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Li C, Shi T, Fan W, Yuan M, Li L, Yu Z, Chen Z, Xu Q. High-level and -yield orotic acid production in Escherichia coli through systematic modular engineering and "Chaos to Order Cycles" fermentation. BIORESOURCE TECHNOLOGY 2024; 411:131345. [PMID: 39182798 DOI: 10.1016/j.biortech.2024.131345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 08/03/2024] [Accepted: 08/22/2024] [Indexed: 08/27/2024]
Abstract
Orotic acid is widely used in healthcare and cosmetic industries. However, orotic acid-producing microorganisms are auxotrophic, which results in inefficient microbial production. Herein, a plasmid-free, uninduced, non-auxotrophic orotic acid hyperproducer was constructed from Escherichia coli W3110. Initially, the orotic acid degradation pathway was blocked and the carbamoyl phosphate supply was enriched. Subsequently, pyr operon from Bacillus subtilis F126 was heterologously expressed and precursors' supply was optimized. Thereafter, pyrE was dynamically regulated to reconstruct the non-auxotrophic pathway. Employing fed-batch cultivation, orotic acid titer, yield, and productivity of strain Ora21 reached 182.5 g/L, 0.58 g/g, and 3.80 g/L/h, respectively, the highest levels reported so far. Finally, a novel "Chaos to Order Cycles (COC)" fermentation was developed, which effectively increased the yield to 0.63 g/g. This research is a remarkable achievement in orotic acid production by microbial fermentation and has vast potential for industrial applications.
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Affiliation(s)
- Changgeng Li
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China; Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Tangen Shi
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China; Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Wenjing Fan
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China; Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Meng Yuan
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China; Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Lanxiao Li
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China; Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Zichen Yu
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China; Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Zhichao Chen
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China; Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Qingyang Xu
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China; Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science & Technology, Tianjin 300457, PR China.
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2
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Liu D, Wang L, Ma L, Wang X, Li S, Zhou J. Metabolic network rewiring and temperature-dependent regulation for enhanced 3-dehydroshikimate production in Escherichia coli. BIORESOURCE TECHNOLOGY 2024; 412:131403. [PMID: 39222859 DOI: 10.1016/j.biortech.2024.131403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 08/28/2024] [Accepted: 08/30/2024] [Indexed: 09/04/2024]
Abstract
The cyclohexane organic acid 3-dehydroshikimate (DHS) has potent antioxidant activity and is widely utilised in chemical and pharmaceutical industries. However, its production requires a long fermentation with a suboptimal yield and low productivity, and a disproportionate growth-to-production ratio impedes the upscaling of DHS synthesis in microbial cell factories. To overcome these limitations, competing and degradation pathways were knocked-out and key enzymes were balanced in an engineered Escherichia coli production strain, resulting in 12.2 g/L DHS. Furthermore, to achieve equilibrium between cell growth and DHS production, a CRISPRi-based temperature-responsive multi-component repressor system was developed to dynamically control the expression of critical genes (pykF and aroE), resulting in a 30-fold increase in DHS titer. After 33 h fermentation in 5 L bioreactor, the DHS titer, productivity and yield reached 94.2 g/L, 2.8 g/L/h and 55 % glucose conversion, respectively. The results provided valuable insight into the production of DHS and its derivatives.
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Affiliation(s)
- Dongming Liu
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education On Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Lian Wang
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education On Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Lingling Ma
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education On Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Xuyang Wang
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education On Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shan Li
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education On Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education On Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China.
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3
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Mao J, Zhang H, Chen Y, Wei L, Liu J, Nielsen J, Chen Y, Xu N. Relieving metabolic burden to improve robustness and bioproduction by industrial microorganisms. Biotechnol Adv 2024; 74:108401. [PMID: 38944217 DOI: 10.1016/j.biotechadv.2024.108401] [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: 02/01/2024] [Revised: 05/04/2024] [Accepted: 06/25/2024] [Indexed: 07/01/2024]
Abstract
Metabolic burden is defined by the influence of genetic manipulation and environmental perturbations on the distribution of cellular resources. The rewiring of microbial metabolism for bio-based chemical production often leads to a metabolic burden, followed by adverse physiological effects, such as impaired cell growth and low product yields. Alleviating the burden imposed by undesirable metabolic changes has become an increasingly attractive approach for constructing robust microbial cell factories. In this review, we provide a brief overview of metabolic burden engineering, focusing specifically on recent developments and strategies for diminishing the burden while improving robustness and yield. A variety of examples are presented to showcase the promise of metabolic burden engineering in facilitating the design and construction of robust microbial cell factories. Finally, challenges and limitations encountered in metabolic burden engineering are discussed.
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Affiliation(s)
- Jiwei Mao
- Department of Life Sciences, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Hongyu Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yu Chen
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, PR China
| | - Liang Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Jun Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Jens Nielsen
- Department of Life Sciences, Chalmers University of Technology, SE412 96 Gothenburg, Sweden; BioInnovation Institute, Ole Maaløes Vej 3, DK2200 Copenhagen, Denmark.
| | - Yun Chen
- Department of Life Sciences, Chalmers University of Technology, SE412 96 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Kongens Lyngby, Denmark.
| | - Ning Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China.
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4
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Park JH, Holló G, Schaerli Y. From resonance to chaos by modulating spatiotemporal patterns through a synthetic optogenetic oscillator. Nat Commun 2024; 15:7284. [PMID: 39179558 PMCID: PMC11343849 DOI: 10.1038/s41467-024-51626-w] [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: 04/09/2024] [Accepted: 08/14/2024] [Indexed: 08/26/2024] Open
Abstract
Oscillations are a recurrent phenomenon in biological systems across scales, but deciphering their fundamental principles is very challenging. Here, we tackle this challenge by redesigning the wellcharacterised synthetic oscillator known as "repressilator" in Escherichia coli and controlling it using optogenetics, creating the "optoscillator". Bacterial colonies manifest oscillations as spatial ring patterns. When we apply periodic light pulses, the optoscillator behaves as a forced oscillator and we systematically investigate the properties of the rings under various light conditions. Combining experiments with mathematical modeling, we demonstrate that this simple oscillatory circuit can generate complex dynamics that are transformed into distinct spatial patterns. We report the observation of synchronisation, resonance, subharmonic resonance and period doubling. Furthermore, we present evidence of a chaotic regime. This work highlights the intricate spatiotemporal patterns accessible by synthetic oscillators and underscores the potential of our approach in revealing fundamental principles of biological oscillations.
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Affiliation(s)
- Jung Hun Park
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Gábor Holló
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
| | - Yolanda Schaerli
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
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5
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Joshi SHN, Jenkins C, Ulaeto D, Gorochowski TE. Accelerating Genetic Sensor Development, Scale-up, and Deployment Using Synthetic Biology. BIODESIGN RESEARCH 2024; 6:0037. [PMID: 38919711 PMCID: PMC11197468 DOI: 10.34133/bdr.0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/23/2024] [Indexed: 06/27/2024] Open
Abstract
Living cells are exquisitely tuned to sense and respond to changes in their environment. Repurposing these systems to create engineered biosensors has seen growing interest in the field of synthetic biology and provides a foundation for many innovative applications spanning environmental monitoring to improved biobased production. In this review, we present a detailed overview of currently available biosensors and the methods that have supported their development, scale-up, and deployment. We focus on genetic sensors in living cells whose outputs affect gene expression. We find that emerging high-throughput experimental assays and evolutionary approaches combined with advanced bioinformatics and machine learning are establishing pipelines to produce genetic sensors for virtually any small molecule, protein, or nucleic acid. However, more complex sensing tasks based on classifying compositions of many stimuli and the reliable deployment of these systems into real-world settings remain challenges. We suggest that recent advances in our ability to precisely modify nonmodel organisms and the integration of proven control engineering principles (e.g., feedback) into the broader design of genetic sensing systems will be necessary to overcome these hurdles and realize the immense potential of the field.
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Affiliation(s)
| | - Christopher Jenkins
- CBR Division, Defence Science and Technology Laboratory, Porton Down, Wiltshire SP4 0JQ, UK
| | - David Ulaeto
- CBR Division, Defence Science and Technology Laboratory, Porton Down, Wiltshire SP4 0JQ, UK
| | - Thomas E. Gorochowski
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
- BrisEngBio,
School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
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6
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Toya Y, Shimizu H. Coupling and uncoupling growth and product formation for producing chemicals. Curr Opin Biotechnol 2024; 87:103133. [PMID: 38640846 DOI: 10.1016/j.copbio.2024.103133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/31/2024] [Accepted: 04/01/2024] [Indexed: 04/21/2024]
Abstract
Microbial fermentation employs two strategies: growth- and nongrowth-coupled productions. Stoichiometric metabolic models with flux balance analysis enable pathway engineering to couple target synthesis with growth, yielding numerous successful results. Growth-coupled engineering also contributes to improving bottleneck flux through subsequent adaptive evolution. However, because growth-coupled production inevitably shares resources between biomass and target syntheses, the cost-effective production of bulk chemicals mandates a nongrowth-coupled approach. In such processes, understanding how and when to transition the metabolic state from growth to production modes becomes crucial, as does maintaining cellular activity during the nongrowing state to achieve high productivity. In this paper, we review recent technologies for growth-coupled and nongrowth-coupled production, considering their advantages and disadvantages.
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Affiliation(s)
- Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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7
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Ji L, Zhang W, Zhang Y, Nian B, Hu Y. Functionalized Ionic Liquids-Modified Metal-Organic Framework Material Boosted the Enzymatic Performance of Lipase. Molecules 2024; 29:2381. [PMID: 38792242 PMCID: PMC11124374 DOI: 10.3390/molecules29102381] [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: 04/15/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
The development of immobilized enzymes with high activity and stability is critical. Metal-organic frameworks (MOFs) have attracted much academic and industrial interest in the field of enzyme immobilization due to their unique properties. In this study, the amino-functionalized ionic liquid (NIL)-modified metal-organic framework (UiO-66-NH2) was prepared to immobilize Candida rugosa lipase (CRL), using dialdehyde starch (DAS) as the cross-linker. The results of the Fourier transform infrared (FT-IR) spectra, X-ray powder diffraction (XRD), and scanning electronic microscopy (SEM) confirmed that the NIL was successfully grafted to UiO-66-NH2. The CRL immobilized on NIL-modified UiO-66-NH2 (UiO-66-NH2-NIL-DAS@CRL) exhibited satisfactory activity recovery (79.33%), stability, reusability, and excellent organic solvent tolerance. The research results indicated that ionic liquid-modified UiO-66-NH2 had practical potential for application in enzyme immobilization.
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Affiliation(s)
| | | | | | - Binbin Nian
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, China; (L.J.); (W.Z.); (Y.Z.)
| | - Yi Hu
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, China; (L.J.); (W.Z.); (Y.Z.)
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8
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Yu L, Gao Y, He Y, Liu Y, Shen J, Liang H, Gong R, Duan H, Price NPJ, Song X, Deng Z, Chen W. Developing the E. coli platform for efficient production of UMP-derived chemicals. Metab Eng 2024; 83:61-74. [PMID: 38522576 DOI: 10.1016/j.ymben.2024.03.004] [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: 11/03/2023] [Revised: 03/10/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024]
Abstract
5-Methyluridine (5-MU) is a prominent intermediate for industrial synthesis of several antiviral-drugs, however, its availability over the past decades has overwhelmingly relied on chemical and enzymatic strategies. Here, we have realized efficient production of 5-MU in E. coli, for the first time, via a designer artificial pathway consisting of a two-enzyme cascade (UMP 5-methylase and phosphatase). More importantly, we have engineered the E. coli cell factory to boost 5-MU production by systematic evaluation of multiple strategies, and as a proof of concept, we have further developed an antibiotic-free fermentation strategy to realize 5-MU production (10.71 g/L) in E. coli MB229 (a ΔthyA strain). Remarkably, we have also established a versatile and robust platform with exploitation of the engineered E. coli for efficient production of diversified UMP-derived chemicals. This study paves the way for future engineering of E. coli as a synthetic biology platform for acceleratively accessing UMP-derived chemical diversities.
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Affiliation(s)
- Le Yu
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yaojie Gao
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yuanyuan He
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yang Liu
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Jianning Shen
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Han Liang
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Rong Gong
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - He Duan
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Neil P J Price
- US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Xuemin Song
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Zixin Deng
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Wenqing Chen
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
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9
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Buson F, Gao Y, Wang B. Genetic Parts and Enabling Tools for Biocircuit Design. ACS Synth Biol 2024; 13:697-713. [PMID: 38427821 DOI: 10.1021/acssynbio.3c00691] [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: 03/03/2024]
Abstract
Synthetic biology aims to engineer biological systems for customized tasks through the bottom-up assembly of fundamental building blocks, which requires high-quality libraries of reliable, modular, and standardized genetic parts. To establish sets of parts that work well together, synthetic biologists created standardized part libraries in which every component is analyzed in the same metrics and context. Here we present a state-of-the-art review of the currently available part libraries for designing biocircuits and their gene expression regulation paradigms at transcriptional, translational, and post-translational levels in Escherichia coli. We discuss the necessary facets to integrate these parts into complex devices and systems along with the current efforts to catalogue and standardize measurement data. To better display the range of available parts and to facilitate part selection in synthetic biology workflows, we established biopartsDB, a curated database of well-characterized and useful genetic part and device libraries with detailed quantitative data validated by the published literature.
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Affiliation(s)
- Felipe Buson
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, U.K
| | - Yuanli Gao
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, U.K
| | - Baojun Wang
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
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10
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Zhao C, Li X, Guo L, Gao C, Song W, Wei W, Wu J, Liu L, Chen X. Reprogramming Metabolic Flux in Escherichia Coli to Enhance Chondroitin Production. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307351. [PMID: 38145357 PMCID: PMC10933623 DOI: 10.1002/advs.202307351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/14/2023] [Indexed: 12/26/2023]
Abstract
Reprogramming metabolic flux is a promising approach for constructing efficient microbial cell factories (MCFs) to produce chemicals. However, how to boost the transmission efficiency of metabolic flux is still challenging in complex metabolic pathways. In this study, metabolic flux is systematically reprogrammed by regulating flux size, flux direction, and flux rate to build an efficient MCF for chondroitin production. The ammoniation pool for UDP-GalNAc synthesis and the carbonization pool for UDP-GlcA synthesis are first enlarged to increase flux size for providing enough precursors for chondroitin biosynthesis. Then, the ammoniation pool and the carbonization pool are rematched using molecular valves to shift flux direction from cell growth to chondroitin biosynthesis. Next, the adaptability of polymerization pool with the ammoniation and carbonization pools is fine-tuned by dynamic and static valve-based adapters to accelerate flux rate for polymerizing UDP-GalNAc and UDP-GlcA to produce chondroitin. Finally, the engineered strain E. coli F51 is able to produce 9.2 g L-1 chondroitin in a 5-L bioreactor. This strategy shown here provides a systematical approach for regulating metabolic flux in complex metabolic pathways for efficient biosynthesis of chemicals.
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Affiliation(s)
- Chunlei Zhao
- State Key Laboratory of Food Science and ResourcesJiangnan UniversityWuxi214122China
- International Joint Laboratory on Food SafetyJiangnan UniversityWuxi214122China
| | - Xiaomin Li
- State Key Laboratory of Food Science and ResourcesJiangnan UniversityWuxi214122China
- International Joint Laboratory on Food SafetyJiangnan UniversityWuxi214122China
| | - Liang Guo
- State Key Laboratory of Food Science and ResourcesJiangnan UniversityWuxi214122China
- International Joint Laboratory on Food SafetyJiangnan UniversityWuxi214122China
| | - Cong Gao
- State Key Laboratory of Food Science and ResourcesJiangnan UniversityWuxi214122China
- International Joint Laboratory on Food SafetyJiangnan UniversityWuxi214122China
| | - Wei Song
- School of Life Sciences and Health EngineeringJiangnan UniversityWuxi214122China
| | - Wanqing Wei
- State Key Laboratory of Food Science and ResourcesJiangnan UniversityWuxi214122China
- International Joint Laboratory on Food SafetyJiangnan UniversityWuxi214122China
| | - Jing Wu
- School of Life Sciences and Health EngineeringJiangnan UniversityWuxi214122China
| | - Liming Liu
- State Key Laboratory of Food Science and ResourcesJiangnan UniversityWuxi214122China
- International Joint Laboratory on Food SafetyJiangnan UniversityWuxi214122China
| | - Xiulai Chen
- State Key Laboratory of Food Science and ResourcesJiangnan UniversityWuxi214122China
- International Joint Laboratory on Food SafetyJiangnan UniversityWuxi214122China
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11
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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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12
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Ma Y, Ye JW, Lin Y, Yi X, Wang X, Wang H, Huang R, Wu F, Wu Q, Liu X, Chen GQ. Flux optimization using multiple promoters in Halomonas bluephagenesis as a model chassis of the next generation industrial biotechnology. Metab Eng 2024; 81:249-261. [PMID: 38159902 DOI: 10.1016/j.ymben.2023.12.011] [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: 10/15/2023] [Revised: 12/16/2023] [Accepted: 12/24/2023] [Indexed: 01/03/2024]
Abstract
Predictability and robustness are challenges for bioproduction because of the unstable intracellular synthetic activities. With the deeper understanding of the gene expression process, fine-tuning has become a meaningful tool for biosynthesis optimization. This study characterized several gene expression elements and constructed a multiple inducible system that responds to ten different small chemical inducers in halophile bacterium Halomonas bluephagenesis. Genome insertion of regulators was conducted for the purpose of gene cluster stabilization and regulatory plasmid simplification. Additionally, dynamic ranges of the multiple inducible systems were tuned by promoter sequence mutations to achieve diverse scopes for high-resolution gene expression control. The multiple inducible system was successfully employed to precisely control chromoprotein expression, lycopene and poly-3-hydroxybutyrate (PHB) biosynthesis, resulting in colorful bacterial pictures, optimized cell growth, lycopene and PHB accumulation. This study demonstrates a desirable approach for fine-tuning of rational and efficient gene expressions, displaying the significance for metabolic pathway optimization.
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Affiliation(s)
- Yueyuan Ma
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jian-Wen Ye
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yina Lin
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xueqing Yi
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xuan Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Huan Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Ruiyan Huang
- Garrison Forest School, Owings Mills, MD, 21117, USA
| | - Fuqing Wu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiong Wu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xu Liu
- PhaBuilder Biotech Co. Ltd., Beijing, 101309, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China; MOE Key Laboratory for Industrial Biocatalysts, Dept Chemical Engineering, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
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13
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Gao Y, Wang L, Wang B. Customizing cellular signal processing by synthetic multi-level regulatory circuits. Nat Commun 2023; 14:8415. [PMID: 38110405 PMCID: PMC10728147 DOI: 10.1038/s41467-023-44256-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023] Open
Abstract
As synthetic biology permeates society, the signal processing circuits in engineered living systems must be customized to meet practical demands. Towards this mission, novel regulatory mechanisms and genetic circuits with unprecedented complexity have been implemented over the past decade. These regulatory mechanisms, such as transcription and translation control, could be integrated into hybrid circuits termed "multi-level circuits". The multi-level circuit design will tremendously benefit the current genetic circuit design paradigm, from modifying basic circuit dynamics to facilitating real-world applications, unleashing our capabilities to customize cellular signal processing and address global challenges through synthetic biology.
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Affiliation(s)
- Yuanli Gao
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310058, China
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Lei Wang
- Center of Synthetic Biology and Integrated Bioengineering & School of Engineering, Westlake University, Hangzhou, 310030, China.
| | - Baojun Wang
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310058, China.
- Research Center for Biological Computation, Zhejiang Lab, Hangzhou, 311100, China.
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14
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Effendi SSW, Ng IS. Challenges and opportunities for engineered Escherichia coli as a pivotal chassis toward versatile tyrosine-derived chemicals production. Biotechnol Adv 2023; 69:108270. [PMID: 37852421 DOI: 10.1016/j.biotechadv.2023.108270] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/30/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
Growing concerns over limited fossil resources and associated environmental problems are motivating the development of sustainable processes for the production of high-volume fuels and high-value-added compounds. The shikimate pathway, an imperative pathway in most microorganisms, is branched with tyrosine as the rate-limiting step precursor of valuable aromatic substances. Such occurrence suggests the shikimate pathway as a promising route in developing microbial cell factories with multiple applications in the nutraceutical, pharmaceutical, and chemical industries. Therefore, an increasing number of studies have focused on this pathway to enable the biotechnological manufacture of pivotal and versatile aromatic products. With advances in genome databases and synthetic biology tools, genetically programmed Escherichia coli strains are gaining immense interest in the sustainable synthesis of chemicals. Engineered E. coli is expected to be the next bio-successor of fossil fuels and plants in commercial aromatics synthesis. This review summarizes successful and applicable genetic and metabolic engineering strategies to generate new chassis and engineer the iterative pathway of the tyrosine route in E. coli, thus addressing the opportunities and current challenges toward the realization of sustainable tyrosine-derived aromatics.
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Affiliation(s)
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan.
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15
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Arboleda-García A, Alarcon-Ruiz I, Boada-Acosta L, Boada Y, Vignoni A, Jantus-Lewintre E. Advancements in synthetic biology-based bacterial cancer therapy: A modular design approach. Crit Rev Oncol Hematol 2023; 190:104088. [PMID: 37541537 DOI: 10.1016/j.critrevonc.2023.104088] [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: 06/10/2023] [Revised: 07/18/2023] [Accepted: 07/31/2023] [Indexed: 08/06/2023] Open
Abstract
Synthetic biology aims to program living bacteria cells with artificial genetic circuits for user-defined functions, transforming them into powerful tools with numerous applications in various fields, including oncology. Cancer treatments have serious side effects on patients due to the systemic action of the drugs involved. To address this, new systems that provide localized antitumoral action while minimizing damage to healthy tissues are required. Bacteria, often considered pathogenic agents, have been used as cancer treatments since the early 20th century. Advances in genetic engineering, synthetic biology, microbiology, and oncology have improved bacterial therapies, making them safer and more effective. Here we propose six modules for a successful synthetic biology-based bacterial cancer therapy, the modules include Payload, Release, Tumor-targeting, Biocontainment, Memory, and Genetic Circuit Stability Module. These will ensure antitumor activity, safety for the environment and patient, prevent bacterial colonization, maintain cell stability, and prevent loss or defunctionalization of the genetic circuit.
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Affiliation(s)
- Andrés Arboleda-García
- Systems Biology and Biosystems Control Lab, Instituto de Automática e Informática Industrial, Universitat Politècnica de València, Spain
| | - Ivan Alarcon-Ruiz
- Gene Regulation in Cardiovascular Remodeling and Inflammation Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain; Departamento de Biología Molecular, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Lissette Boada-Acosta
- Centro de Investigación Biomédica en Red Cáncer, CIBERONC, Madrid, Spain; TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación Investigación del Hospital General Universitario de Valencia, Valencia, Spain; Molecular Oncology Laboratory, Fundación Investigación del Hospital General Universitario de Valencia, Valencia, Spain
| | - Yadira Boada
- Systems Biology and Biosystems Control Lab, Instituto de Automática e Informática Industrial, Universitat Politècnica de València, Spain
| | - Alejandro Vignoni
- Systems Biology and Biosystems Control Lab, Instituto de Automática e Informática Industrial, Universitat Politècnica de València, Spain.
| | - Eloisa Jantus-Lewintre
- Centro de Investigación Biomédica en Red Cáncer, CIBERONC, Madrid, Spain; TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación Investigación del Hospital General Universitario de Valencia, Valencia, Spain; Molecular Oncology Laboratory, Fundación Investigación del Hospital General Universitario de Valencia, Valencia, Spain; Department of Biotechnology, Universitat Politècnica de València, Valencia, Spain
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16
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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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17
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Jiang T, Li C, Teng Y, Zhang J, Logan DA, Yan Y. Dynamic Metabolic Control: From the Perspective of Regulation Logic. SYNTHETIC BIOLOGY AND ENGINEERING 2023; 1:10012. [PMID: 38572077 PMCID: PMC10986841 DOI: 10.35534/sbe.2023.10012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Establishing microbial cell factories has become a sustainable and increasingly promising approach for the synthesis of valuable chemicals. However, introducing heterologous pathways into these cell factories can disrupt the endogenous cellular metabolism, leading to suboptimal production performance. To address this challenge, dynamic pathway regulation has been developed and proven effective in improving microbial biosynthesis. In this review, we summarized typical dynamic regulation strategies based on their control logic. The applicable scenarios for each control logic were highlighted and perspectives for future research direction in this area were discussed.
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Affiliation(s)
- Tian Jiang
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Chenyi Li
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Yuxi Teng
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Jianli Zhang
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Diana Alexis Logan
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Yajun Yan
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
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18
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Rao Y, Wang J, Yang X, Xie X, Zhan Y, Ma X, Cai D, Chen S. A novel toolbox for precise regulation of gene expression and metabolic engineering in Bacillus licheniformis. Metab Eng 2023; 78:159-170. [PMID: 37307865 DOI: 10.1016/j.ymben.2023.06.004] [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: 02/01/2023] [Revised: 05/15/2023] [Accepted: 06/05/2023] [Indexed: 06/14/2023]
Abstract
Despite industrial bio-manufacturing progress using Bacillus licheniformis, the absence of a well-characterized toolbox allowing precise regulation of multiple genes limits its expansion for basic research and application. Here, a novel gene expression toolbox (GET) was developed for precise regulation of gene expression and high-level production of 2-phenylethanol. Firstly, we established a novel promoter core region mosaic combination model to combine, characterize and analyze different core regions. Characterization and orthogonal design of promoter ribbons allowed convenient construction of an adaptable and robust GET, gene gfp expression intensity was 0.64%-16755.77%, with a dynamic range of 2.61 × 104 times, which is the largest regulatory range of GET in Bacillus based on modification of promoter P43. Then we verified the protein and species universality of GET using different proteins expressed in B. licheniformis and Bacillus subtilis. Finally, the GET for 2-phenylethanol metabolic breeding, resulting in a plasmid-free strain producing 6.95 g/L 2-phenylethanol with a yield and productivity of 0.15 g/g glucose and 0.14 g/L/h, respectively, the highest de novo synthesis yield of 2-phenylethanol reported. Taken together, this is the first report elucidating the impact of mosaic combination and tandem of multiple core regions to initiate transcription and improve the output of proteins and metabolites, which provides strong support for gene regulation and diversified product production in Bacillus.
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Affiliation(s)
- Yi Rao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Jiaqi Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Xinyuan Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Xinxin Xie
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Yangyang Zhan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Xin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Dongbo Cai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China.
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China.
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19
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Bo T, Wu C, Wang Z, Jiang H, Wang F, Chen N, Li Y. Multiple Metabolic Engineering Strategies to Improve Shikimate Titer in Escherichia coli. Metabolites 2023; 13:747. [PMID: 37367905 DOI: 10.3390/metabo13060747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/28/2023] Open
Abstract
Shikimate is a valuable chiral precursor for synthesizing oseltamivir (Tamiflu®) and other chemicals. High production of shikimate via microbial fermentation has attracted increasing attention to overcome the unstable and expensive supply of shikimate extracted from plant resources. The current cost of microbial production of shikimate via engineered strains is still unsatisfactory, and thus more metabolic strategies need to be investigated to further increase the production efficiency. In this study, we first constructed a shikimate E. coli producer through the application of the non-phosphoenolpyruvate: carbohydrate phosphotransferase system (non-PTS) glucose uptake pathway, the attenuation of the shikimate degradation metabolism, and the introduction of a mutant of feedback-resistant 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase. Inspired by the natural presence of bifunctional 3-dehydroquinate dehydratase (DHD)-shikimate dehydrogenase (SDH) enzyme in plants, we then designed an artificial fusion protein of DHD-SDH to decrease the accumulation of the byproduct 3-dehydroshikimate (DHS). Subsequently, a repressed shikimate kinase (SK) mutant was selected to promote shikimate accumulation without the supplementation of expensive aromatic substances. Furthermore, EsaR-based quorum sensing (QS) circuits were employed to regulate the metabolic flux distribution between cell growth and product synthesis. The final engineered strain dSA10 produced 60.31 g/L shikimate with a yield of 0.30 g/g glucose in a 5 L bioreactor.
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Affiliation(s)
- Taidong Bo
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Chen Wu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zeting Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Hao Jiang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Feiao Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Ning Chen
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yanjun Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China
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20
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Han Y, Jiang SZ, Zhong X, Chen X, Ma CK, Yang YM, Mao YC, Zhou SD, Zhou L, Zhang YF, Huang XH, Zhang H, Li LG, Zhu J, Yang ZN. Low temperature compensates for defective tapetum initiation to restore the fertility of the novel TGMS line ostms15. PLANT BIOTECHNOLOGY JOURNAL 2023. [PMID: 37205779 PMCID: PMC10363753 DOI: 10.1111/pbi.14066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/29/2023] [Accepted: 04/24/2023] [Indexed: 05/21/2023]
Abstract
In rice breeding, thermosensitive genic male sterility (TGMS) lines based on the tms5 locus have been extensively employed. Here, we reported a novel rice TGMS line ostms15 (Oryza sativa ssp. japonica ZH11) which show male sterility under high temperature and fertility under low temperature. Field evaluation from 2018 to 2021 revealed that its sterility under high temperature is more stable than that of tms5 (ZH11), even with occasional low temperature periods, indicating its considerable value for rice breeding. OsTMS15 encodes an LRR-RLK protein MULTIPLE SPOROCYTE1 (MSP1) which was reported to interact with its ligand to initiate tapetum development for pollen formation. In ostms15, a point mutation from GTA (Val) to GAA (Glu) in its TIR motif of the LRR region led to the TGMS phenotype. Cellular observation and gene expression analysis showed that the tapetum is still present in ostms15, while its function was substantially impaired under high temperature. However, its tapetum function was restored under low temperature. The interaction between mOsTMS15 and its ligand was reduced while this interaction was partially restored under low temperature. Slow development was reported to be a general mechanism of P/TGMS fertility restoration. We propose that the recovered protein interaction together with slow development under low temperature compensates for the defective tapetum initiation, which further restores ostms15 fertility. We used base editing to create a number of TGMS lines with different base substitutions based on the OsTMS15 locus. This work may also facilitate the mechanistic investigation and breeding of other crops.
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Affiliation(s)
- Yu Han
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Sheng-Zhe Jiang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xiang Zhong
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xing Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chang-Kai Ma
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yan-Ming Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yi-Chen Mao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Si-Da Zhou
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Lei Zhou
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yan-Fei Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xue-Hui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Hui Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Lai-Geng Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jun Zhu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Zhong-Nan Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
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21
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Wang J, Wang Y, Wu Q, Zhang Y. Multidimensional engineering of Escherichia coli for efficient biosynthesis of cis-3-hydroxypipecolic acid. BIORESOURCE TECHNOLOGY 2023; 382:129173. [PMID: 37187331 DOI: 10.1016/j.biortech.2023.129173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/17/2023]
Abstract
Cis-3-hydroxypipecolic acid (cis-3-HyPip) is the crucial part of many alkaloids and drugs. However, its bio-based industrial production remains challenging. Here, lysine cyclodeaminase from Streptomyces malaysiensis (SmLCD) and pipecolic acid hydroxylase from Streptomyces sp. L-49973 (StGetF) were screened to achieve the conversion of L-lysine to cis-3-HyPip. Considering the high-cost of cofactors, NAD(P)H oxidase from Lactobacillus sanfranciscensis (LsNox) was further overexpressed in chassis strain Escherichia coli W3110 ΔsucCD (α-ketoglutarate-producing strain) to construct the NAD+ regeneration system, thus realizing the bioconversion of cis-3-HyPip from low-cost substrate L-lysine without NAD+ and α-ketoglutarate addition. To further accelerate the transmission efficiency of cis-3-HyPip biosynthetic pathway, multiple-enzyme expression optimization and transporter dynamic regulation via promoter engineering were conducted. Through fermentation optimization, the final engineered strain HP-13 generated 78.4 g/L cis-3-HyPip with 78.9% conversion in a 5-L fermenter, representing the highest production level achieved so far. These strategies described herein show promising potentials for large-scale production of cis-3-HyPip.
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Affiliation(s)
- Jiaping Wang
- Hangzhou Wahaha Group Co. Ltd., Hangzhou 310018, China; Hangzhou Wahaha Technology Co. Ltd., Hangzhou 310018, China; Key Laboratory of Food and Biological Engineering of Zhejiang Province, Hangzhou 310018, China
| | - Yaqiong Wang
- Hangzhou Wahaha Group Co. Ltd., Hangzhou 310018, China; Hangzhou Wahaha Technology Co. Ltd., Hangzhou 310018, China; Key Laboratory of Food and Biological Engineering of Zhejiang Province, Hangzhou 310018, China
| | - Qin Wu
- Hangzhou Wahaha Group Co. Ltd., Hangzhou 310018, China; Hangzhou Wahaha Technology Co. Ltd., Hangzhou 310018, China; Key Laboratory of Food and Biological Engineering of Zhejiang Province, Hangzhou 310018, China
| | - Yimin Zhang
- Hangzhou Wahaha Group Co. Ltd., Hangzhou 310018, China; Hangzhou Wahaha Technology Co. Ltd., Hangzhou 310018, China; Key Laboratory of Food and Biological Engineering of Zhejiang Province, Hangzhou 310018, China.
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22
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Gu F, Jiang W, Kang F, Su T, Yang X, Qi Q, Liang Q. A synthetic population-level oscillator in non-microfluidic environments. Commun Biol 2023; 6:515. [PMID: 37179427 PMCID: PMC10183009 DOI: 10.1038/s42003-023-04904-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Synthetic oscillators have become a research hotspot because of their complexity and importance. The construction and stable operation of oscillators in large-scale environments are important and challenging. Here, we introduce a synthetic population-level oscillator in Escherichia coli that operates stably during continuous culture in non-microfluidic environments without the addition of inducers or frequent dilution. Specifically, quorum-sensing components and protease regulating elements are employed, which form delayed negative feedback to trigger oscillation and accomplish the reset of signals through transcriptional and post-translational regulation. We test the circuit in devices with 1 mL, 50 mL, 400 mL of medium, and demonstrate that the circuit could maintain stable population-level oscillations. Finally, we explore potential applications of the circuit in regulating cellular morphology and metabolism. Our work contributes to the design and testing of synthetic biological clocks that function in large populations.
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Affiliation(s)
- Fei Gu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72, Binhai Road, 266237, Qingdao, China
| | - Wei Jiang
- Research Center of Basic Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Fangbing Kang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72, Binhai Road, 266237, Qingdao, China
| | - Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, No. 72, Binhai Road, 266237, Qingdao, China
| | - Xiaoya Yang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72, Binhai Road, 266237, Qingdao, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, No. 72, Binhai Road, 266237, Qingdao, China.
| | - Quanfeng Liang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72, Binhai Road, 266237, Qingdao, China.
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23
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Huang T, Ma Y. Advances in biosynthesis of higher alcohols in Escherichia coli. World J Microbiol Biotechnol 2023; 39:125. [PMID: 36941474 DOI: 10.1007/s11274-023-03580-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/13/2023] [Indexed: 03/23/2023]
Abstract
In recent years, the development of green energy to replace fossil fuels has been the focus of research. Higher alcohols are important biofuels and chemicals. The production of higher alcohols in microbes has gained attention due to its environmentally friendly character. Higher alcohols have been synthesized in model microorganism Escherichia coli, and the production has reached the gram level through enhancement of metabolic flow, the balance of reducing power and the optimization of fermentation processes. Sustainable bio-higher alcohols production is expected to replace fossil fuels as a green and renewable energy source. Therefore, this review summarizes the latest developments in producing higher alcohols (C3-C6) by E. coli, elucidate the main bottlenecks limiting the biosynthesis of higher alcohols, and proposes potential engineering strategies of improving the production of biological higher alcohols. This review would provide a theoretical basis for further research on higher alcohols production by E. coli.
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Affiliation(s)
- Tong Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Yuanyuan Ma
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
- School of Marin Science and Technology, Tianjin University, Tianjin, 300072, China.
- R&D Center for Petrochemical Technology, Tianjin University, Tianjin, 300072, China.
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González-Arrué N, Inostroza I, Conejeros R, Rivas-Astroza M. Phenotype-specific estimation of metabolic fluxes using gene expression data. iScience 2023; 26:106201. [PMID: 36915687 PMCID: PMC10006673 DOI: 10.1016/j.isci.2023.106201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/30/2022] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
A cell's genome influences its metabolism via the expression of enzyme-related genes, but transcriptome and fluxome are not perfectly correlated as post-transcriptional mechanisms also regulate reaction's kinetics. Here, we addressed the question: given a transcriptome, how unobserved mechanisms of reaction kinetics should be systematically accounted for when inferring the fluxome? To infer the most likely and least biased fluxome, we present Pheflux, a constraint-based model maximizing Shannon's entropy of fluxes per mRNA. Benchmarked against 13C fluxes of yeast and bacteria, Pheflux accurately estimates the carbon core metabolism. We applied Pheflux to thousands of normal and tumor cell transcriptomes obtained from The Cancer Genome Atlas. Pheflux showed statistically significantly higher glucose yields on lactate in breast, kidney, and bronchus-lung tumoral cells than their normal counterparts. Results are consistent with the Warburg effect, a hallmark of cancer metabolism, suggesting that Pheflux can be efficiently used to study the metabolism of eukaryotic cells.
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Affiliation(s)
- Nicolás González-Arrué
- Universidad Tecnológica Metropolitana, Departamento de Biotecnología, Ñuñoa, Santiago 7800003, Chile
| | - Isidora Inostroza
- Universidad Tecnológica Metropolitana, Departamento de Biotecnología, Ñuñoa, Santiago 7800003, Chile
| | - Raúl Conejeros
- Pontificia Universidad Católica de Valparaíso, Escuela de Ingeniería Bioquímica, Valparaíso, 2362803, Chile
| | - Marcelo Rivas-Astroza
- Universidad Tecnológica Metropolitana, Departamento de Biotecnología, Ñuñoa, Santiago 7800003, Chile
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25
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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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26
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Sheng Q, Yi L, Zhong B, Wu X, Liu L, Zhang B. Shikimic acid biosynthesis in microorganisms: Current status and future direction. Biotechnol Adv 2023; 62:108073. [PMID: 36464143 DOI: 10.1016/j.biotechadv.2022.108073] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/03/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022]
Abstract
Shikimic acid (SA), a hydroaromatic natural product, is used as a chiral precursor for organic synthesis of oseltamivir (Tamiflu®, an antiviral drug). The process of microbial production of SA has recently undergone vigorous development. Particularly, the sustainable construction of recombinant Corynebacterium glutamicum (141.2 g/L) and Escherichia coli (87 g/L) laid a solid foundation for the microbial fermentation production of SA. However, its industrial application is restricted by limitations such as the lack of fermentation tests for industrial-scale and the requirement of growth-limiting factors, antibiotics, and inducers. Therefore, the development of SA biosensors and dynamic molecular switches, as well as genetic modification strategies and optimization of the fermentation process based on omics technology could improve the performance of SA-producing strains. In this review, recent advances in the development of SA-producing strains, including genetic modification strategies, metabolic pathway construction, and biosensor-assisted evolution, are discussed and critically reviewed. Finally, future challenges and perspectives for further reinforcing the development of robust SA-producing strains are predicted, providing theoretical guidance for the industrial production of SA.
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Affiliation(s)
- Qi Sheng
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Lingxin Yi
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Bin Zhong
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiaoyu Wu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Bin Zhang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China.
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27
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Li Z, Gao C, Ye C, Guo L, Liu J, Chen X, Song W, Wu J, Liu L. Systems engineering of Escherichia coli for high-level shikimate production. Metab Eng 2023; 75:1-11. [PMID: 36328295 DOI: 10.1016/j.ymben.2022.10.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/03/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
To further increase the production efficiency of microbial shikimate, a valuable compound widely used in the pharmaceutical and chemical industries, ten key target genes contributing to shikimate production were identified by exploiting the enzyme constraint model ec_iML1515, and subsequently used for promoting metabolic flux towards shikimate biosynthesis in the tryptophan-overproducing strain Escherichia coli TRP0. The engineered E. coli SA05 produced 78.4 g/L shikimate via fed-batch fermentation. Deletion of quinate dehydrogenase and introduction of the hydroaromatic equilibration-alleviating shikimate dehydrogenase mutant AroET61W/L241I reduced the contents of byproducts quinate (7.5 g/L) and 3-dehydroshikimic acid (21.4 g/L) by 89.1% and 52.1%, respectively. Furthermore, a high concentration shikimate responsive promoter PrpoS was recruited to dynamically regulate the expression of the tolerance target ProV to enhance shikimate productivity by 23.2% (to 2 g/L/h). Finally, the shikimate titer was increased to 126.4 g/L, with a yield of 0.50 g/g glucose and productivity of 2.63 g/L/h, using a 30-L fermenter and the engineered strain E. coli SA09. This is, to the best of our knowledge, the highest reported shikimate titer and productivity in E. coli.
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Affiliation(s)
- Zhendong Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 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
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
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28
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Tan C, Xu P, Tao F. Harnessing Interactional Sensory Genes for Rationally Reprogramming Chaotic Metabolism. RESEARCH (WASHINGTON, D.C.) 2022; 2022:0017. [PMID: 39290971 PMCID: PMC11407584 DOI: 10.34133/research.0017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/07/2022] [Indexed: 09/19/2024]
Abstract
Rationally controlling cellular metabolism is of great importance but challenging owing to its highly complex and chaotic nature. Natural existing sensory proteins like histidine kinases (HKs) are understood as "sensitive nodes" of biological networks that can trigger disruptive metabolic reprogramming (MRP) upon perceiving environmental fluctuation. Here, the "sensitive node" genes were adopted to devise a global MRP platform consisting of a CRISPR interference-mediated dual-gene combinational knockdown toolbox and survivorship-based metabolic interaction decoding algorithm. The platform allows users to decode the interfering effects of n × n gene pairs while only requiring the synthesis of n pairs of primers. A total of 35 HK genes and 24 glycine metabolic genes were selected as the targets to determine the effectiveness of our platform in a Vibrio sp. FA2. The platform was applied to decode the interfering impact of HKs on antibiotic resistance in strain FA2. A pattern of combined knockdown of HK genes (sasA_8 and 04288) was demonstrated to be capable of reducing antibiotic resistance of Vibrio by 108-fold. Patterns of combined knockdown of glycine pathway genes (e.g., gcvT and ltaE) and several HK genes (e.g., cpxA and btsS) were also revealed to increase glycine production. Our platform may enable an efficient and rational approach for global MRP based on the elucidation of high-order gene interactions. A web-based 1-stop service (https://smrp.sjtu.edu.cn) is also provided to simplify the implementation of this smart strategy in a broad range of cells.
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Affiliation(s)
- Chunlin Tan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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29
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Suo H, Geng X, Sun Y, Zhang L, Yang J, Yang F, Yan H, Hu Y, Xu L. Surface Modification of Magnetic ZIF-90 Nanoparticles Improves the Microenvironment of Immobilized Lipase and Its Application in Esterification. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:15384-15393. [PMID: 36448653 DOI: 10.1021/acs.langmuir.2c02672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Interactions of enzymes with supports significantly affect the activity and stability of immobilized enzymes. Herein, amino-functionalized ionic liquid (IL)-grafted magnetic zeolitic imidazolate framework-90 (MZIF-90) was prepared and used to immobilize porcine pancreatic lipase (PPL). The nanocomposites were fully characterized; meanwhile, the interactions between ILs and ZIF-90 were calculated based on density functional theory. The prepared biocatalyst (PPL-ILs/MZIF-90) had a lipase loading of 178.3 mg/g and hydrolysis activity up to 287.5 U/g. When the biocatalyst was used to synthesize isoamyl acetate, the reaction media, molar ratio of alcohol/acid, temperature, and reaction time were optimized. Under the optimized reaction conditions (in hexane, alcohol/acid = 3:1, under 45 °C, reacted for 9 h), the ester yield reached 85.5%. The results of the stability test showed that PPL-ILs/MZIF-90 retained 88.7% of the initial activity after storing for 35 days and 92.5% of the initial activity after reusing for seven cycles for synthesizing isoamyl acetate. Moreover, the secondary structure analysis showed that the synthesized supports protected the active conformation of immobilized lipase, which lead to the enhanced catalytic performance. Additionally, the biocatalyst can be easily separated with a magnet, which facilitated the reusability. This study provides insights regarding the application of metal organic framework composites in the field of enzyme catalysis.
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Affiliation(s)
- Hongbo Suo
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, China
| | - Xinyue Geng
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, China
| | - Yinghui Sun
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, China
| | - Lu Zhang
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, China
| | - Jie Yang
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, China
| | - Fan Yang
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, China
| | - Hui Yan
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, China
| | - Yi Hu
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, China
| | - Lili Xu
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, China
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30
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Tan C, Xu P, Tao F. Carbon-negative synthetic biology: challenges and emerging trends of cyanobacterial technology. Trends Biotechnol 2022; 40:1488-1502. [PMID: 36253158 DOI: 10.1016/j.tibtech.2022.09.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/05/2022] [Accepted: 09/20/2022] [Indexed: 11/06/2022]
Abstract
Global warming and climate instability have spurred interest in using renewable carbon resources for the sustainable production of chemicals. Cyanobacteria are ideal cellular factories for carbon-negative production of chemicals owing to their great potentials for directly utilizing light and CO2 as sole energy and carbon sources, respectively. However, several challenges in adapting cyanobacterial technology to industry, such as low productivity, poor tolerance, and product harvesting difficulty, remain. Synthetic biology may finally address these challenges. Here, we summarize recent advances in the production of value-added chemicals using cyanobacterial cell factories, particularly in carbon-negative synthetic biology and emerging trends in cyanobacterial applications. We also propose several perspectives on the future development of cyanobacterial technology for commercialization.
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Affiliation(s)
- Chunlin Tan
- The State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Xu
- The State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fei Tao
- The State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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31
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Moškon M, Pušnik Ž, Stanovnik L, Zimic N, Mraz M. A computational design of a programmable biological processor. Biosystems 2022; 221:104778. [PMID: 36099979 DOI: 10.1016/j.biosystems.2022.104778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/02/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022]
Abstract
Basic synthetic information processing structures, such as logic gates, oscillators and flip-flops, have already been implemented in living organisms. Current implementations of these structures have yet to be extended to more complex processing structures that would constitute a biological computer. We make a step forward towards the construction of a biological computer. We describe a model-based computational design of a biological processor that uses transcription and translation resources of the host cell to perform its operations. The proposed processor is composed of an instruction memory containing a biological program, a program counter that is used to address this memory, and a biological oscillator that triggers the execution of the next instruction in the memory. We additionally describe the implementation of a biological compiler that compiles a sequence of human-readable instructions into ordinary differential equation-based models, which can be used to simulate and analyse the dynamics of the processor. The proposed implementation presents the first programmable biological processor that exploits cellular resources to execute the specified instructions. We demonstrate the application of the described processor on a set of simple yet scalable biological programs. Biological descriptions of these programs can be produced manually or automatically using the provided compiler.
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Affiliation(s)
- Miha Moškon
- University of Ljubljana, Faculty of Computer and Information Science, Večna pot 113, Ljubljana, SI-1000, Slovenia.
| | - Žiga Pušnik
- University of Ljubljana, Faculty of Computer and Information Science, Večna pot 113, Ljubljana, SI-1000, Slovenia
| | - Lidija Stanovnik
- University of Ljubljana, Faculty of Computer and Information Science, Večna pot 113, Ljubljana, SI-1000, Slovenia
| | - Nikolaj Zimic
- University of Ljubljana, Faculty of Computer and Information Science, Večna pot 113, Ljubljana, SI-1000, Slovenia
| | - Miha Mraz
- University of Ljubljana, Faculty of Computer and Information Science, Večna pot 113, Ljubljana, SI-1000, Slovenia
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32
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Lu J, Wang Y, Xu M, Fei Q, Gu Y, Luo Y, Wu H. Efficient biosynthesis of 3-hydroxypropionic acid from ethanol in metabolically engineered Escherichia coli. BIORESOURCE TECHNOLOGY 2022; 363:127907. [PMID: 36087655 DOI: 10.1016/j.biortech.2022.127907] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Engineering microbial cell factories to convert CO2-based feedstock into chemicals and fuels provide a feasible carbon-neutral route for the third-generation biorefineries. Ethanol became one of the major products of syngas fermentation by engineered acetogens. The key building block chemical 3-hydroxypropionic acid (3-HP) can be synthesized from ethanol by the malonyl-CoA pathway with CO2 fixation. In this study, the effect of two ethanol consumption pathways on 3-HP synthesis were studied as well as the effect of TCA cycle, gluconeogenesis pathway, and transhydrogenase. And the 3-HP synthesis pathway was also optimized. The engineered strain synthesized 1.66 g/L of 3-HP with a yield of 0.24 g/g. Furthermore, the titer and the yield of 3-HP increased to 13.17 g/L and 0.57 g/g in the whole-cell biocatalysis system. This study indicated that ethanol as feedstock had the potential to synthesize 3-HP, which provided an alternative route for future biorefinery.
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Affiliation(s)
- Juefeng Lu
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yuying Wang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Mingcheng Xu
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qiang Fei
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Yang Gu
- Key Laboratory of Synthetic Biology, The State Key Laboratory of Plant Carbon-Nitrogen Assimilation, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yuanchan Luo
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Hui Wu
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai 200237, China; Key Laboratory of Bio-based Material Engineering of China National Light Industry Council, 130 Meilong Road, Shanghai 200237, China.
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33
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Zhao M, Li Y, Wang F, Ren Y, Wei D. A CRISPRi mediated self-inducible system for dynamic regulation of TCA cycle and improvement of itaconic acid production in Escherichia coli. Synth Syst Biotechnol 2022; 7:982-988. [PMID: 35782485 PMCID: PMC9213231 DOI: 10.1016/j.synbio.2022.05.008] [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: 02/28/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 11/17/2022] Open
Abstract
Itaconic acid (ITA), an effective alternative fossil fuel, derives from the bypass pathway of the tricarboxylic acid (TCA) cycle. Therefore, the imbalance of metabolic flux between TCA cycle and ITA biosynthetic pathway seriously limits the production of ITA. The optimization of flux distribution between biomass and production has the potential to the productivity of ITA. Based on the previously constructed strain Escherichia coli MG1655 Δ1-SAS-3 (ITA titer: 1.87 g/L), a CRISPRi-mediated self-inducible system (CiMS), which contained a responsive module based on the ITA biosensor YpItcR/P ccl and a regulative CRISPRi-mediated interferential module, was developed to regulate the flux of the TCA cycle and to enhance the capacity of the strain to produce ITA. First, a higher ITA-yielding strain, Δ4-P rmd -SAS-3 (ITA titer: 3.20 g/L), derived from Δ1-SAS-3, was constructed by replacing the promoter P J23100 , for the expression of ITA synthesis genes, with P rmd and knocking out the three bypass genes poxB, pflB, and ldhA. Subsequently, the CiMS was used to inhibit the expression of key genes icd, pykA, and sucCD to dynamically balance the metabolic flux between TCA cycle and ITA biosynthetic pathway during the ITA production stage. The constructed strain Δ4-P rmd -SAS-3 under the dynamic regulation of the CiMS, showed a 23% increase in the ITA titer, which reached 3.93 g/L. This study indicated that CiMS was a practical strategy to dynamically and precisely regulated the metabolic flux in microbial cell factories.
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Affiliation(s)
- Ming Zhao
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
- Anhui Engineering Laboratory for Industrial Microbiology Molecular Breeding, College of Biology and Food Engineering, Anhui Polytechnic University, Wuhu, 241000, China
| | - Yuting Li
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Fengqing Wang
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuhong Ren
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Dongzhi Wei
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
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34
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Ding Q, Li Z, Guo L, Song W, Wu J, Chen X, Liu L, Gao C. Engineering Escherichia coli asymmetry distribution-based synthetic consortium for shikimate production. Biotechnol Bioeng 2022; 119:3230-3240. [PMID: 35982023 DOI: 10.1002/bit.28211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 11/09/2022]
Abstract
Microbial consortia constitute a promising tool for achieving high-value chemical bio-production. However, customizing the consortium ratio remains challenging. Herein, an asymmetry distribution-based synthetic consortium (ADSC) was developed to switch cell phenotypes using shikimate synthesis for proof of concept. First, the cell pole-organizing protein PopZ was screened as a mediator of asymmetric protein distribution in Escherichia coli. The ADSC was then constructed to incorporate PopZ-mediated asymmetry distribution and a TetR-based transcription repression switch to achieve the dynamical control of microbial population ratio. Finally, the ADSC was used to decouple cell growth from shikimate synthesis by effectively coordinating the ratio of growing cells and production cells at the consortium level, thereby increasing shikimate titer to 30.1 g/L in the 7.5-L bioreactor with a minimal medium. This titer was further improved to 82.5 g/L when using rich medium fermentation. Our results illustrate a novel approach to control consortium structure through ADSC-mediated regulation, highlighting its potential as an efficient strategy for controlling metabolic state in microbes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Qiang Ding
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China.,School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Zhendong Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, 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, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, 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.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 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, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
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35
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An international comprehensive benchmarking analysis of synthetic biology in China from 2015 to 2020. Chin J Chem Eng 2022. [DOI: 10.1016/j.cjche.2021.05.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Trichez D, Carneiro CVGC, Braga M, Almeida JRM. Recent progress in the microbial production of xylonic acid. World J Microbiol Biotechnol 2022; 38:127. [PMID: 35668329 DOI: 10.1007/s11274-022-03313-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/19/2022] [Indexed: 01/03/2023]
Abstract
Interest in the production of renewable chemicals from biomass has increased in the past years. Among these chemicals, carboxylic acids represent a significant part of the most desirable bio-based products. Xylonic acid is a five-carbon sugar-acid obtained from xylose oxidation that can be used in several industrial applications, including food, pharmaceutical, and construction industries. So far, the production of xylonic acid has not yet been available at an industrial scale; however, several microbial bio-based production processes are under development. This review summarizes the recent advances in pathway characterization, genetic engineering, and fermentative strategies to improve xylonic acid production by microorganisms from xylose or lignocellulosic hydrolysates. In addition, the strengths of the available microbial strains and processes and the major requirements for achieving biotechnological production of xylonic acid at a commercial scale are discussed. Efficient native and engineered microbial strains have been reported. Xylonic acid titers as high as 586 and 171 g L-1 were obtained from bacterial and yeast strains, respectively, in a laboratory medium. Furthermore, relevant academic and industrial players associated with xylonic acid production will be presented.
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Affiliation(s)
- Débora Trichez
- Laboratory of Genetics and Biotechnology, EMBRAPA Agroenergia, Brasília, Brazil
| | - Clara Vida G C Carneiro
- Laboratory of Genetics and Biotechnology, EMBRAPA Agroenergia, Brasília, Brazil.,Graduate Program of Microbial Biology, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, Brazil
| | - Melissa Braga
- Innovation and Business Office, EMBRAPA Agroenergia, Brasília, Brazil
| | - João Ricardo M Almeida
- Laboratory of Genetics and Biotechnology, EMBRAPA Agroenergia, Brasília, Brazil. .,Graduate Program of Microbial Biology, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, Brazil.
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Cofactor Self-Sufficient Whole-Cell Biocatalysts for the Relay-Race Synthesis of Shikimic Acid. FERMENTATION 2022. [DOI: 10.3390/fermentation8050229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Shikimic acid (SA) is a key intermediate in the aromatic amino-acid biosynthetic pathway, as well as an important precursor for synthesizing many valuable antiviral drugs. The asymmetric reduction of 3-dehydroshikimic acid (DHS) to SA is catalyzed by shikimate dehydrogenase (AroE) using NADPH as the cofactor; however, the intracellular NADPH supply limits the biosynthetic capability of SA. Glucose dehydrogenase (GDH) is an efficient enzyme which is typically used for NAD(P)H regeneration in biocatalytic processes. In this study, a series of NADPH self-sufficient whole-cell biocatalysts were constructed, and the biocatalyst co-expressing Bmgdh–aroE showed the highest conversion rate for the reduction of DHS to SA. Then, the preparation of whole-cell biocatalysts by fed-batch fermentation without supplementing antibiotics was developed on the basis of the growth-coupled l-serine auxotroph. After optimizing the whole-cell biocatalytic conditions, a titer of 81.6 g/L SA was obtained from the supernatant of fermentative broth in 98.4% yield (mol/mol) from DHS with a productivity of 40.8 g/L/h, and cofactor NADP+ or NADPH was not exogenously supplemented during the whole biocatalytic process. The efficient relay-race synthesis of SA from glucose by coupling microbial fermentation with a biocatalytic process was finally achieved. This work provides an effective strategy for the biosynthesis of fine chemicals that are difficult to obtain through de novo biosynthesis from renewable feedstocks, as well as for biocatalytic studies that strictly rely on NAD(P)H regeneration.
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38
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Lv X, Hueso-Gil A, Bi X, Wu Y, Liu Y, Liu L, Ledesma-Amaro R. New synthetic biology tools for metabolic control. Curr Opin Biotechnol 2022; 76:102724. [PMID: 35489308 DOI: 10.1016/j.copbio.2022.102724] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/28/2022] [Accepted: 03/20/2022] [Indexed: 11/29/2022]
Abstract
In industrial bioprocesses, microbial metabolism dictates the product yields, and therefore, our capacity to control it has an enormous potential to help us move towards a bio-based economy. The rapid development of multiomics data has accelerated our systematic understanding of complex metabolic regulatory mechanisms, which allow us to develop tools to manipulate them. In the last few years, machine learning-based metabolic modeling, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) derived synthetic biology tools, and synthetic genetic circuits have been widely used to control the metabolism of microorganisms, manipulate gene expression, and build synthetic pathways for bioproduction. This review describes the latest developments for metabolic control, and focuses on the trends and challenges of metabolic engineering strategies.
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Affiliation(s)
- Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Angeles Hueso-Gil
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW72AZ, UK
| | - Xinyu Bi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yaokang Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW72AZ, UK.
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Zhang Y, Zou ZP, Chen SY, Wei WP, Zhou Y, Ye BC. Design and optimization of E. coli artificial genetic circuits for detection of explosive composition 2,4-dinitrotoluene. Biosens Bioelectron 2022; 207:114205. [PMID: 35339074 DOI: 10.1016/j.bios.2022.114205] [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: 12/13/2021] [Revised: 03/07/2022] [Accepted: 03/18/2022] [Indexed: 11/26/2022]
Abstract
The detection of mine-based explosives poses a serious threat to the lives of deminers, and carcinogenic residues may cause severe environmental pollution. Whole-cell biosensors that can detect on-site in dangerous or inaccessible environments have great potential to replace conventional methods. Synthetic biology based on engineering modularity serves as a new tool that could be used to engineer microbes to acquire desired functions through artificial design and precise regulation. In this study, we designed artificial genetic circuits in Escherichia coli MG1655 by reconstructing the transcription factor YhaJ-based system to detect explosive composition 2,4-dinitrotoluene (2,4-DNT). These genetic circuits were optimized at the transcriptional, translational, and post-translational levels. The binding affinity of the transcription factor YhaJ with inducer 2,4-DNT metabolites was enhanced via directed evolution, and several activator binding sites were inserted in sensing yqjF promoter (PyqjF) to further improve the output level. The optimized biosensor PyqjF×2-TEV-(mYhaJ + GFP)-Ssr had a maximum induction ratio of 189 with green fluorescent signal output, and it could perceive at least 1 μg/mL 2,4-DNT. Its effective and robust performance was verified in different water samples. Our results demonstrate the use of synthetic biology tools to systematically optimize the performance of sensors for 2,4-DNT detection, that lay the foundation for practical applications.
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Affiliation(s)
- Yan Zhang
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China; School of Chemistry and Chemical Engineering/Key Laboratory of Environmental Monitoring and Pollutant Control of Xinjiang Bingtuan, Shihezi University, Shihezi, 832003, China
| | - Zhen-Ping Zou
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Sheng-Yan Chen
- School of Chemistry and Chemical Engineering/Key Laboratory of Environmental Monitoring and Pollutant Control of Xinjiang Bingtuan, Shihezi University, Shihezi, 832003, China
| | - Wen-Ping Wei
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
| | - Ying Zhou
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China; School of Chemistry and Chemical Engineering/Key Laboratory of Environmental Monitoring and Pollutant Control of Xinjiang Bingtuan, Shihezi University, Shihezi, 832003, China; Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China.
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40
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Wu T, Chen Z, Guo S, Zhang C, Huo YX. Engineering Transcription Factor BmoR Mutants for Constructing Multifunctional Alcohol Biosensors. ACS Synth Biol 2022; 11:1251-1260. [PMID: 35175734 DOI: 10.1021/acssynbio.1c00549] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Native transcription factor-based biosensors (TFBs) have the potential for the in situ detection of value-added chemicals or byproducts. However, their industrial application is limited by their ligand promiscuity, low sensitivity, and narrow detection range. Alcohols exhibit similar structures, and no reported TFB can distinguish a specific alcohol from its analogues. Here, we engineered an alcohol-regulated transcription factor, BmoR, and obtained various mutants with remarkable properties. For example, the generated signal-molecule-specific BmoRs could distinguish the constitutional isomers n-butanol and isobutanol, with insensitivity up to an ethanol concentration of 800 mM (36.9 g/L). Linear detection of 0-60 mM of a specific higher alcohol could be achieved in the presence of up to 500 mM (23.0 g/L) ethanol as background noise. Furthermore, we obtained two mutants with raised outputs and over 107-fold higher sensitivity and one mutant with an increased upper detection limit (14.8 g/L n-butanol or isobutanol). Using BmoR as an example, this study systematically explored the ultimate detection limit of a TFB toward its small-molecule ligands, paving the way for in situ detection in biofuel and wine industries.
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Affiliation(s)
- Tong Wu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081 Beijing, China
| | - Zhenya Chen
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081 Beijing, China
| | - Shuyuan Guo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081 Beijing, China
| | - Cuiying Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, No. 9 13th Street, Tianjin Economic and Technological Development Zone, 300457 Tianjin, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081 Beijing, China
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41
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Mao X, Zhang B, Zhao C, Lin J, Wei D. Overexpression of mGDH in Gluconobacter oxydans to improve D-xylonic acid production from corn stover hydrolysate. Microb Cell Fact 2022; 21:35. [PMID: 35264166 PMCID: PMC8905809 DOI: 10.1186/s12934-022-01763-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 02/24/2022] [Indexed: 11/17/2022] Open
Abstract
Background d-Xylonic acid is a versatile platform chemical with broad potential applications as a water reducer and disperser for cement and as a precursor for 1,4-butanediol and 1,2,4-tributantriol. Microbial production of d-xylonic acid with bacteria such as Gluconobacter oxydans from inexpensive lignocellulosic feedstock is generally regarded as one of the most promising and cost-effective methods for industrial production. However, high substrate concentrations and hydrolysate inhibitors reduce xylonic acid productivity. Results The d-xylonic acid productivity of G. oxydans DSM2003 was improved by overexpressing the mGDH gene, which encodes membrane-bound glucose dehydrogenase. Using the mutated plasmids based on pBBR1MCS-5 in our previous work, the recombinant strain G. oxydans/pBBR-R3510-mGDH was obtained with a significant improvement in d-xylonic acid production and a strengthened tolerance to hydrolysate inhibitors. The fed-batch biotransformation of d-xylose by this recombinant strain reached a high titer (588.7 g/L), yield (99.4%), and volumetric productivity (8.66 g/L/h). Moreover, up to 246.4 g/L d-xylonic acid was produced directly from corn stover hydrolysate without detoxification at a yield of 98.9% and volumetric productivity of 11.2 g/L/h. In addition, G. oxydans/pBBR-R3510-mGDH exhibited a strong tolerance to typical inhibitors, i.e., formic acid, furfural, and 5-hydroxymethylfurfural. Conclusion Through overexpressing mgdh in G. oxydans, we obtained the recombinant strain G. oxydans/pBBR-R3510-mGDH, and it was capable of efficiently producing xylonic acid from corn stover hydrolysate under high inhibitor concentrations. The high d-xylonic acid productivity of G. oxydans/pBBR-R3510-mGDH made it an attractive choice for biotechnological production. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01763-y.
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Affiliation(s)
- Xinlei Mao
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Baoqi Zhang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Chenxiu Zhao
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Jinping Lin
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
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42
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Harnessing plasmid replication mechanism to enable dynamic control of gene copy in bacteria. Metab Eng 2022; 70:67-78. [PMID: 35033655 PMCID: PMC8844098 DOI: 10.1016/j.ymben.2022.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/17/2021] [Accepted: 01/09/2022] [Indexed: 01/03/2023]
Abstract
Dynamic regulation has been proved efficient in controlling gene expression at transcriptional, translational, and post-translational level. However, the dynamic regulation at gene replication level has been rarely explored so far. In this study, we established dynamic regulation at gene copy level through engineering controllable plasmid replication to dynamically control the gene expression. Prototypic genetic circuits with different control logic were applied to enable diversified dynamic behaviors of gene copy. To explore the applicability of this strategy, the dynamic gene copy control was employed in regulating the biosynthesis of p-coumaric acid, which resulted in an up to 78% increase in p-coumaric acid titer to 1.69 g/L in shake flasks. These results indicated the great potential of applying dynamic gene copy control for engineering biosynthesis of valuable compounds in metabolic engineering.
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43
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Dyer RP, Weiss GA. Making the cut with protease engineering. Cell Chem Biol 2022; 29:177-190. [PMID: 34921772 PMCID: PMC9127713 DOI: 10.1016/j.chembiol.2021.12.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 07/30/2021] [Accepted: 11/29/2021] [Indexed: 12/30/2022]
Abstract
Proteases cut with enviable precision and regulate diverse molecular events in biology. Such qualities drive a seemingly inexhaustible appetite for proteases with new activities and capabilities. Comprising 25% of the total industrial enzyme market, proteases appear in consumer goods, such as detergents, textile processing, and numerous foods; additionally, proteases include 25 US Food and Drug Administration-approved medicines and various research tools. Recent advances in protease engineering strategies address target specificity, catalytic efficiency, and stability. This guide to protease engineering surveys best practices and emerging strategies. We further highlight gaps and flexibilities inherent to each system that suggest opportunities for new technology development along with engineered proteases to solve challenges in proteomics, protein sequencing, and synthetic gene circuits.
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Affiliation(s)
- Rebekah P Dyer
- Department of Molecular Biology and Biochemistry, University of California, Irvine, 1102 NS-2, Irvine, CA 92697-2025, USA
| | - Gregory A Weiss
- Department of Chemistry, University of California, Irvine, 1102 NS-2, Irvine, CA 92697-2025, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, 1102 NS-2, Irvine, CA 92697-2025, USA; Department of Pharmaceutical Sciences, University of California, Irvine, 1102 NS-2, Irvine, CA 92697-2025, USA.
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44
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Komera I, Gao C, Guo L, Hu G, Chen X, Liu L. Bifunctional optogenetic switch for improving shikimic acid production in E. coli. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:13. [PMID: 35418155 PMCID: PMC8822657 DOI: 10.1186/s13068-022-02111-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 01/28/2022] [Indexed: 12/19/2022]
Abstract
BACKGROUND Biomass formation and product synthesis decoupling have been proven to be promising to increase the titer of desired value add products. Optogenetics provides a potential strategy to develop light-induced circuits that conditionally control metabolic flux redistribution for enhanced microbial production. However, the limited number of light-sensitive proteins available to date hinders the progress of light-controlled tools. RESULTS To address these issues, two optogenetic systems (TPRS and TPAS) were constructed by reprogramming the widely used repressor TetR and protease TEVp to expand the current optogenetic toolkit. By merging the two systems, a bifunctional optogenetic switch was constructed to enable orthogonally regulated gene transcription and protein accumulation. Application of this bifunctional switch to decouple biomass formation and shikimic acid biosynthesis allowed 35 g/L of shikimic acid production in a minimal medium from glucose, representing the highest titer reported to date by E. coli without the addition of any chemical inducers and expensive aromatic amino acids. This titer was further boosted to 76 g/L when using rich medium fermentation. CONCLUSION The cost effective and light-controlled switch reported here provides important insights into environmentally friendly tools for metabolic pathway regulation and should be applicable to the production of other value-add chemicals.
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Affiliation(s)
- Irene Komera
- State Key Laboratory of Food Science and Technology, Jiangnan University, 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, 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, Wuxi, 214122, China.,International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Guipeng Hu
- School of Pharmaceutical Science, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 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, Wuxi, 214122, China. .,International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China.
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45
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Hu G, Guo L, Gao C, Song W, Liu L, Chen X. Synergistic Metabolism of Glucose and Formate Increases the Yield of Short-Chain Organic Acids in Escherichia coli. ACS Synth Biol 2022; 11:135-143. [PMID: 34979802 DOI: 10.1021/acssynbio.1c00289] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Microbial cell factories using a single carbon source (e.g., sugars) have been used to produce a wide variety of chemicals. However, this process is often accompanied by stoichiometric constraints on carbons and redox cofactors. Here, a synthetic pathway was designed and constructed in Escherichia coli to synergistically use glucose and formate as mixed carbon sources. By optimizing this synthetic pathway via enzyme mining, protein engineering, and bioprocess approaches, the yield of pyruvate from glucose was enhanced to 94% of the theoretical glycolysis yield, reaching 1.88 mol/mol. Finally, the optimized synthetic pathway was integrated with a phosphite reductase-based NADH regeneration system in malate-producing E. coli, resulting in the conversion of glucose into l-malate with a high yield of up to 1.65 mol/mol. This synergistic carbon metabolism strategy can be used to establish carbon- and energy-efficient productive processes.
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Affiliation(s)
- Guipeng Hu
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, 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, 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, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Wei Song
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, 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, 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, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
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46
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Advances in microbial production of feed amino acid. ADVANCES IN APPLIED MICROBIOLOGY 2022; 119:1-33. [DOI: 10.1016/bs.aambs.2022.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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47
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Li C, Jiang T, Li M, Zou Y, Yan Y. Fine-tuning gene expression for improved biosynthesis of natural products: From transcriptional to post-translational regulation. Biotechnol Adv 2022; 54:107853. [PMID: 34637919 PMCID: PMC8724446 DOI: 10.1016/j.biotechadv.2021.107853] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 02/08/2023]
Abstract
Microbial production of natural compounds has attracted extensive attention due to their high value in pharmaceutical, cosmetic, and food industries. Constructing efficient microbial cell factories for biosynthesis of natural products requires the fine-tuning of gene expressions to minimize the accumulation of toxic metabolites, reduce the competition between cell growth and product generation, as well as achieve the balance of redox or co-factors. In this review, we focus on recent advances in fine-tuning gene expression at the DNA, RNA, and protein levels to improve the microbial biosynthesis of natural products. Commonly used regulatory toolsets in each level are discussed, and perspectives for future direction in this area are provided.
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Affiliation(s)
- Chenyi Li
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Tian Jiang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Michelle Li
- North Oconee High School, Bogart, GA 30622, USA
| | - Yusong Zou
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA.
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48
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Guo L, Ding S, Liu Y, Gao C, Hu G, Song W, Liu J, Chen X, Liu L. Enhancing tryptophan production by balancing precursors in Escherichia coli. Biotechnol Bioeng 2021; 119:983-993. [PMID: 34936092 DOI: 10.1002/bit.28019] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/20/2021] [Accepted: 11/27/2021] [Indexed: 11/11/2022]
Abstract
Tryptophan, an essential aromatic amino acid, is widely used in animal feed, food additives, and pharmaceuticals. Although sustainable and environmentally friendly, microbial tryptophan production from renewable feedstocks is limited by low biosynthesis and transport rates. Here, an Escherichia coli strain capable of efficient tryptophan production was generated by improving and balancing the supply of precursors and by engineering membrane transporters. Tryptophan biosynthesis was increased by eliminating negative regulatory factors, blocking competing pathways, and preventing tryptophan degradation. Promoter engineering balanced the supply of the precursors erythrose-4-phosphate and phosphoenolpyruvate, as well as the availability of serine. Finally, the engineering of tryptophan transporters prevented feedback inhibition and growth toxicity. Fed-batch fermentation of the final strain (TRP12) in a 5 L bioreactor produced 52.1 g·L-1 of tryptophan, with a yield of 0.171 g·g-1 glucose and productivity of 1.45 g·L-1 ·h-1 . The metabolic engineering strategy described here paves the way for high-performance microbial cell factories aimed at the production of tryptophan as well as other valuable chemicals.
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Affiliation(s)
- Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Shuang Ding
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Yadi Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Guipeng Hu
- School of Pharmaceutical Science, Jiangnan University, Wuxi, China
| | - Wei Song
- School of Pharmaceutical Science, Jiangnan University, Wuxi, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
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Pillay CS, John N. Can thiol-based redox systems be utilized as parts for synthetic biology applications? Redox Rep 2021; 26:147-159. [PMID: 34378494 PMCID: PMC8366655 DOI: 10.1080/13510002.2021.1966183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVES Synthetic biology has emerged from molecular biology and engineering approaches and aims to develop novel, biologically-inspired systems for industrial and basic research applications ranging from biocomputing to drug production. Surprisingly, redoxin (thioredoxin, glutaredoxin, peroxiredoxin) and other thiol-based redox systems have not been widely utilized in many of these synthetic biology applications. METHODS We reviewed thiol-based redox systems and the development of synthetic biology applications that have used thiol-dependent parts. RESULTS The development of circuits to facilitate cytoplasmic disulfide bonding, biocomputing and the treatment of intestinal bowel disease are amongst the applications that have used thiol-based parts. We propose that genetically encoded redox sensors, thiol-based biomaterials and intracellular hydrogen peroxide generators may also be valuable components for synthetic biology applications. DISCUSSION Thiol-based systems play multiple roles in cellular redox metabolism, antioxidant defense and signaling and could therefore offer a vast and diverse portfolio of components, parts and devices for synthetic biology applications. However, factors limiting the adoption of redoxin systems for synthetic biology applications include the orthogonality of thiol-based components, limitations in the methods to characterize thiol-based systems and an incomplete understanding of the design principles of these systems.
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Affiliation(s)
- Ché S. Pillay
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Nolyn John
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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Reprogramming microbial populations using a programmed lysis system to improve chemical production. Nat Commun 2021; 12:6886. [PMID: 34824227 PMCID: PMC8617184 DOI: 10.1038/s41467-021-27226-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 11/10/2021] [Indexed: 11/08/2022] Open
Abstract
Microbial populations are a promising model for achieving microbial cooperation to produce valuable chemicals. However, regulating the phenotypic structure of microbial populations remains challenging. In this study, a programmed lysis system (PLS) is developed to reprogram microbial cooperation to enhance chemical production. First, a colicin M -based lysis unit is constructed to lyse Escherichia coli. Then, a programmed switch, based on proteases, is designed to regulate the effective lysis unit time. Next, a PLS is constructed for chemical production by combining the lysis unit with a programmed switch. As a result, poly (lactate-co-3-hydroxybutyrate) production is switched from PLH synthesis to PLH release, and the content of free PLH is increased by 283%. Furthermore, butyrate production with E. coli consortia is switched from E. coli BUT003 to E. coli BUT004, thereby increasing butyrate production to 41.61 g/L. These results indicate the applicability of engineered microbial populations for improving the metabolic division of labor to increase the efficiency of microbial cell factories.
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