1
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Kuang Z, Yan X, Yuan Y, Wang R, Zhu H, Wang Y, Li J, Ye J, Yue H, Yang X. Advances in stress-tolerance elements for microbial cell factories. Synth Syst Biotechnol 2024; 9:793-808. [PMID: 39072145 PMCID: PMC11277822 DOI: 10.1016/j.synbio.2024.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/10/2024] [Accepted: 06/27/2024] [Indexed: 07/30/2024] Open
Abstract
Microorganisms, particularly extremophiles, have evolved multiple adaptation mechanisms to address diverse stress conditions during survival in unique environments. Their responses to environmental coercion decide not only survival in severe conditions but are also an essential factor determining bioproduction performance. The design of robust cell factories should take the balance of their growing and bioproduction into account. Thus, mining and redesigning stress-tolerance elements to optimize the performance of cell factories under various extreme conditions is necessary. Here, we reviewed several stress-tolerance elements, including acid-tolerant elements, saline-alkali-resistant elements, thermotolerant elements, antioxidant elements, and so on, providing potential materials for the construction of cell factories and the development of synthetic biology. Strategies for mining and redesigning stress-tolerance elements were also discussed. Moreover, several applications of stress-tolerance elements were provided, and perspectives and discussions for potential strategies for screening stress-tolerance elements were made.
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Affiliation(s)
- Zheyi Kuang
- School of Intelligence Science and Technology, Xinjiang University, Urumqi, 830017, China
| | - Xiaofang Yan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yanfei Yuan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Ruiqi Wang
- School of Intelligence Science and Technology, Xinjiang University, Urumqi, 830017, China
| | - Haifan Zhu
- School of Intelligence Science and Technology, Xinjiang University, Urumqi, 830017, China
| | - Youyang Wang
- School of Intelligence Science and Technology, Xinjiang University, Urumqi, 830017, China
| | - Jianfeng Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Jianwen Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Haitao Yue
- School of Intelligence Science and Technology, Xinjiang University, Urumqi, 830017, China
- Laboratory of Synthetic Biology, School of Life Science and Technology, Xinjiang University, Urumqi, 830017, China
| | - Xiaofeng Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
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2
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Gola KK, Patel A, Sen S. Tradeoffs in the design of RNA thermometers. Phys Biol 2024; 21:044001. [PMID: 38949434 DOI: 10.1088/1478-3975/ad5d6b] [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: 02/14/2024] [Accepted: 07/01/2024] [Indexed: 07/02/2024]
Abstract
The synthesis of RNA thermometers is aimed at achieving temperature responses with desired thresholds and sensitivities. Although previous works have generated thermometers with a variety of thresholds and sensitivities as well as guidelines for design, possible constraints in the achievable thresholds and sensitivities remain unclear. We addressed this issue using a two-state model and its variants, as well as melt profiles generated from thermodynamic computations. In the two-state model, we found that the threshold was inversely proportional to the sensitivity, in the case of a fixed energy difference between the two states. Notably, this constraint could persist in variations of the two-state model with sequentially unfolding states and branched parallel pathways. Furthermore, the melt profiles generated from a library of thermometers exhibited a similar constraint. These results should inform the design of RNA thermometers as well as other responses that are mediated in a similar fashion.
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Affiliation(s)
- Krishan Kumar Gola
- Department of Electrical Engineering, Indian Institute of Technology Delhi, New Delhi, Delhi 110016, India
| | - Abhilash Patel
- Department of Electrical Engineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Shaunak Sen
- Department of Electrical Engineering, Indian Institute of Technology Delhi, New Delhi, Delhi 110016, India
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3
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Yue K, Chen J, Li Y, Kai L. Advancing synthetic biology through cell-free protein synthesis. Comput Struct Biotechnol J 2023; 21:2899-2908. [PMID: 37216017 PMCID: PMC10196276 DOI: 10.1016/j.csbj.2023.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
The rapid development of synthetic biology has enabled the production of compounds with revolutionary improvements in biotechnology. DNA manipulation tools have expedited the engineering of cellular systems for this purpose. Nonetheless, the inherent constraints of cellular systems persist, imposing an upper limit on mass and energy conversion efficiencies. Cell-free protein synthesis (CFPS) has demonstrated its potential to overcome these inherent constraints and has been instrumental in the further advancement of synthetic biology. Via the removal of the cell membranes and redundant parts of cells, CFPS has provided flexibility in directly dissecting and manipulating the Central Dogma with rapid feedback. This mini-review summarizes recent achievements of the CFPS technique and its application to a wide range of synthetic biology projects, such as minimal cell assembly, metabolic engineering, and recombinant protein production for therapeutics, as well as biosensor development for in vitro diagnostics. In addition, current challenges and future perspectives in developing a generalized cell-free synthetic biology are outlined.
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Affiliation(s)
- Ke Yue
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Junyu Chen
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Yingqiu Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Lei Kai
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
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4
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Volk MJ, Tran VG, Tan SI, Mishra S, Fatma Z, Boob A, Li H, Xue P, Martin TA, Zhao H. Metabolic Engineering: Methodologies and Applications. Chem Rev 2022; 123:5521-5570. [PMID: 36584306 DOI: 10.1021/acs.chemrev.2c00403] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Metabolic engineering aims to improve the production of economically valuable molecules through the genetic manipulation of microbial metabolism. While the discipline is a little over 30 years old, advancements in metabolic engineering have given way to industrial-level molecule production benefitting multiple industries such as chemical, agriculture, food, pharmaceutical, and energy industries. This review describes the design, build, test, and learn steps necessary for leading a successful metabolic engineering campaign. Moreover, we highlight major applications of metabolic engineering, including synthesizing chemicals and fuels, broadening substrate utilization, and improving host robustness with a focus on specific case studies. Finally, we conclude with a discussion on perspectives and future challenges related to metabolic engineering.
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Affiliation(s)
- Michael J Volk
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Vinh G Tran
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shih-I Tan
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - Shekhar Mishra
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Zia Fatma
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Aashutosh Boob
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hongxiang Li
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pu Xue
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Teresa A Martin
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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5
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Chee WKD, Yeoh JW, Dao VL, Poh CL. Thermogenetics: Applications come of age. Biotechnol Adv 2022; 55:107907. [PMID: 35041863 DOI: 10.1016/j.biotechadv.2022.107907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/13/2021] [Accepted: 01/09/2022] [Indexed: 12/20/2022]
Abstract
Temperature is a ubiquitous physical cue that is non-invasive, penetrative and easy to apply. In the growing field of thermogenetics, through beneficial repurposing of natural thermosensing mechanisms, synthetic biology is bringing new opportunities to design and build robust temperature-sensitive (TS) sensors which forms a thermogenetic toolbox of well characterised biological parts. Recent advancements in technological platforms available have expedited the discovery of novel or de novo thermosensors which are increasingly deployed in many practical temperature-dependent biomedical, industrial and biosafety applications. In all, the review aims to convey both the exhilarating recent technological developments underlying the advancement of thermosensors and the exciting opportunities the nascent thermogenetic field holds for biomedical and biotechnology applications.
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Affiliation(s)
- Wai Kit David Chee
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Jing Wui Yeoh
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Viet Linh Dao
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Chueh Loo Poh
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
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6
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Sun J, Sun W, Zhang G, Lv B, Li C. High efficient production of plant flavonoids by microbial cell factories: Challenges and opportunities. Metab Eng 2022; 70:143-154. [DOI: 10.1016/j.ymben.2022.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 01/12/2022] [Accepted: 01/21/2022] [Indexed: 12/27/2022]
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7
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Sen S, Patel A, Gola KK. Design of a Toolbox of RNA Thermometers. Methods Mol Biol 2022; 2518:125-133. [PMID: 35666443 DOI: 10.1007/978-1-0716-2421-0_8] [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] [Indexed: 06/15/2023]
Abstract
RNA thermometers are RNA regulatory elements that convert temperature into a functional biological response through a temperature-induced conformational change. These regulatory elements have been investigated in numerous natural contexts and have been designed for synthetic biology as well. A basic challenge has been the design of an RNA thermometer whose final activity in response to temperature matches a prespecified response, in terms of its sensitivity, threshold, and leakiness. This chapter provides a methodology for the design of a toolbox of RNA thermometers. We describe considerations for the conceptual design, a computational assessment, and strategies for experimental synthesis and measurement.
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Affiliation(s)
- Shaunak Sen
- Department of Electrical Engineering, IIT Delhi, New Delhi, India.
| | - Abhilash Patel
- Department of Bioengineering, Imperial College, London, UK
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8
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Chen L, Pang Y, Luo Y, Cheng X, Lv B, Li C. Separation and purification of plant terpenoids from biotransformation. Eng Life Sci 2021; 21:724-738. [PMID: 34764825 PMCID: PMC8576074 DOI: 10.1002/elsc.202100014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/10/2021] [Accepted: 05/17/2021] [Indexed: 11/06/2022] Open
Abstract
The production of plant terpenoids through biotransformation has undoubtedly become one of the research hotspots, and the continuous upgrading of the corresponding downstream technology is also particularly important. Downstream technology is the indispensable technical channel for the industrialization of plant terpenoids. How to efficiently separate high-purity products from complex microbial fermentation broths or enzyme-catalyzed reactions to achieve high separation rates, high returns and environmental friendliness has become the focus of research in recent years. This review mainly introduces the common separation methods of plant terpenoids based on biotransformation from the perspectives of engineering strain construction, unit separation technology, product properties and added value. Then, further attention was paid to the application prospects of intelligent cell factories and control in the separation of plant terpenoids. Finally, some current challenges and prospects are proposed, which provide possible directions and guidance for the separation and purification of terpenoids and even industrialization.
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Affiliation(s)
- Linhao Chen
- Key Laboratory of Medical Molecule Science and Pharmaceutics EngineeringMinistry of Industry and Information TechnologyInstitute of Biochemical EngineeringSchool of Chemistry and Chemical EngineeringBeijing Institute of TechnologyBeijingP. R. China
| | - Yaru Pang
- Key Laboratory of Medical Molecule Science and Pharmaceutics EngineeringMinistry of Industry and Information TechnologyInstitute of Biochemical EngineeringSchool of Chemistry and Chemical EngineeringBeijing Institute of TechnologyBeijingP. R. China
| | - Yan Luo
- Key Laboratory of Medical Molecule Science and Pharmaceutics EngineeringMinistry of Industry and Information TechnologyInstitute of Biochemical EngineeringSchool of Chemistry and Chemical EngineeringBeijing Institute of TechnologyBeijingP. R. China
| | - Xu Cheng
- Key Laboratory of Medical Molecule Science and Pharmaceutics EngineeringMinistry of Industry and Information TechnologyInstitute of Biochemical EngineeringSchool of Chemistry and Chemical EngineeringBeijing Institute of TechnologyBeijingP. R. China
| | - Bo Lv
- Key Laboratory of Medical Molecule Science and Pharmaceutics EngineeringMinistry of Industry and Information TechnologyInstitute of Biochemical EngineeringSchool of Chemistry and Chemical EngineeringBeijing Institute of TechnologyBeijingP. R. China
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics EngineeringMinistry of Industry and Information TechnologyInstitute of Biochemical EngineeringSchool of Chemistry and Chemical EngineeringBeijing Institute of TechnologyBeijingP. R. China
- Key Lab for Industrial BiocatalysisMinistry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijingP. R. China
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9
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Liu HR, Ahmad N, Lv B, Li C. Advances in production and structural derivatization of the promising molecule ursolic acid. Biotechnol J 2021; 16:e2000657. [PMID: 34096160 DOI: 10.1002/biot.202000657] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 05/16/2021] [Accepted: 05/18/2021] [Indexed: 02/05/2023]
Abstract
Ursolic acid (UA) is a ursane-type pentacyclic triterpenoid compound, naturally produced in plants via specialized metabolism and exhibits vast range of remarkable physiological activities and pharmacological manifestations. Owing to significant safety and efficacy in different medical conditions, UA may serve as a backbone to produce its derivatives with novel therapeutic functions. This review aims to provide ideas for exploring more diverse structures to improve UA pharmacological activity and increasing its biological yield to meet the industrial requirements by systematically reviewing the current research progress of UA. We first provides an overview of the pharmacological activities, acquisition methods and structural modifications of UA. Among them, we focused on the synthetic modifications of UA to yield valuable derivatives with enhanced therapeutic potential. Furthermore, harnessing the essential advances for green synthesis of UA and its derivatives by advent of metabolic engineering and synthetic biology are of great concern. In this regard, all pivotal advances for enhancing the production of UA have been discussed. In combination with the advantages of UA biosynthesis and transformation strategy, large-scale microbial production of UA is a promising platform for further exploration.
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Affiliation(s)
- Hao-Ran Liu
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Nadeem Ahmad
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Bo Lv
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, P. R. China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China
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10
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Hu X, Tang X, Bi Z, Zhao Q, Ren L. Adaptive evolution of microalgae Schizochytrium sp. under high temperature for efficient production of docosahexaeonic acid. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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11
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Li C, Gao X, Peng X, Li J, Bai W, Zhong J, He M, Xu K, Wang Y, Li C. Intelligent microbial cell factory with genetic pH shooting (GPS) for cell self-responsive base/acid regulation. Microb Cell Fact 2020; 19:202. [PMID: 33138821 PMCID: PMC7607686 DOI: 10.1186/s12934-020-01457-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 10/17/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND In industrial fermentation, pH fluctuation resulted from microbial metabolism influences the strain performance and the final production. The common way to control pH is adding acid or alkali after probe detection, which is not a fine-tuned method and often leads to increased costs and complex downstream processing. Here, we constructed an intelligent pH-sensing and controlling genetic circuits called "Genetic pH Shooting (GPS)" to realize microbial self-regulation of pH. RESULTS In order to achieve the self-regulation of pH, GPS circuits consisting of pH-sensing promoters and acid-/alkali-producing genes were designed and constructed. Designed pH-sensing promoters in the GPS can respond to high or low pHs and generate acidic or alkaline substances, achieving endogenously self-responsive pH adjustments. Base shooting circuit (BSC) and acid shooting circuit (ASC) were constructed and enabled better cell growth under alkaline or acidic conditions, respectively. Furthermore, the genetic circuits including GPS, BSC and ASC were applied to lycopene production with a higher yield without an artificial pH regulation compared with the control under pH values ranging from 5.0 to 9.0. In scale-up fermentations, the lycopene titer in the engineered strain harboring GPS was increased by 137.3% and ammonia usage decreased by 35.6%. CONCLUSIONS The pH self-regulation achieved through the GPS circuits is helpful to construct intelligent microbial cell factories and reduce the production costs, which would be much useful in industrial applications.
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Affiliation(s)
- Chenyi Li
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, People's Republic of China
| | - Xiaopeng Gao
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, People's Republic of China.,School of Life Science, Yan'an University, Shanxi, 716000, People's Republic of China
| | - Xiao Peng
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, People's Republic of China
| | - Jinlin Li
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, People's Republic of China
| | - Wenxin Bai
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, People's Republic of China
| | - Jiadong Zhong
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, People's Republic of China
| | - Mengchao He
- School of Life Science, Yan'an University, Shanxi, 716000, People's Republic of China
| | - Ke Xu
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, People's Republic of China.,Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, People's Republic of China
| | - Ying Wang
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, People's Republic of China.
| | - Chun Li
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, People's Republic of China. .,School of Life Science, Yan'an University, Shanxi, 716000, People's Republic of China. .,Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, People's Republic of China.
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12
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Gayán E, Van den Bergh B, Michiels J, Michiels CW, Aertsen A. Synthetic reconstruction of extreme high hydrostatic pressure resistance in Escherichia coli. Metab Eng 2020; 62:287-297. [PMID: 32979485 DOI: 10.1016/j.ymben.2020.09.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/17/2022]
Abstract
Although high hydrostatic pressure (HHP) is an interesting parameter to be applied in bioprocessing, its potential is currently limited by the lack of bacterial chassis capable of surviving and maintaining homeostasis under pressure. While several efforts have been made to genetically engineer microorganisms able to grow at sublethal pressures, there is little information for designing backgrounds that survive more extreme pressures. In this investigation, we analyzed the genome of an extreme HHP-resistant mutant of E. coli MG1655 (designated as DVL1), from which we identified four mutations (in the cra, cyaA, aceA and rpoD loci) causally linked to increased HHP resistance. Analysing the functional effect of these mutations we found that the coupled effect of downregulation of cAMP/CRP, Cra and the glyoxylate shunt activity, together with the upregulation of RpoH and RpoS activity, could mechanistically explain the increased HHP resistance of the mutant. Using combinations of three mutations, we could synthetically engineer E. coli strains able to comfortably survive pressures of 600-800 MPa, which could serve as genetic backgrounds for HHP-based biotechnological applications.
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Affiliation(s)
- Elisa Gayán
- Department of Microbial and Molecular Systems, KU Leuven. Faculty of Bioscience Engineering, Kasteelpark Arenberg 20, 3001, Leuven, Belgium.
| | - Bram Van den Bergh
- Department of Microbial and Molecular Systems, KU Leuven. Faculty of Bioscience Engineering, Kasteelpark Arenberg 20, 3001, Leuven, Belgium; VIB Center for Microbiology, Flanders Institute for Biotechnology, Kasteelpark Arenberg 20, 3001, Leuven, Belgium
| | - Jan Michiels
- Department of Microbial and Molecular Systems, KU Leuven. Faculty of Bioscience Engineering, Kasteelpark Arenberg 20, 3001, Leuven, Belgium; VIB Center for Microbiology, Flanders Institute for Biotechnology, Kasteelpark Arenberg 20, 3001, Leuven, Belgium
| | - Chris W Michiels
- Department of Microbial and Molecular Systems, KU Leuven. Faculty of Bioscience Engineering, Kasteelpark Arenberg 20, 3001, Leuven, Belgium
| | - Abram Aertsen
- Department of Microbial and Molecular Systems, KU Leuven. Faculty of Bioscience Engineering, Kasteelpark Arenberg 20, 3001, Leuven, Belgium.
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13
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de Siqueira GMV, Silva-Rocha R, Guazzaroni ME. Turning the Screw: Engineering Extreme pH Resistance in Escherichia coli through Combinatorial Synthetic Operons. ACS Synth Biol 2020; 9:1254-1262. [PMID: 32438805 DOI: 10.1021/acssynbio.0c00089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Adoption of microorganisms as platforms for sustainable biobased production requires host cells to be able to withstand harsh conditions, usually very distant from those in which these organisms are naturally adapted to thrive. However, novel survival mechanisms unearthed by the study of microbiomes from extreme habitats may be exploited to enhance microbial robustness under the strict conditions needed for different industrial appplications. In this work, synthetic biology approaches were used to engineer enhanced acidic resistance in Escherichia coli through the characterization of a collection of unique operons composed of combinatorial assemblies of three novel genes from an extreme environment and three synthetic ribosome binding sites. The results here presented illustrate the efficacy of combining different metagenomic genes for resistance in synthetic operons, as expression of these gene clusters increased hundred-fold the survival percentage of cells exposed to an acidic shock in minimal media at pH 1.9 under aerobic conditions.
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Affiliation(s)
- Guilherme M. V. de Siqueira
- Departamento de Bioquı́mica, Faculdade de Medicina de Ribeirão Preto (FMRP-USP), Ribeirão Preto, SP 14049-900, Brasil
| | - Rafael Silva-Rocha
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto (FMRP-USP), Ribeirão Preto, SP 14049-900, Brasil
| | - María-Eugenia Guazzaroni
- Departamento de Biologia, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto (FFCLRP-USP), Ribeirão Preto, SP 14040-901, Brasil
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14
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Li P, Fu X, Zhang L, Li S. CRISPR/Cas-based screening of a gene activation library in Saccharomyces cerevisiae identifies a crucial role of OLE1 in thermotolerance. Microb Biotechnol 2019; 12:1154-1163. [PMID: 30394685 PMCID: PMC6801138 DOI: 10.1111/1751-7915.13333] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/11/2018] [Accepted: 10/16/2018] [Indexed: 11/30/2022] Open
Abstract
CRISPR/Cas-based (clustered regularly interspaced short palindromic repeats/CRISPR-associated) screening has been proved to be an efficient method to study functional genomics from yeast to human. In this study, we report the development of a focused CRISPR/Cas-based gene activation library in Saccharomyces cerevisiae and its application in gene identification based on functional screening towards improved thermotolerance. The gene activation library was subjected to screening at 42°C, and the same library cultured at 30°C was set as a control group. After five successive subcultures, five clones were randomly picked from the libraries cultured at 30 and 42°C, respectively. The five clones selected at 30°C contain the specificity sequences of five different single guide RNAs, whereas all the five clones selected at 42°C contain the specificity sequence of one sgRNA that targets the promoter region of OLE1. A crucial role of OLE1 in thermotolerance was identified: the overexpression of OLE1 increased fatty acid unsaturation, and thereby helped counter lipid peroxidation caused by heat stress, rendering the yeast thermotolerant. This study described the application of CRISPR/Cas-based gene activation screening with an example of thermotolerant yeast screening, demonstrating that this method can be used to identify functional genes in yeast.
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Affiliation(s)
- Pengsong Li
- MOST‐USDA Joint Research Center for BiofuelsBeijing Engineering Research Center for BiofuelsInstitute of New Energy TechnologyTsinghua UniversityBeijing100084China
| | - Xiaofen Fu
- MOST‐USDA Joint Research Center for BiofuelsBeijing Engineering Research Center for BiofuelsInstitute of New Energy TechnologyTsinghua UniversityBeijing100084China
| | - Lei Zhang
- MOST‐USDA Joint Research Center for BiofuelsBeijing Engineering Research Center for BiofuelsInstitute of New Energy TechnologyTsinghua UniversityBeijing100084China
| | - Shizhong Li
- MOST‐USDA Joint Research Center for BiofuelsBeijing Engineering Research Center for BiofuelsInstitute of New Energy TechnologyTsinghua UniversityBeijing100084China
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15
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Gao C, Xu P, Ye C, Chen X, Liu L. Genetic Circuit-Assisted Smart Microbial Engineering. Trends Microbiol 2019; 27:1011-1024. [PMID: 31421969 DOI: 10.1016/j.tim.2019.07.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/27/2019] [Accepted: 07/19/2019] [Indexed: 12/22/2022]
Abstract
Rapid advances in DNA synthesis, genetic manipulation, and biosensors have greatly improved the ability to engineer microorganisms with complex functions. By accurately integrating quality biosensors and complex genetic circuits, recently emerged smart microorganisms have enabled exciting opportunities for dissecting complex signaling networks and making responses without artificial intervention. However, because of the lack of design principles, developing such smart microorganisms remains challenging. In this review, we propose the concept of smart microbial engineering (SME) and describe the general features of basic SME, including the circuit architecture, components, and design process. We also summarize the latest SME achievements, remaining challenges, and potential solutions in this growing field.
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Affiliation(s)
- Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Peng Xu
- Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Chao Ye
- State Key Laboratory of Food Science and Technology, 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 Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China.
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16
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Jia H, Heymann M, Härtel T, Kai L, Schwille P. Temperature-sensitive protein expression in protocells. Chem Commun (Camb) 2019; 55:6421-6424. [PMID: 31094370 DOI: 10.1039/c9cc02734c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We engineered a synthetic temperature regulation toolbox to enable protocells to sense and respond to heat, utilizing RNA thermometers. The thermo-sensitive protocells were generated by encapsulating temperature feedback transcription/translation machinery in droplets. Based on these temperature-sensing devices, the protocells can be operated with logic AND gates, differentially processing temperature stimuli into biological signals.
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Affiliation(s)
- Haiyang Jia
- Dept. Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D - 82152 Martinsried, Germany.
| | - Michael Heymann
- Dept. Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D - 82152 Martinsried, Germany.
| | - Tobias Härtel
- Dept. Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D - 82152 Martinsried, Germany.
| | - Lei Kai
- Dept. Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D - 82152 Martinsried, Germany.
| | - Petra Schwille
- Dept. Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D - 82152 Martinsried, Germany.
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17
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Ding M, Chen B, Ji X, Zhou J, Wang H, Tian X, Feng X, Yue H, Zhou Y, Wang H, Wu J, Yang P, Jiang Y, Mao X, Xiao G, Zhong C, Xiao W, Li B, Qin L, Cheng J, Yao M, Wang Y, Liu H, Zhang L, Yu L, Chen T, Dong X, Jia X, Zhang S, Liu Y, Chen Y, Chen K, Wu J, Zhu C, Zhuang W, Xu S, Jiao P, Zhang L, Song H, Yang S, Xiong Y, Li Y, Zhang Y, Zhuang Y, Su H, Fu W, Huang Y, Li C, Zhao ZK, Sun Y, Chen GQ, Zhao X, Huang H, Zheng Y, Yang L, Su Z, Ma G, Ying H, Chen J, Tan T, Yuan Y. Biochemical engineering in China. REV CHEM ENG 2019. [DOI: 10.1515/revce-2017-0035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Abstract
Chinese biochemical engineering is committed to supporting the chemical and food industries, to advance science and technology frontiers, and to meet major demands of Chinese society and national economic development. This paper reviews the development of biochemical engineering, strategic deployment of these technologies by the government, industrial demand, research progress, and breakthroughs in key technologies in China. Furthermore, the outlook for future developments in biochemical engineering in China is also discussed.
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Affiliation(s)
- Mingzhu Ding
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University , Tianjin 300072 , China
| | - Biqiang Chen
- Beijing University of Chemical Technology , Beijing 100029 , China
| | - Xiaojun Ji
- College of Pharmaceutical Sciences, Nanjing Tech University , Nanjing 211816 , China
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , Nanjing 210009 , China
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University , Nanjing 210009 , China
| | - Jingwen Zhou
- School of Biotechnology, Jiangnan University , Wuxi 214122 , China
| | - Huiyuan Wang
- Shanghai Information Center of Life Sciences (SICLS), Shanghai Institute of Biology Sciences (SIBS), Chinese Academy of Sciences , Shanghai 200031 , China
| | - Xiwei Tian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai 200237 , China
| | - Xudong Feng
- School of Life Science, Beijing Institute of Technology , Beijing 100081 , China
| | - Hua Yue
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences , Beijing 100190 , China
| | - Yongjin Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023 , China
| | - Hailong Wang
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University , Jinan 250100 , China
| | - Jianping Wu
- Institute of Biology Engineering, College of Chemical and Biological Engineering, Zhejiang University , Hangzhou 310027 , China
| | - Pengpeng Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , Nanjing 210009 , China
- National Engineering Technique Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University , Nanjing 210009 , China
| | - Yu Jiang
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai 200032 , China
| | - Xuming Mao
- Institute of Pharmaceutical Biotechnology, Zhejiang University , Hangzhou 310058 , China
| | - Gang Xiao
- Beijing University of Chemical Technology , Beijing 100029 , China
| | - Cheng Zhong
- Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science and Technology , Tianjin 300457 , China
| | - Wenhai Xiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University , Tianjin 300072 , China
| | - Bingzhi Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University , Tianjin 300072 , China
| | - Lei Qin
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University , Tianjin 300072 , China
| | - Jingsheng Cheng
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University , Tianjin 300072 , China
| | - Mingdong Yao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University , Tianjin 300072 , China
| | - Ying Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University , Tianjin 300072 , China
| | - Hong Liu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University , Tianjin 300072 , China
| | - Lin Zhang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
| | - Linling Yu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
| | - Tao Chen
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
| | - Xiaoyan Dong
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
| | - Xiaoqiang Jia
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
| | - Songping Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences , Beijing 100190 , China
| | - Yanfeng Liu
- School of Biotechnology, Jiangnan University , Wuxi 214122 , China
| | - Yong Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , Nanjing 210009 , China
- National Engineering Technique Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University , Nanjing 210009 , China
| | - Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , Nanjing 210009 , China
- National Engineering Technique Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University , Nanjing 210009 , China
| | - Jinglan Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , Nanjing 210009 , China
- National Engineering Technique Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University , Nanjing 210009 , China
| | - Chenjie Zhu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , Nanjing 210009 , China
- National Engineering Technique Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University , Nanjing 210009 , China
| | - Wei Zhuang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , Nanjing 210009 , China
- National Engineering Technique Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University , Nanjing 210009 , China
| | - Sheng Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , Nanjing 210009 , China
- National Engineering Technique Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University , Nanjing 210009 , China
| | - Pengfei Jiao
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , Nanjing 210009 , China
- National Engineering Technique Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University , Nanjing 210009 , China
| | - Lei Zhang
- Tianjin Ltd. of BoyaLife Inc. , Tianjin 300457 , China
| | - Hao Song
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University , Tianjin 300072 , China
| | - Sheng Yang
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai 200032 , China
| | - Yan Xiong
- Shanghai Information Center of Life Sciences (SICLS), Shanghai Institute of Biology Sciences (SIBS), Chinese Academy of Sciences , Shanghai 200031 , China
| | - Yongquan Li
- Institute of Pharmaceutical Biotechnology, Zhejiang University , Hangzhou 310058 , China
| | - Youming Zhang
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University , Jinan 250100 , China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai 200237 , China
| | - Haijia Su
- Beijing University of Chemical Technology , Beijing 100029 , China
| | - Weiping Fu
- China National Center of Biotechnology Development , Beijing , China
| | - Yingming Huang
- China National Center of Biotechnology Development , Beijing , China
| | - Chun Li
- School of Life Science, Beijing Institute of Technology , Beijing 100081 , China
| | - Zongbao K. Zhao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023 , China
| | - Yan Sun
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
| | - Guo-Qiang Chen
- Center of Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing 100084 , China
| | - Xueming Zhao
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
| | - He Huang
- College of Pharmaceutical Sciences, Nanjing Tech University , Nanjing 211816 , China
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , Nanjing 210009 , China
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University , Nanjing 210009 , China
| | - Yuguo Zheng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology , Hangzhou 310014 , China
| | - Lirong Yang
- Institute of Biology Engineering, College of Chemical and Biological Engineering, Zhejiang University , Hangzhou 310027 , China
| | - Zhiguo Su
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences , Beijing 100190 , China
| | - Guanghui Ma
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences , Beijing 100190 , China
| | - Hanjie Ying
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , Nanjing 210009 , China
- National Engineering Technique Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University , Nanjing 210009 , China
| | - Jian Chen
- School of Biotechnology, Jiangnan University , Wuxi 214122 , China
| | - Tianwei Tan
- Beijing University of Chemical Technology , Beijing 100029 , China
| | - Yingjin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University , Tianjin 300072 , China
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18
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Xu K, Lee YS, Li J, Li C. Resistance mechanisms and reprogramming of microorganisms for efficient biorefinery under multiple environmental stresses. Synth Syst Biotechnol 2019; 4:92-98. [PMID: 30899819 PMCID: PMC6407310 DOI: 10.1016/j.synbio.2019.02.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/01/2019] [Accepted: 02/20/2019] [Indexed: 01/14/2023] Open
Abstract
In the fermentation process of biorefinery, industrial strains are normally subjected to adverse environmental stresses, which leads to their slow growth, yield decline, a substantial increase in energy consumption, and other negative consequences, which ultimately seriously hamper the development of biorefinery. How to minimize the impact of stress on microorganisms is of great significance. This review not only reveals the damaging effects of different environmental stresses on microbial strains but also introduces commonly used strategies to improve microbial tolerance, including adaptive evolution, reprogramming of the industrial host based on genetic circuits, global transcription machinery engineering (gTME) and bioprocess integration. Furthermore, by integrating the advantages of these strategies and reducing the cost of system operation, the tolerance of industrial strains, combined with production efficiency and process stability, will be greatly improved, and the development prospects of biorefinery will be more widespread.
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Affiliation(s)
- Ke Xu
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, PR China.,Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, PR China
| | - Yun Seo Lee
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, PR China
| | - Jun Li
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, PR China
| | - Chun Li
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, PR China
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19
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Xu K, Lv B, Huo YX, Li C. Toward the lowest energy consumption and emission in biofuel production: combination of ideal reactors and robust hosts. Curr Opin Biotechnol 2018; 50:19-24. [DOI: 10.1016/j.copbio.2017.08.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 10/18/2022]
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20
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Li P, Fu X, Zhang L, Zhang Z, Li J, Li S. The transcription factors Hsf1 and Msn2 of thermotolerant Kluyveromyces marxianus promote cell growth and ethanol fermentation of Saccharomyces cerevisiae at high temperatures. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:289. [PMID: 29213328 PMCID: PMC5713069 DOI: 10.1186/s13068-017-0984-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/26/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND High temperature inhibits cell growth and ethanol fermentation of Saccharomyces cerevisiae. As a complex phenotype, thermotolerance usually involves synergistic actions of many genes, thereby being difficult to engineer. The overexpression of either endogenous or exogenous stress-related transcription factor genes in yeasts was found to be able to improve relevant stress tolerance of the hosts. RESULTS To increase ethanol yield of high-temperature fermentation, we constructed a series of strains of S. cerevisiae by expressing 8 transcription factor genes from S. cerevisiae and 7 transcription factor genes from thermotolerant K. marxianus in S. cerevisiae. The results of growth curve measurements and spotting test show that KmHsf1 and KmMsn2 can enhance cell growth of S. cerevisiae at 40-42 °C. According to the results of batch fermentation at 43 °C with an initial glucose concentration of 104.8 g/l, the fermentation broths of KmHSF1 and KmMSN2-expressing strains could reach final ethanol concentrations of 27.2 ± 1.4 and 27.6 ± 1.2 g/l, respectively, while the control strain just produced 18.9 ± 0.3 g/l ethanol. Transcriptomic analysis found that the expression of KmHSF1 and KmMSN2 resulted in 55 (including 31 up-regulated and 24 down-regulated) and 50 (including 32 up-regulated and 18 down-regulated) genes with different expression levels, respectively (padj < 0.05). The results of transcriptomic analysis also reveal that KmHsf1 might increase ethanol production by regulating genes related to transporter activity to limit excessive ATP consumption and promote the uptake of glucose; while KmMsn2 might promote ethanol fermentation by regulating genes associated with glucose metabolic process and glycolysis/gluconeogenesis. In addition, KmMsn2 might also help to cope with high temperature by regulating genes associated with lipid metabolism to change the membrane fluidity. CONCLUSIONS The transcription factors KmHsf1 and KmMsn2 of thermotolerant K. marxianus can promote both cell growth and ethanol fermentation of S. cerevisiae at high temperatures. Different mechanisms of KmHsf1 and KmMsn2 in promoting high-temperature ethanol fermentation of S. cerevisiae were revealed by transcriptomic analysis.
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Affiliation(s)
- Pengsong Li
- Institute of New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Xiaofen Fu
- Institute of New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Lei Zhang
- Institute of New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Zhiyu Zhang
- Institute of New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Jihong Li
- Institute of New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Shizhong Li
- Institute of New Energy Technology, Tsinghua University, Beijing, 100084 China
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21
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Cell-free protein synthesis in micro compartments: building a minimal cell from biobricks. N Biotechnol 2017; 39:199-205. [DOI: 10.1016/j.nbt.2017.06.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 05/10/2017] [Accepted: 06/30/2017] [Indexed: 12/16/2022]
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22
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Engineering a riboswitch-based genetic platform for the self-directed evolution of acid-tolerant phenotypes. Nat Commun 2017; 8:411. [PMID: 28871084 PMCID: PMC5583362 DOI: 10.1038/s41467-017-00511-w] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 07/05/2017] [Indexed: 12/12/2022] Open
Abstract
Environmental pH is a fundamental signal continuously directing the metabolism and behavior of living cells. Programming the precise cellular response toward environmental pH is, therefore, crucial for engineering cells for increasingly sophisticated functions. Herein, we engineer a set of riboswitch-based pH-sensing genetic devices to enable the control of gene expression according to differential environmental pH. We next develop a digital pH-sensing system to utilize the analogue-sensing behavior of these devices for high-resolution recording of host cell exposure to discrete external pH levels. The application of this digital pH-sensing system is demonstrated in a genetic program that autonomously regulated the evolutionary engineering of host cells for improved tolerance to a broad spectrum of organic acids, a valuable phenotype for metabolic engineering and bioremediation applications. Cells are exposed to shifts in environmental pH, which direct their metabolism and behavior. Here the authors design pH-sensing riboswitches to create a gene expression program, digitalize the system to respond to a narrow pH range and apply it to evolve host cells with improved tolerance to a variety of organic acids.
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Abstract
Biomolecular temperature sensors can be used for efficient control of large-volume bioreactors, for spatiotemporal imaging and control of gene expression, and to engineer robustness to temperature in biomolecular circuit design. Although RNA-based sensors, called "thermometers", have been investigated in both natural and synthetic contexts, an important challenge is to design diverse responses to temperature differing in sensitivity and threshold. We address this issue by constructing a library of RNA thermometers based on thermodynamic computations and experimentally measuring their activities in cell-free biomolecular "breadboards". Using free energies of the minimum free energy structures as well as melt profile computations, we estimated that a diverse set of temperature responses were possible. We experimentally found a wide range of responses to temperature in the range 29-37 °C with fold-changes varying over 3-fold around the starting thermometer. The sensitivities of these responses ranged over 10-fold around the starting thermometer. We correlated these measurements with computational expectations, finding that although there was no strong correlation for the individual thermometers, overall trends of diversity, fold-changes, and sensitivities were similar. These results present a toolbox of RNA-based circuit elements with diverse temperature responses.
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Affiliation(s)
- Shaunak Sen
- Department
of Electrical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Divyansh Apurva
- Department
of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Rohit Satija
- Department
of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
- Institute
for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Dan Siegal
- Division
of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
- Schafer Corporation, Arlington, Virginia 22203, United States
| | - Richard M. Murray
- Division
of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
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24
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Guzmán-Trampe S, Ceapa CD, Manzo-Ruiz M, Sánchez S. Synthetic biology era: Improving antibiotic’s world. Biochem Pharmacol 2017; 134:99-113. [DOI: 10.1016/j.bcp.2017.01.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 01/26/2017] [Indexed: 12/12/2022]
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Sun H, Jia H, Li J, Feng X, Liu Y, Zhou X, Li C. Rational synthetic combination genetic devices boosting high temperature ethanol fermentation. Synth Syst Biotechnol 2017; 2:121-129. [PMID: 29062969 PMCID: PMC5636948 DOI: 10.1016/j.synbio.2017.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 03/21/2017] [Accepted: 04/25/2017] [Indexed: 11/27/2022] Open
Abstract
The growth and production of yeast in the industrial fermentation are seriously restrained by heat stress and exacerbated by heat induced oxidative stress. In this study, a novel synthetic biology approach was developed to globally boost the viability and production ability of S. cerevisiae at high temperature through rationally designing and combing heat shock protein (HSP) and superoxide dismutase (SOD) genetic devices to ultimately synergistically alleviate both heat stress and oxidative stress. HSP and SOD from extremophiles were constructed to be different genetic devices and they were preliminary screened by heat resistant experiments and anti-oxidative experiments, respectively. Then in order to customize and further improve thermotolerance of S. cerevisiae, the HSP genetic device and SOD genetic device were rationally combined. The results show the simply assemble of the same function genetic devices to solve heat stress or oxidative stress could not enhance the thermotolerance considerably. Only S. cerevisiae with the combination genetic device (FBA1p-sod-MB4-FBA1p-shsp-HB8) solving both stress showed 250% better thermotolerance than the control and displayed further 55% enhanced cell density compared with the strains with single FBA1p-sod-MB4 or FBA1p-shsp-HB8 at 42 °C. Then the most excellent combination genetic device was introduced into lab S. cerevisiae and industrial S. cerevisiae for ethanol fermentation. The ethanol yields of the two strains were increased by 20.6% and 26.3% compared with the control under high temperature, respectively. These results indicate synergistically defensing both heat stress and oxidative stress is absolutely necessary to enhance the thermotolerance and production of S. cerevisiae.
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Affiliation(s)
- Huan Sun
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Haiyang Jia
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Jun Li
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Xudong Feng
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Yueqin Liu
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, China
| | - Xiaohong Zhou
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, China
| | - Chun Li
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, China
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26
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Kuwahara H, Umarov R, Almasri I, Gao X. ACRE: Absolute concentration robustness exploration in module-based combinatorial networks. Synth Biol (Oxf) 2017; 2:ysx001. [PMID: 32995502 PMCID: PMC7513739 DOI: 10.1093/synbio/ysx001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 12/03/2016] [Accepted: 01/03/2017] [Indexed: 11/26/2022] Open
Abstract
To engineer cells for industrial-scale application, a deep understanding of how to design molecular control mechanisms to tightly maintain functional stability under various fluctuations is crucial. Absolute concentration robustness (ACR) is a category of robustness in reaction network models in which the steady-state concentration of a molecular species is guaranteed to be invariant even with perturbations in the other molecular species in the network. Here, we introduce a software tool, absolute concentration robustness explorer (ACRE), which efficiently explores combinatorial biochemical networks for the ACR property. ACRE has a user-friendly interface, and it can facilitate efficient analysis of key structural features that guarantee the presence and the absence of the ACR property from combinatorial networks. Such analysis is expected to be useful in synthetic biology as it can increase our understanding of how to design molecular mechanisms to tightly control the concentration of molecular species. ACRE is freely available at https://github.com/ramzan1990/ACRE.
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Affiliation(s)
- Hiroyuki Kuwahara
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia.,Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Ramzan Umarov
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia.,Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Islam Almasri
- Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia.,Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
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27
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Ma ZP, Lao YM, Jin H, Lin GH, Cai ZH, Zhou J. Diverse Profiles of AI-1 Type Quorum Sensing Molecules in Cultivable Bacteria from the Mangrove ( Kandelia obovata) Rhizosphere Environment. Front Microbiol 2016; 7:1957. [PMID: 27994584 PMCID: PMC5136546 DOI: 10.3389/fmicb.2016.01957] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/22/2016] [Indexed: 11/25/2022] Open
Abstract
Mangrove rhizosphere environment harbors diverse populations of microbes, and some evidence showed that rhizobacteria behavior was regulated by quorum sensing (QS). Investigating the diverse profiles of QS molecules in mangrove ecosystems may shed light on the bacterial roles and lead to a better understanding of the symbiotic interactions between plants and microbes. The aims of the current study focus on identifying AI-1 type QS signals, i.e., acyl homoserine lactones (AHLs), in Kandelia obovata rhizosphere environment. Approximately 1200 rhizobacteria were screened and 184 strains (15.3%) tested were positive. Subsequent 16s rRNA gene sequencing and dereplication analyses identified 24 species from the positive isolates, which were affiliated to three different phyla, including Proteobacteria, Firmicutes, and Actinobacteria. Thin-layer chromatography separation of extracts revealed diverse AHL profiles and detected at least one active compound in the supernatant of these 24 cultivable AHL-producers. The active extracts from these bacterial isolates were further evaluated by ultra performance liquid chromatography-mass spectrometry, and the carbon side chain length ranged from C4 to C14. This is the first report on the diversity of AI-1 type auto-inducers in the mangrove plant K. obovata, and it is imperative to expand our knowledge of plant-bacteria interactions with respect to the maintenance of wetland ecosystem health.
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Affiliation(s)
- Zhi P Ma
- The Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua UniversityShenzhen, China; Shenzhen Public Platform for Screening and Application of Marine Microbial ResourcesShenzhen, China
| | - Yong M Lao
- The Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua UniversityShenzhen, China; Shenzhen Public Platform for Screening and Application of Marine Microbial ResourcesShenzhen, China
| | - Hui Jin
- The Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua UniversityShenzhen, China; Shenzhen Public Platform for Screening and Application of Marine Microbial ResourcesShenzhen, China
| | - Guang H Lin
- The Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua University Shenzhen, China
| | - Zhong H Cai
- The Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua UniversityShenzhen, China; Shenzhen Public Platform for Screening and Application of Marine Microbial ResourcesShenzhen, China
| | - Jin Zhou
- The Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua UniversityShenzhen, China; Shenzhen Public Platform for Screening and Application of Marine Microbial ResourcesShenzhen, China
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