results could accurately and seamlessly be bridged with in vivo or in vitro experiments. We believe this platform will provide a user-friendly, powerful and flexible tool for large-scale mutation analysis in the industrial workhorse C. glutamicum via robotic/software-assisted systems.
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Affiliation(s)
- Yi Yang
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yufeng Mao
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Ye Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Ruoyu Wang
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Hui Lu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Haoran Li
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jiahao Luo
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Meng Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xiaoping Liao
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Hongwu Ma
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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13
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Kladko DV, Falchevskaya AS, Serov NS, Prilepskii AY. Nanomaterial Shape Influence on Cell Behavior. Int J Mol Sci 2021; 22:5266. [PMID: 34067696 PMCID: PMC8156540 DOI: 10.3390/ijms22105266] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 12/18/2022] Open
Abstract
Nanomaterials are proven to affect the biological activity of mammalian and microbial cells profoundly. Despite this fact, only surface chemistry, charge, and area are often linked to these phenomena. Moreover, most attention in this field is directed exclusively at nanomaterial cytotoxicity. At the same time, there is a large body of studies showing the influence of nanomaterials on cellular metabolism, proliferation, differentiation, reprogramming, gene transfer, and many other processes. Furthermore, it has been revealed that in all these cases, the shape of the nanomaterial plays a crucial role. In this paper, the mechanisms of nanomaterials shape control, approaches toward its synthesis, and the influence of nanomaterial shape on various biological activities of mammalian and microbial cells, such as proliferation, differentiation, and metabolism, as well as the prospects of this emerging field, are reviewed.
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Affiliation(s)
| | | | | | - Artur Y. Prilepskii
- International Institute “Solution Chemistry of Advanced Materials and Technologies”, ITMO University, 191002 Saint Petersburg, Russia; (D.V.K.); (A.S.F.); (N.S.S.)
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14
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Cao Y, Zhang B, Zhu Z, Xin X, Wu H, Chen B. Microfluidic Based Whole-Cell Biosensors for Simultaneously On-Site Monitoring of Multiple Environmental Contaminants. Front Bioeng Biotechnol 2021; 9:622108. [PMID: 33791284 PMCID: PMC8006271 DOI: 10.3389/fbioe.2021.622108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/18/2021] [Indexed: 12/20/2022] Open
Abstract
Monitoring of environmental contaminants serves a vital role in proactive environmental management and pollution control. Research efforts have been centered on the development of robust whole-cell biosensors in recent years. However, data acquisition, multiple contaminants detection and biosafety issues limit the on-site application of such biosensors. Microfluidic system exhibits great potential to face these challenges via coupling biosensors. Here, we prospect a novel microfluidic based whole-cell biosensor (MWCB) for multiplexing monitoring of diverse contaminants, and design strategies to further increase the specificity, sensitivity and accuracy, reduce signal delay and expand shelf life of the proposed MWCB for on-site environmental applications. The development of MWCB demands multidisciplinary cooperation, and the sensing platforms are highly promising for real-world contaminants monitoring.
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Affiliation(s)
- Yiqi Cao
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Baiyu Zhang
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Zhiwen Zhu
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Xiayin Xin
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Hongjing Wu
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Bing Chen
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL, Canada
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