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Lee Y, Kim K, Choi M, Seo SW. Natural transformation of Vibrio natriegens with large genetic cluster enables alginate assimilation for isopentenol production. BIORESOURCE TECHNOLOGY 2024; 406:130988. [PMID: 38885723 DOI: 10.1016/j.biortech.2024.130988] [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: 03/20/2024] [Revised: 06/14/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024]
Abstract
Alginate is a major component of brown macroalgae, and its efficient utilization is critical for developing sustainable technologies. Vibrio natriegens is a fast-growing marine bacterium that has gained massive attention due to its potential as an alternative industrial chassis. However, V. natriegens cannot naturally metabolize alginate, limiting its usage in marine biomass conversion. In this study, V. natriegens was engineered to utilize marine biomass, kelp, as a carbon source. A total of 33.8 kb of the genetic cluster for alginate assimilation from Vibrio sp. dhg was integrated into V. natriegens by natural transformation. Engineered V. natriegens was further modified to produce 1.8 mg/L of isopentenol from 16 g/L of crude kelp powder. This study not only presents the very first case in which V. natriegens can be naturally transformed with large DNA fragments but also highlights the potential of this strain for converting marine biomass into valuable products.
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Affiliation(s)
- Yungyu Lee
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Keonwoo Kim
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Mincheol Choi
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; Bio-MAX Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; Institute of Bio Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
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2
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Wang G, Wang Q, Qi Q, Wang Q. Dynamic plasmid copy number control for synthetic biology. Trends Biotechnol 2024; 42:147-150. [PMID: 37689527 DOI: 10.1016/j.tibtech.2023.08.004] [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: 07/10/2023] [Revised: 08/18/2023] [Accepted: 08/22/2023] [Indexed: 09/11/2023]
Abstract
Plasmids that replicate independently from chromosomes are valuable genetic tools for biological research. Dynamic control of plasmid copy number facilitates flexible regulation of the gene of interest or the genetic circuit installed in the plasmid. This useful strategy is being integrated into synthetic biology for metabolic reprogramming and biosensing applications.
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Affiliation(s)
- Gege Wang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, PR China
| | - Qi Wang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, PR China
| | - Qingsheng Qi
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, PR China
| | - Qian Wang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, PR China.
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3
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Hahn J, Ding S, Im J, Harimoto T, Leong KW, Danino T. Bacterial therapies at the interface of synthetic biology and nanomedicine. NATURE REVIEWS BIOENGINEERING 2024; 2:120-135. [PMID: 38962719 PMCID: PMC11218715 DOI: 10.1038/s44222-023-00119-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/08/2023] [Indexed: 07/05/2024]
Abstract
Bacteria are emerging as living drugs to treat a broad range of disease indications. However, the inherent advantages of these replicating and immunostimulatory therapies also carry the potential for toxicity. Advances in synthetic biology and the integration of nanomedicine can address this challenge through the engineering of controllable systems that regulate spatial and temporal activation for improved safety and efficacy. Here, we review recent progress in nanobiotechnology-driven engineering of bacteria-based therapies, highlighting limitations and opportunities that will facilitate clinical translation.
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Affiliation(s)
- Jaeseung Hahn
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Suwan Ding
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Jongwon Im
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Tetsuhiro Harimoto
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Kam W. Leong
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - Tal Danino
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Data Science Institute, Columbia University, New York, NY, USA
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4
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Brechun KE, Förschle M, Schmidt M, Kranz H. Method for plasmid-based antibiotic-free fermentation. Microb Cell Fact 2024; 23:18. [PMID: 38212806 PMCID: PMC10782701 DOI: 10.1186/s12934-023-02291-z] [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: 11/24/2023] [Accepted: 12/29/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Antibiotic-based plasmid selection and maintenance is a core tool in molecular biology; however, while convenient, this strategy has numerous drawbacks for biological manufacturing. Overuse of antibiotics and antibiotic resistance genes (ARG) contributes to the development of antimicrobial resistance, which is a growing threat to modern medicine. Antibiotics themselves are costly and therefore often omitted in fermentations, leading to plasmid loss and a corresponding loss in product yield. Furthermore, constitutive expression of a plasmid-encoded antibiotic resistance gene imposes a significant metabolic burden on the cells. For many fermentation products (e.g., in nutrition and medicine), the use of antibiotic resistance genes is subject to strict regulations and should be avoided. We present a method for plasmid selection and maintenance with stringent selection pressure that is independent of antibiotics and ARG. Furthermore, it can be used without any restrictions regarding culture medium and temperature. RESULTS The developed method involves modification of a bacterial strain such that an essential gene is expressed genomically under the control of an inducible promoter. A copy of the same essential gene with the endogenous promoter is supplied on a plasmid for selection. In the absence of the inducer for the genomic copy of the essential gene, cells rely on expression of the plasmid-encoded gene copy, leading to tight selection for plasmid maintenance. Induction of the genomic copy of the essential gene enables the engineered strain to be propagated in the absence of a plasmid. Here, we describe the genetic setup and demonstrate long-term, tight selection for plasmid maintenance with a variety of different plasmids and E. coli strains. CONCLUSIONS This method facilitates plasmid-based fermentations by eliminating the need for antibiotic selection and improving plasmid maintenance.
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Affiliation(s)
- Katherine E Brechun
- Gen-H Genetic Engineering Heidelberg GmbH, Im Neuenheimer Feld 584, 69120, Heidelberg, Germany
| | - Marion Förschle
- Gen-H Genetic Engineering Heidelberg GmbH, Im Neuenheimer Feld 584, 69120, Heidelberg, Germany
| | - Marlen Schmidt
- Gen-H Genetic Engineering Heidelberg GmbH, Im Neuenheimer Feld 584, 69120, Heidelberg, Germany
| | - Harald Kranz
- Gen-H Genetic Engineering Heidelberg GmbH, Im Neuenheimer Feld 584, 69120, Heidelberg, Germany.
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5
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Amrofell MB, Rengarajan S, Vo ST, Ramirez Tovar ES, LoBello L, Dantas G, Moon TS. Engineering E. coli strains using antibiotic-resistance-gene-free plasmids. CELL REPORTS METHODS 2023; 3:100669. [PMID: 38086386 PMCID: PMC10753387 DOI: 10.1016/j.crmeth.2023.100669] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/29/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023]
Abstract
We created a generalizable pipeline for antibiotic-resistance-gene-free plasmid (ARGFP)-based cloning using a dual auxotrophic- and essential-gene-based selection strategy. We use auxotrophic selection to construct plasmids in engineered E. coli DH10B cloning strains and both auxotrophic- and essential-gene-based selection to (1) select for recombinant strains and (2) maintain a plasmid in E. coli Nissle 1917, a common chassis for engineered probiotic applications, and E. coli MG1655, the laboratory "wild-type" E. coli strain. We show that our approach has comparable efficiency to that of antibiotic-resistance-gene-based cloning. We also show that the double-knockout Nissle and MG1655 strains are simple to transform with plasmids of interest. Notably, we show that the engineered Nissle strains are amenable to long-term plasmid maintenance in repeated culturing as well as in the mouse gut, demonstrating the potential for broad applications while minimizing the risk of antibiotic resistance spread via horizontal gene transfer.
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Affiliation(s)
- Matthew B Amrofell
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Sunaina Rengarajan
- Department of Medicine, Division of Dermatology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Steven T Vo
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Erick S Ramirez Tovar
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Larissa LoBello
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gautam Dantas
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA; Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA; Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA.
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6
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Song X, Kong SJ, Seo S, Prabhakar RG, Shamoo Y. Methyl halide transferase-based gas reporters for quantification of filamentous bacteria in microdroplet emulsions. Appl Environ Microbiol 2023; 89:e0076423. [PMID: 37699129 PMCID: PMC10537575 DOI: 10.1128/aem.00764-23] [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: 05/10/2023] [Accepted: 07/19/2023] [Indexed: 09/14/2023] Open
Abstract
The application of microfluidic techniques in experimental and environmental studies is a rapidly emerging field. Water-in-oil microdroplets can serve readily as controllable micro-vessels for studies that require spatial structure. In many applications, it is useful to monitor cell growth without breaking or disrupting the microdroplets. To this end, optical reporters based on color, fluorescence, or luminescence have been developed. However, optical reporters suffer from limitations when used in microdroplets such as inaccurate readings due to strong background interference or limited sensitivity during early growth stages. In addition, optical detection is typically not amenable to filamentous or biofilm-producing organisms that have significant nonlinear changes in opacity and light scattering during growth. To overcome such limitations, we show that volatile methyl halide gases produced by reporter cells expressing a methyl halide transferase (MHT) can serve as an alternative nonoptical detection approach suitable for microdroplets. In this study, an MHT-labeled Streptomyces venezuelae reporter strain was constructed and characterized. Protocols were established for the encapsulation and incubation of S. venezuelae in microdroplets. We observed the complete life cycle for S. venezuelae including the vegetative expansion of mycelia, mycelial fragmentation, and late-stage sporulation. Methyl bromide (MeBr) production was detected by gas chromatography-mass spectrometry (GC-MS) from S. venezuelae gas reporters incubated in either liquid suspension or microdroplets and used to quantitatively estimate bacterial density. Overall, using MeBr production as a means of quantifying bacterial growth provided a 100- to 1,000-fold increase in sensitivity over optical or fluorescence measurements of a comparable reporter strain expressing fluorescent proteins. IMPORTANCE Quantitative measurement of bacterial growth in microdroplets in situ is desirable but challenging. Current optical reporter systems suffer from limitations when applied to filamentous or biofilm-producing organisms. In this study, we demonstrate that volatile methyl halide gas production can serve as a quantitative nonoptical growth assay for filamentous bacteria encapsulated in microdroplets. We constructed an S. venezuelae gas reporter strain and observed a complete life cycle for encapsulated S. venezuelae in microdroplets, establishing microdroplets as an alternative growth environment for Streptomyces spp. that can provide spatial structure. We detected MeBr production from both liquid suspension and microdroplets with a 100- to 1,000-fold increase in signal-to-noise ratio compared to optical assays. Importantly, we could reliably detect bacteria with densities down to 106 CFU/mL. The combination of quantitative gas reporting and microdroplet systems provides a valuable approach to studying fastidious organisms that require spatial structure such as those found typically in soils.
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Affiliation(s)
- Xinhao Song
- Department of BioSciences, Rice University, Houston, Texas, USA
| | - Sarah J. Kong
- Department of BioSciences, Rice University, Houston, Texas, USA
| | - Seokju Seo
- Department of BioSciences, Rice University, Houston, Texas, USA
| | | | - Yousif Shamoo
- Department of BioSciences, Rice University, Houston, Texas, USA
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7
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Madhavan A, Arun KB, Alex D, Anoopkumar AN, Emmanual S, Chaturvedi P, Varjani S, Tiwari A, Kumar V, Reshmy R, Awasthi MK, Binod P, Aneesh EM, Sindhu R. Microbial production of nutraceuticals: Metabolic engineering interventions in phenolic compounds, poly unsaturated fatty acids and carotenoids synthesis. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2023; 60:2092-2104. [PMID: 37273565 PMCID: PMC10232702 DOI: 10.1007/s13197-022-05482-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 04/20/2022] [Accepted: 05/07/2022] [Indexed: 06/06/2023]
Abstract
Nutraceuticals have attained substantial attention due to their health-boosting or disease-prevention characteristics. Growing awareness about the potential of nutraceuticals for the prevention and management of diseases affecting human has led to an increase in the market value of nutraceuticals in several billion dollars. Nevertheless, limitations in supply and isolation complications from plants, animals or fungi, limit the large-scale production of nutraceuticals. Microbial engineering at metabolic level has been proved as an environment friendly substitute for the chemical synthesis of nutraceuticals. Extensively used microbial systems such as E. coli and S. cerevisiae have been modified as versatile cell factories for the synthesis of diverse nutraceuticals. This review describes current interventions in metabolic engineering for synthesising some of the therapeutically important nutraceuticals (phenolic compounds, polyunsaturated fatty acids and carotenoids). We focus on the interventions in enhancing product yield through engineering at gene level or pathway level.
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Affiliation(s)
- Aravind Madhavan
- Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014 India
| | - K. B. Arun
- Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014 India
| | - Deepthy Alex
- Department of Biotechnology, Mar Ivanios College, Trivandrum, Kerala 695015 India
| | - A. N. Anoopkumar
- Department of Zoology, Centre for Research in Emerging Tropical Diseases (CRET‑D), University of Calicut, Malappuram, Kerala India
| | - Shibitha Emmanual
- Department of Zoology, St. Joseph’s College, Thrissur, Kerala 680121 India
| | - Preeti Chaturvedi
- Aquatic Toxicology Laboratory, Environmental Toxicology Group, CSIR- Indian Institute for Toxicology Research (CSIR-IITR), 31 MG Marg, Lucknow, 226001 India
| | - Sunita Varjani
- Gujarat Pollution Control Board, Paryavaran Bhavan, CHH Road, Sector 10 A, Gandhinagar, Gujarat 382010 India
| | - Archana Tiwari
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Uttar Pradesh, Noida, 201301 India
| | - Vinod Kumar
- Fermentation Technology Division, CSIR- Indian Institute of Integrative Medicine (CSIR-IIIM), Jammu, J & K 180001 India
| | - R. Reshmy
- Department of Science and Humanities, Providence College of Engineering, Chengannur, Kerala 689122 India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, Kerala 695019 India
| | - Embalil Mathachan Aneesh
- Department of Zoology, Centre for Research in Emerging Tropical Diseases (CRET‑D), University of Calicut, Malappuram, Kerala India
| | - Raveendran Sindhu
- Department of Food Technology, T K M Institute of Technology, Kollam, Kerala 691505 India
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8
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Singh B, Kumar A, Saini AK, Saini RV, Thakur R, Mohammed SA, Tuli HS, Gupta VK, Areeshi MY, Faidah H, Jalal NA, Haque S. Strengthening microbial cell factories for efficient production of bioactive molecules. Biotechnol Genet Eng Rev 2023:1-34. [PMID: 36809927 DOI: 10.1080/02648725.2023.2177039] [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: 08/11/2022] [Accepted: 01/21/2023] [Indexed: 02/24/2023]
Abstract
High demand of bioactive molecules (food additives, antibiotics, plant growth enhancers, cosmetics, pigments and other commercial products) is the prime need for the betterment of human life where the applicability of the synthetic chemical product is on the saturation due to associated toxicity and ornamentations. It has been noticed that the discovery and productivity of such molecules in natural scenarios are limited due to low cellular yields as well as less optimized conventional methods. In this respect, microbial cell factories timely fulfilling the requirement of synthesizing bioactive molecules by improving production yield and screening more promising structural homologues of the native molecule. Where the robustness of the microbial host can be potentially achieved by taking advantage of cell engineering approaches such as tuning functional and adjustable factors, metabolic balancing, adapting cellular transcription machinery, applying high throughput OMICs tools, stability of genotype/phenotype, organelle optimizations, genome editing (CRISPER/Cas mediated system) and also by developing accurate model systems via machine-learning tools. In this article, we provide an overview from traditional to recent trends and the application of newly developed technologies, for strengthening the systemic approaches and providing future directions for enhancing the robustness of microbial cell factories to speed up the production of biomolecules for commercial purposes.
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Affiliation(s)
- Bharat Singh
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Ankit Kumar
- TERI-Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gurugram, India
| | - Adesh Kumar Saini
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Reena Vohra Saini
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Rahul Thakur
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Shakeel A Mohammed
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Hardeep Singh Tuli
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Centre, Scotland's Rural College (SRUC), Edinburgh, UK
| | - Mohammed Y Areeshi
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Hani Faidah
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Naif A Jalal
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
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9
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Sun BY, Wang FQ, Zhao J, Tao XY, Liu M, Wei DZ. Engineering Escherichia coli for l-homoserine production. J Basic Microbiol 2023; 63:168-178. [PMID: 36284486 DOI: 10.1002/jobm.202200488] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/13/2022] [Accepted: 10/01/2022] [Indexed: 02/03/2023]
Abstract
l-homoserine, a nonprotein amino acid, is used to synthesize many active substances in the industry. Here, to develop a robust l-homoserine-producing strain, Escherichia coli W3110 was used as a chassis to be engineered. Based on a previous construct with blocked competing routes for l-homoserine synthesis, five genes were overexpressed by promoter replacement strategy to increase the l-homoserine production, including enhancement of precursors for l-homoserine synthesis (ppc, thrA, and asd), reinforcement of the NADPH supply (pntAB) and efflux transporters (rhtA) to improve the l-homoserine production. However, the plasmid losing was to blame for the wildly fluctuating fermentation performance of engineered strains, ranging between 2.1 and 6.2 g/L. Then, a hok/sok toxin/antitoxin system was introduced into the free plasmid expression cassette to maintain the genetic stability of the episomal plasmid; consequently, the plasmid-losing rate sharply decreased, resulting in the engineered strain SHL17, which exhibited excellent stability in l-homoserine production, with 6.3 g/L in shake flasks and 44.4 g/L in a 5-L fermenter without antibiotic addition. This work verified the effective use of the hok/sok toxin/antitoxin system combined with promoter engineering to improve the genetic stability of E. coli episomal plasmids without antibiotics.
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Affiliation(s)
- Bing-Yao Sun
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Feng-Qing Wang
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Jian Zhao
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Xin-Yi Tao
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Min Liu
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Dong-Zhi Wei
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
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10
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Park MR, Gauttam R, Fong B, Chen Y, Lim HG, Feist AM, Mukhopadhyay A, Petzold CJ, Simmons BA, Singer SW. Revealing oxidative pentose metabolism in new Pseudomonas putida isolates. Environ Microbiol 2023; 25:493-504. [PMID: 36465038 PMCID: PMC10107873 DOI: 10.1111/1462-2920.16296] [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: 10/04/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
The Pseudomonas putida group in the Gammaproteobacteria has been intensively studied for bioremediation and plant growth promotion. Members of this group have recently emerged as promising hosts to convert intermediates derived from plant biomass to biofuels and biochemicals. However, most strains of P. putida cannot metabolize pentose sugars derived from hemicellulose. Here, we describe three isolates that provide a broader view of the pentose sugar catabolism in the P. putida group. One of these isolates clusters with the well-characterized P. alloputida KT2440 (Strain BP6); the second isolate clustered with plant growth-promoting strain P. putida W619 (Strain M2), while the third isolate represents a new species in the group (Strain BP8). Each of these isolates possessed homologous genes for oxidative xylose catabolism (xylDXA) and a potential xylonate transporter. Strain M2 grew on arabinose and had genes for oxidative arabinose catabolism (araDXA). A CRISPR interference (CRISPRi) system was developed for strain M2 and identified conditionally essential genes for xylose growth. A glucose dehydrogenase was found to be responsible for initial oxidation of xylose and arabinose in strain M2. These isolates have illuminated inherent diversity in pentose catabolism in the P. putida group and may provide alternative hosts for biomass conversion.
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Affiliation(s)
- Mee-Rye Park
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Rahul Gauttam
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Bonnie Fong
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yan Chen
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Hyun Gyu Lim
- Joint BioEnergy Institute, Emeryville, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Adam M Feist
- Joint BioEnergy Institute, Emeryville, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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11
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Kang CW, Lim HG, Won J, Cha S, Shin G, Yang JS, Sung J, Jung GY. Circuit-guided population acclimation of a synthetic microbial consortium for improved biochemical production. Nat Commun 2022; 13:6506. [PMID: 36344561 PMCID: PMC9640620 DOI: 10.1038/s41467-022-34190-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 10/14/2022] [Indexed: 11/09/2022] Open
Abstract
Microbial consortia have been considered potential platforms for bioprocessing applications. However, the complexity in process control owing to the use of multiple strains necessitates the use of an efficient population control strategy. Herein, we report circuit-guided synthetic acclimation as a strategy to improve biochemical production by a microbial consortium. We designed a consortium comprising alginate-utilizing Vibrio sp. dhg and 3-hydroxypropionic acid (3-HP)-producing Escherichia coli strains for the direct conversion of alginate to 3-HP. We introduced a genetic circuit, named "Population guider", in the E. coli strain, which degrades ampicillin only when 3-HP is produced. In the presence of ampicillin as a selection pressure, the consortium was successfully acclimated for increased 3-HP production by 4.3-fold compared to that by a simple co-culturing consortium during a 48-h fermentation. We believe this concept is a useful strategy for the development of robust consortium-based bioprocesses.
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Affiliation(s)
- Chae Won Kang
- grid.49100.3c0000 0001 0742 4007Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Korea
| | - Hyun Gyu Lim
- grid.49100.3c0000 0001 0742 4007Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Korea
| | - Jaehyuk Won
- grid.254224.70000 0001 0789 9563Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, 84 Heukseok-Ro, Dongjak-gu, Seoul 06974 Republic of Korea ,grid.254224.70000 0001 0789 9563Department of Chemistry, Chung-Ang University, 84 Heukseok-Ro, Dongjak-gu, Seoul 06974 Republic of Korea
| | - Sanghak Cha
- grid.49100.3c0000 0001 0742 4007Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Korea
| | - Giyoung Shin
- grid.49100.3c0000 0001 0742 4007School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Korea
| | - Jae-Seong Yang
- grid.423637.70000 0004 1763 5862Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193 Spain
| | - Jaeyoung Sung
- grid.254224.70000 0001 0789 9563Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, 84 Heukseok-Ro, Dongjak-gu, Seoul 06974 Republic of Korea ,grid.254224.70000 0001 0789 9563Department of Chemistry, Chung-Ang University, 84 Heukseok-Ro, Dongjak-gu, Seoul 06974 Republic of Korea
| | - Gyoo Yeol Jung
- grid.49100.3c0000 0001 0742 4007Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Korea ,grid.49100.3c0000 0001 0742 4007School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Korea
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12
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Sri Wahyu Effendi S, Lin JY, Ng IS. Simultaneous carbon dioxide sequestration and utilization for cadaverine production using dual promoters in engineered Escherichia coli strains. BIORESOURCE TECHNOLOGY 2022; 363:127980. [PMID: 36137445 DOI: 10.1016/j.biortech.2022.127980] [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: 08/19/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Human carbonic anhydrase II (hCAII) is a rapid-acting zinc-metalloenzyme that catalyzes CO2 hydration reversibly, with encouraging applications in carbon capture, sequestration, and utilization (CCSU). However, biocatalyst durability is a major challenge. Herein, hCAII is emphasized in 4 different Escherichia coli strains and designated under dual promoters from sigma factor 70 (σ70) and heat shock protein (HSP70A) to suppress the usage of inducer and stimulate activity in heat environments. As a result, hCAII under high-efficient dual promoters regulation retained high residual activity in CO2 biomineralization of 68.8 % after 4 cycles at 40 °C. Moreover, co-expression of CAC9 with lysine decarboxylase (CadA) simultaneously sequestered CO2 release up to 95.7 % and increased cadaverine titer from 18.0 to 36.7 g/L by using E. coli MG1655. The remnant biomass from cadaverine synthesis sustained converting CO2 to 57.9 mg-CaCO3. Thus, the dual promoters design demonstrated the promising potential for CCSU through simultaneous CO2 utilization and cadaverine synthesis.
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Affiliation(s)
| | - Jia-Yi Lin
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan.
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13
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Effendi SSW, Ng IS. Reprogramming T7RNA Polymerase in Escherichia coli Nissle 1917 under Specific Lac Operon for Efficient p-Coumaric Acid Production. ACS Synth Biol 2022; 11:3471-3481. [PMID: 36087056 DOI: 10.1021/acssynbio.2c00363] [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] [Indexed: 01/24/2023]
Abstract
Lac operon is the standard regulator used to control the orthogonality of T7RNA polymerase (T7RNAP) and T7 promoter inEscherichia coli BL21(DE3) strain for protein expression. However,E. coliNissle 1917 (EcN), the unique probiotic strain, has seldom been precisely adapted to the T7 system. Herein, we applied bioinformatics analysis on Lac operon from different strains, and it was observed that a weak promoter for LacI repressor existed in EcN. Furthermore, X-gal assay revealed a strong expression of lacZ in EcN. We demonstrated that Lac operon significantly affected the protein expression in the two T7-derived EcN, in which T7RNAP was integrated at lambda (ET7L) and HK022 (ET7H), respectively. Different combinations of replication origin, chaperonin GroELS, inducer, and medium were explored to fine-tune the best strain with tyrosine ammonia-lyase (TAL) for p-coumaric acid (pCA) production, which is one of the essential bioactive compounds for human health. Finally, the highest pCA conversion of 78.8% was achieved using RRtL (plasmid form) under the optimum condition, and a 51.5% conversion was obtained with L::Rt strain which has integrated T7-RtTAL at HK022 of ET7L in the simulated gut environment. The appropriate reprogramming of T7RNAP expedites EcN as an effective and promising cell factory for live bacterial therapeutics in the future.
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Affiliation(s)
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
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14
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Ye DY, Noh MH, Moon JH, Milito A, Kim M, Lee JW, Yang JS, Jung GY. Kinetic compartmentalization by unnatural reaction for itaconate production. Nat Commun 2022; 13:5353. [PMID: 36097012 PMCID: PMC9468356 DOI: 10.1038/s41467-022-33033-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 08/29/2022] [Indexed: 11/09/2022] Open
Abstract
Physical compartmentalization of metabolism using membranous organelles in eukaryotes is helpful for chemical biosynthesis to ensure the availability of substrates from competitive metabolic reactions. Bacterial hosts lack such a membranous system, which is one of the major limitations for efficient metabolic engineering. Here, we employ kinetic compartmentalization with the introduction of an unnatural enzymatic reaction by an engineered enzyme as an alternative strategy to enable substrate availability from competitive reactions through kinetic isolation of metabolic pathways. As a proof of concept, we kinetically isolate the itaconate synthetic pathway from the tricarboxylic acid cycle in Escherichia coli, which is natively separated by mitochondrial membranes in Aspergillus terreus. Specifically, 2-methylcitrate dehydratase is engineered to alternatively catalyze citrate and kinetically secure cis-aconitate for efficient production using a high-throughput screening system. Itaconate production can be significantly improved with kinetic compartmentalization and its strategy has the potential to be widely applicable.
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Affiliation(s)
- Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Myung Hyun Noh
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Jo Hyun Moon
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Alfonsina Milito
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Minsun Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Jeong Wook Lee
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea.,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Jae-Seong Yang
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain.
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea. .,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea.
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15
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Cho JS, Kim GB, Eun H, Moon CW, Lee SY. Designing Microbial Cell Factories for the Production of Chemicals. JACS AU 2022; 2:1781-1799. [PMID: 36032533 PMCID: PMC9400054 DOI: 10.1021/jacsau.2c00344] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 05/24/2023]
Abstract
The sustainable production of chemicals from renewable, nonedible biomass has emerged as an essential alternative to address pressing environmental issues arising from our heavy dependence on fossil resources. Microbial cell factories are engineered microorganisms harboring biosynthetic pathways streamlined to produce chemicals of interests from renewable carbon sources. The biosynthetic pathways for the production of chemicals can be defined into three categories with reference to the microbial host selected for engineering: native-existing pathways, nonnative-existing pathways, and nonnative-created pathways. Recent trends in leveraging native-existing pathways, discovering nonnative-existing pathways, and designing de novo pathways (as nonnative-created pathways) are discussed in this Perspective. We highlight key approaches and successful case studies that exemplify these concepts. Once these pathways are designed and constructed in the microbial cell factory, systems metabolic engineering strategies can be used to improve the performance of the strain to meet industrial production standards. In the second part of the Perspective, current trends in design tools and strategies for systems metabolic engineering are discussed with an eye toward the future. Finally, we survey current and future challenges that need to be addressed to advance microbial cell factories for the sustainable production of chemicals.
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Affiliation(s)
- Jae Sung Cho
- Metabolic
and Biomolecular Engineering National Research Laboratory and Systems
Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative
Laboratory, Department of Chemical and Biomolecular Engineering (BK21
four), Korea Advanced Institute of Science
and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST
Institute for the BioCentury and KAIST Institute for Artificial Intelligence, Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 34141, Republic of Korea
- BioProcess
Engineering Research Center and BioInformatics Research Center, Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 34141, Republic of Korea
| | - Gi Bae Kim
- Metabolic
and Biomolecular Engineering National Research Laboratory and Systems
Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative
Laboratory, Department of Chemical and Biomolecular Engineering (BK21
four), Korea Advanced Institute of Science
and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST
Institute for the BioCentury and KAIST Institute for Artificial Intelligence, Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 34141, Republic of Korea
| | - Hyunmin Eun
- Metabolic
and Biomolecular Engineering National Research Laboratory and Systems
Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative
Laboratory, Department of Chemical and Biomolecular Engineering (BK21
four), Korea Advanced Institute of Science
and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST
Institute for the BioCentury and KAIST Institute for Artificial Intelligence, Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 34141, Republic of Korea
| | - Cheon Woo Moon
- Metabolic
and Biomolecular Engineering National Research Laboratory and Systems
Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative
Laboratory, Department of Chemical and Biomolecular Engineering (BK21
four), Korea Advanced Institute of Science
and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST
Institute for the BioCentury and KAIST Institute for Artificial Intelligence, Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic
and Biomolecular Engineering National Research Laboratory and Systems
Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative
Laboratory, Department of Chemical and Biomolecular Engineering (BK21
four), Korea Advanced Institute of Science
and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST
Institute for the BioCentury and KAIST Institute for Artificial Intelligence, Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 34141, Republic of Korea
- BioProcess
Engineering Research Center and BioInformatics Research Center, Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 34141, Republic of Korea
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16
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Sathesh-Prabu C, Tiwari R, Lee SK. Substrate-inducible and antibiotic-free high-level 4-hydroxyvaleric acid production in engineered Escherichia coli. Front Bioeng Biotechnol 2022; 10:960907. [PMID: 36017349 PMCID: PMC9398171 DOI: 10.3389/fbioe.2022.960907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
In this study, we developed a levulinic acid (LA)-inducible and antibiotic-free plasmid system mediated by HpdR/PhpdH and infA-complementation to produce 4-hydroxyvaleric acid (4-HV) from LA in an engineered Escherichia coli strain. The system was efficiently induced by the addition of the LA substrate and resulted in tight dose-dependent control and fine-tuning of gene expression. By engineering the 5′ untranslated region (UTR) of hpdR mRNA, the gene expression of green fluorescent protein (GFP) increased by at least two-fold under the hpdH promoter. Furthermore, by evaluating the robustness and plasmid stability of the proposed system, the engineered strain, IRV750f, expressing the engineered 3-hydroxybutyrate dehydrogenase (3HBDH∗) and formate dehydrogenase (CbFDH), produced 82 g/L of 4-HV from LA, with a productivity of 3.4 g/L/h and molar conversion of 92% in the fed-batch cultivation (5 L fermenter) without the addition of antibiotics or external inducers. Overall, the reported system was highly beneficial for the large-scale and cost-effective microbial production of value-added products and bulk chemicals from the renewable substrate, LA.
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17
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Abstract
Plasmids are one of the most commonly used platforms for genetic engineering and recombinant gene expression in bacteria. The range of available copy numbers for cloning vectors is largely restricted to the handful of Origins of Replication (ORIs) that have been isolated from plasmids found in nature. Here, we introduce two systems that allow for the continuous, finely-tuned control of plasmid copy number between 1 and 800 copies per cell: a plasmid with an anhydrotetracycline-controlled copy number, and a parallelized assay that is used to generate a continuous spectrum of 1194 ColE1-based copy number variants. Using these systems, we investigate the effects of plasmid copy number on cellular growth rates, gene expression, biosynthesis, and genetic circuit performance. We perform single-cell timelapse measurements to characterize plasmid loss, runaway plasmid replication, and quantify the impact of plasmid copy number on the variability of gene expression. Using our assay, we find that each plasmid imposes a 0.063% linear metabolic burden on their hosts, hinting at a simple relationship between metabolic burdens and plasmid DNA synthesis. Our systems enable the precise control of gene expression, and our results highlight the importance of tuning plasmid copy number as a powerful tool for the optimization of synthetic biological systems.
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18
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Cheng ZH, Wu J, Liu JQ, Min D, Liu DF, Li WW, Yu HQ. Repurposing CRISPR RNA-guided integrases system for one-step, efficient genomic integration of ultra-long DNA sequences. Nucleic Acids Res 2022; 50:7739-7750. [PMID: 35776123 PMCID: PMC9303307 DOI: 10.1093/nar/gkac554] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/14/2022] [Accepted: 06/16/2022] [Indexed: 01/26/2023] Open
Abstract
Genomic integration techniques offer opportunities for generation of engineered microorganisms with improved or even entirely new functions but are currently limited by inability for efficient insertion of long genetic payloads due to multiplexing. Herein, using Shewanella oneidensis MR-1 as a model, we developed an optimized CRISPR-associated transposase from cyanobacteria Scytonema hofmanni (ShCAST system), which enables programmable, RNA-guided transposition of ultra-long DNA sequences (30 kb) onto bacterial chromosomes at ∼100% efficiency in a single orientation. In this system, a crRNA (CRISPR RNA) was used to target multicopy loci like insertion-sequence elements or combining I-SceI endonuclease, thereby allowing efficient single-step multiplexed or iterative DNA insertions. The engineered strain exhibited drastically improved substrate diversity and extracellular electron transfer ability, verifying the success of this system. Our work greatly expands the application range and flexibility of genetic engineering techniques and may be readily extended to other bacteria for better controlling various microbial processes.
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Affiliation(s)
- Zhou-Hua Cheng
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Jie Wu
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Jia-Qi Liu
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Di Min
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Dong-Feng Liu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China.,Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Wen-Wei Li
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Han-Qing Yu
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
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19
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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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20
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Rottinghaus AG, Ferreiro A, Fishbein SRS, Dantas G, Moon TS. Genetically stable CRISPR-based kill switches for engineered microbes. Nat Commun 2022; 13:672. [PMID: 35115506 PMCID: PMC8813983 DOI: 10.1038/s41467-022-28163-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/13/2022] [Indexed: 12/13/2022] Open
Abstract
Microbial biocontainment is an essential goal for engineering safe, next-generation living therapeutics. However, the genetic stability of biocontainment circuits, including kill switches, is a challenge that must be addressed. Kill switches are among the most difficult circuits to maintain due to the strong selection pressure they impart, leading to high potential for evolution of escape mutant populations. Here we engineer two CRISPR-based kill switches in the probiotic Escherichia coli Nissle 1917, a single-input chemical-responsive switch and a 2-input chemical- and temperature-responsive switch. We employ parallel strategies to address kill switch stability, including functional redundancy within the circuit, modulation of the SOS response, antibiotic-independent plasmid maintenance, and provision of intra-niche competition by a closely related strain. We demonstrate that strains harboring either kill switch can be selectively and efficiently killed inside the murine gut, while strains harboring the 2-input switch are additionally killed upon excretion. Leveraging redundant strategies, we demonstrate robust biocontainment of our kill switch strains and provide a template for future kill switch development.
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Affiliation(s)
- Austin G Rottinghaus
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Aura Ferreiro
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Skye R S Fishbein
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
- Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA.
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
- Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA.
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21
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Zhang Y, Sun Q, Liu Y, Cen X, Liu D, Chen Z. Development of a plasmid stabilization system in Vibrio natriegens for the high production of 1,3-propanediol and 3-hydroxypropionate. BIORESOUR BIOPROCESS 2021; 8:125. [PMID: 38650249 PMCID: PMC10992974 DOI: 10.1186/s40643-021-00485-0] [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: 10/29/2021] [Accepted: 12/07/2021] [Indexed: 11/10/2022] Open
Abstract
Vibrio natriegens is a promising industrial chassis with a super-fast growth rate and high substrate uptake rates. V. natriegens was previously engineered to produce 1,3-propanediol (1,3-PDO) from glycerol by overexpressing the corresponding genes in a plasmid. However, antibiotic selection pressure for plasmid stability was not satisfactory and plasmid loss resulted in reduced productivity of the bioprocess. In this study, we developed an antibiotic-free plasmid stabilization system for V. natriegens. The system was achieved by shifting the glpD gene, one of the essential genes for glycerol degradation, from the chromosome to plasmid. With this system, engineered V. natriegens can stably maintain a large expression plasmid during the whole fed-batch fermentation and accumulated 69.5 g/L 1,3-PDO in 24 h, which was 23% higher than that based on antibiotic selection system. This system was also applied to engineering V. natriegens for the production of 3-hydroxypropionate (3-HP), enabling the engineered strain to accumulate 64.5 g/L 3-HP in 24 h, which was 30% higher than that based on antibiotic system. Overall, the developed strategy could be useful for engineering V. natriegens as a platform for the production of value-added chemicals from glycerol.
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Affiliation(s)
- Ye Zhang
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Qing Sun
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Yu Liu
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xuecong Cen
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Dehua Liu
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
- Tsinghua Innovation Center in Dongguan, Dongguan, 523808, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Zhen Chen
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China.
- Tsinghua Innovation Center in Dongguan, Dongguan, 523808, China.
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.
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22
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Seco EM, Fernández LÁ. Efficient markerless integration of genes in the chromosome of probiotic E. coli Nissle 1917 by bacterial conjugation. Microb Biotechnol 2021; 15:1374-1391. [PMID: 34755474 PMCID: PMC9049610 DOI: 10.1111/1751-7915.13967] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/22/2021] [Accepted: 10/23/2021] [Indexed: 01/30/2023] Open
Abstract
The probiotic strain Escherichia coli Nissle 1917 (EcN) is a common bacterial chassis in synthetic biology developments for therapeutic applications given its long track record of safe administration in humans. Chromosomal integration of the genes of interest (GOIs) in the engineered bacterium offers significant advantages in genetic stability and to control gene dose, but common methodologies relying on the transformation of EcN are inefficient. In this work, we implement in EcN the use of bacterial conjugation in combination with markerless genome engineering to efficiently insert multiple GOIs at different loci of EcN chromosome, leaving no antibiotic resistance genes, vector sequences or scars in the modified bacterium. The resolution of cointegrants that leads to markerless insertion of the GOIs requires expression of I-SceI endonuclease and its efficiency is enhanced by λ Red proteins. We show the potential of this strategy by integrating different genes encoding fluorescent and bioluminescent reporters (i.e. GFP, mKate2, luxCDABE) both individually and sequentially. We also demonstrate its application for gene deletions in EcN (ΔflhDC) and to replace the endogenous regulation of chromosomal locus (i.e. flhDC) by heterologous regulatory elements (e.g. tetR-Ptet) in order to have an ectopic control of gene expression in EcN with an external inducer to alter bacterial behaviour (e.g. flagellar motility). Whole-genome sequencing confirmed the introduction of the designed modifications without off-target alterations in the genome. This straightforward approach accelerates the generation of multiple modifications in EcN chromosome for the generation of living bacterial therapeutics.
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Affiliation(s)
- Elena M Seco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus UAM Cantoblanco, Madrid, 28049, Spain
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus UAM Cantoblanco, Madrid, 28049, Spain
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23
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Cao Y, Tian R, Lv X, Li J, Liu L, Du G, Chen J, Liu Y. Inducible Population Quality Control of Engineered Bacillus subtilis for Improved N-Acetylneuraminic Acid Biosynthesis. ACS Synth Biol 2021; 10:2197-2209. [PMID: 34404207 DOI: 10.1021/acssynbio.1c00086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Biosynthesis by microorganisms using renewable feedstocks is an important approach for realizing sustainable chemical manufacturing. However, cell-to-cell variation in biosynthesis capability during fermentation restricts the robustness and efficiency of bioproduction, hampering the industrialization of biosynthesis. Herein, we developed an inducible population quality control system (iPopQC) for dynamically modulating the producing and nonproducing subpopulations of engineered Bacillus subtilis, which was constructed via inducible promoter- and metabolite-responsive biosensor-based genetic circuit for regulating essential genes. Moreover, iPopQC achieved a 1.97-fold increase in N-acetylneuraminic acid (NeuAc) titer by enriching producing cell subpopulation during cultivation, representing 52% higher than that of previous PopQC. Strains with double-output iPopQC cocoupling the expression of double essential genes with NeuAc production improved production robustness further, retaining NeuAc production throughout 96 h of fermentation, upon which the strains cocoupling one essential gene expression with NeuAc production abolished the production ability.
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Affiliation(s)
- Yanting Cao
- 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
| | - Rongzhen Tian
- 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
| | - 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
| | - Jianghua Li
- 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
| | - Guocheng Du
- 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
| | - Jian Chen
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- National Engineering Laboratory for Cereal Fermentation Technology, 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
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24
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Zeng BX, Yao MD, Xiao WH, Luo YZ, Wang Y, Yuan YJ. Endogenous 2μ Plasmid Editing for Pathway Engineering in Saccharomyces cerevisiae. Front Microbiol 2021; 12:631462. [PMID: 33664720 PMCID: PMC7921170 DOI: 10.3389/fmicb.2021.631462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/22/2021] [Indexed: 02/05/2023] Open
Abstract
In Saccharomyces cerevisiae, conventional 2μ-plasmid based plasmid (pC2μ, such as pRS425) have been widely adopted in pathway engineering for multi-copy overexpression of key genes. However, the loss of partition and copy number control elements of yeast endogenous 2μ plasmid (pE2μ) brings the issues concerning plasmid stability and copy number of pC2μ, especially in long-term fermentation. In this study, we developed a method based on CRISPR/Cas9 to edit pE2μ and built the pE2μ multi-copy system by insertion of the target DNA element and elimination of the original pE2μ plasmid. The resulting plasmid pE2μRAF1 and pE2μREP2 demonstrated higher copy number and slower loss rate than a pC2μ control plasmid pRS425RK, when carrying the same target gene. Then, moving the essential gene TPI1 (encoding triose phosphate isomerase) from chromosome to pE2μRAF1 could increase the plasmid viability to nearly 100% and further increase the plasmid copy number by 73.95%. The expression using pE2μ multi-copy system demonstrated much smaller cell-to-cell variation comparing with pC2μ multi-copy system. With auxotrophic complementation of TPI1, the resulting plasmid pE2μRT could undergo cultivation of 90 generations under non-selective conditions without loss. Applying pE2μ multi-copy system for dihydroartemisinic acid (DHAA) biosynthesis, the production of DHAA was increased to 620.9 mg/L at shake-flask level in non-selective rich medium. This titer was 4.73-fold of the strain constructed based on pC2μ due to the more stable pE2μ plasmid system and with higher plasmid copy number. This study provides an improved expression system in yeast, and set a promising platform to construct biosynthesis pathway for valuable products.
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Affiliation(s)
- Bo-Xuan Zeng
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Ming-Dong Yao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Wen-Hai Xiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Yun-Zi Luo
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Ying Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Ying-Jin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
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25
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Kan A, Gelfat I, Emani S, Praveschotinunt P, Joshi NS. Plasmid Vectors for in Vivo Selection-Free Use with the Probiotic E. coli Nissle 1917. ACS Synth Biol 2021; 10:94-106. [PMID: 33301298 PMCID: PMC7813132 DOI: 10.1021/acssynbio.0c00466] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Escherichia
coli Nissle 1917 (EcN) is a probiotic
bacterium, commonly employed to treat certain gastrointestinal disorders.
It is fast emerging as an important target for the development of
therapeutic engineered bacteria, benefiting from the wealth of knowledge
of E. coli biology and ease of manipulation.
Bacterial synthetic biology projects commonly utilize engineered plasmid
vectors, which are simple to engineer and can reliably achieve high
levels of protein expression. However, plasmids typically require
antibiotics for maintenance, and the administration of an antibiotic
is often incompatible with in vivo experimentation
or treatment. EcN natively contains plasmids pMUT1 and pMUT2, which
have no known function but are stable within the bacteria. Here, we
describe the development of the pMUT plasmids into a robust platform
for engineering EcN for in vivo experimentation,
alongside a CRISPR-Cas9 system to remove the native plasmids. We systematically
engineered both pMUT plasmids to contain selection markers, fluorescent
markers, temperature sensitive expression, and curli secretion systems
to export a customizable functional material into the extracellular
space. We then demonstrate that the engineered plasmids were maintained
in bacteria as the engineered bacteria pass through the mouse GI tract
without selection, and that the secretion system remains functional,
exporting functionalized curli proteins into the gut. Our plasmid
system presents a platform for the rapid development of therapeutic
EcN bacteria.
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Affiliation(s)
- Anton Kan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - Ilia Gelfat
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Sivaram Emani
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Harvard College, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Pichet Praveschotinunt
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Neel S. Joshi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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26
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Noh MH, Cha S, Kim M, Jung GY. Recent Advances in Microbial Cell Growth Regulation Strategies for Metabolic Engineering. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0511-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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27
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Tan SI, Ng IS. Design and optimization of bioreactor to boost carbon dioxide assimilation in RuBisCo-equipped Escherichia coli. BIORESOURCE TECHNOLOGY 2020; 314:123785. [PMID: 32652452 DOI: 10.1016/j.biortech.2020.123785] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 06/30/2020] [Accepted: 07/01/2020] [Indexed: 06/11/2023]
Abstract
Global warming is a surging issue that has provoked the demand of green process to mitigate carbon dioxide. In this context, RuBisCo-equipped Escherichia coli has first developed and evaluated the CO2-assimiliable capability based on the mass balance in three devices: Flask-based in CO2 incubator (FIC), two-layered device (TLD) and CO2 bubbling device (CBD) systematically. With the forced diffusion of 5% CO2 in CBD, which confers an efficient attack of CO2 to RuBisCo, the CO2 assimilation increased from -5.03 to -2.63 g-CO2/g-DCW. Furthermore, boosted CO2 assimilation ability was observed by co-expression of GroELS chaperone with 71% reduction on CO2 release. By DNA sequencing and tandem MS/MS analysis, the toxicity of RuBisCo and PRK was identified to interfere the sugar metabolism and energy producing, while the cell morphology was changed and observed in RuBisCo-equipped E. coli. Our study provides a new perspective of higher CO2 assimilation for sustainable to eco-friendly green bioprocess.
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Affiliation(s)
- Shih-I Tan
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan.
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28
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Tan SI, Yu PJ, Ng IS. CRISPRi-mediated programming essential gene can as a Direct Enzymatic Performance Evaluation & Determination (DEPEND) system. Biotechnol Bioeng 2020; 117:2842-2851. [PMID: 32458463 DOI: 10.1002/bit.27443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/18/2020] [Accepted: 05/24/2020] [Indexed: 12/16/2022]
Abstract
Harnessing enzyme expression for production of target chemicals is a critical and multifarious process, where screening of different genes by inspection of enzymatic activity plays an imperative role. Here, we conceived an idea to improve the time-consuming and labor-intensive process of enzyme screening. Controlling cell growth was achieved by the Cluster Regularly Interspaced Short Palindromic Repeat (CRISPRi) system with different single guide RNA targeting the essential gene can (CRISPRi::CA) that encodes a carbonic anhydrase for CO2 uptake. CRISPRi::CA comprises a whole-cell biosensor to monitor CO2 concentration, ranging from 1% to 5%. On the basis of CRISPRi::CA, an effective and simple Direct Enzymatic Performance Evaluation & Determination (DEPEND) system was developed by a single step of plasmid transformation for targeted enzymes. As a result, the activity of different carbonic anhydrases corresponded to the colony-forming units. Furthermore, the enzymatic performance of 5-aminolevulinic acid synthetase (ALAS), which converts glycine and succinate-CoA to release a molecule of CO2 , has also been distinguished, and the effect of the chaperone GroELS on ALAS enzyme folding was successfully identified in the DEPEND system. We provide a highly feasible, time-saving, and flexible technology for the screening and inspection of high-performance enzymes, which may accelerate protein engineering in the future.
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Affiliation(s)
- Shih-I Tan
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Peng-Jui Yu
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
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29
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Recent advances in improving metabolic robustness of microbial cell factories. Curr Opin Biotechnol 2020; 66:69-77. [PMID: 32683192 DOI: 10.1016/j.copbio.2020.06.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/12/2020] [Accepted: 06/17/2020] [Indexed: 12/20/2022]
Abstract
Engineering microbial cell factories has been widely applied to produce compounds spanning from intricate natural products to bulk commodities. In each case, host robustness is essential to ensure the reliable and sustainable production of targeted metabolites. However, it can be negatively affected by metabolic burden, pathway toxicity, and harsh environment, resulting in a decreased titer and productivity. Enhanced robustness enables host to have better production performance under complicated growth circumstances. Here, we review current strategies for boosting host robustness, including metabolic balancing, genetic and phenotype stability enhancement, and tolerance engineering. In addition, we discuss the challenges and future perspectives on microbial host engineering for increased robustness.
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30
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Li C, Swofford CA, Sinskey AJ. Modular engineering for microbial production of carotenoids. Metab Eng Commun 2020; 10:e00118. [PMID: 31908924 PMCID: PMC6938962 DOI: 10.1016/j.mec.2019.e00118] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/02/2019] [Accepted: 12/08/2019] [Indexed: 12/12/2022] Open
Abstract
There is an increasing demand for carotenoids due to their applications in the food, flavor, pharmaceutical and feed industries, however, the extraction and synthesis of these compounds can be expensive and technically challenging. Microbial production of carotenoids provides an attractive alternative to the negative environmental impacts and cost of chemical synthesis or direct extraction from plants. Metabolic engineering and synthetic biology approaches have been widely utilized to reconstruct and optimize pathways for carotenoid overproduction in microorganisms. This review summarizes the current advances in microbial engineering for carotenoid production and divides the carotenoid biosynthesis building blocks into four distinct metabolic modules: 1) central carbon metabolism, 2) cofactor metabolism, 3) isoprene supplement metabolism and 4) carotenoid biosynthesis. These four modules focus on redirecting carbon flux and optimizing cofactor supplements for isoprene precursors needed for carotenoid synthesis. Future perspectives are also discussed to provide insights into microbial engineering principles for overproduction of carotenoids.
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Affiliation(s)
- Cheng Li
- Department of Biology, Massachusetts Institute of Technology, Boston, MA, 02139, USA
- Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore, 138602, Singapore
| | - Charles A. Swofford
- Department of Biology, Massachusetts Institute of Technology, Boston, MA, 02139, USA
- Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore, 138602, Singapore
| | - Anthony J. Sinskey
- Department of Biology, Massachusetts Institute of Technology, Boston, MA, 02139, USA
- Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore, 138602, Singapore
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31
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Tan SI, Ng IS. New Insight into Plasmid-Driven T7 RNA Polymerase in Escherichia coli and Use as a Genetic Amplifier for a Biosensor. ACS Synth Biol 2020; 9:613-622. [PMID: 32142603 DOI: 10.1021/acssynbio.9b00466] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
T7 RNA polymerase (T7RNAP) and T7 promoter are powerful genetic components, thus a plasmid-driven T7 (PDT7) genetic circuit could be broadly applied for synthetic biology. However, the limited knowledge of the toxicity and instability of such a system still restricts its application. Herein, we constructed 16 constitutive genetic circuts of PDT7 and investigated the orthogonal effects in toxicity and instability. The T7 toxicity was elucidated from the construction processes and cell growth characterization, showing the importance of optimal orthogonality for PDT7. Besides, a protein analysis was performed to validate how the T7 system affected cell metabolism and led to the instability. The application of constitutive PDT7 in functional protein expressions, including carbonic anhydrase, lysine decarboxylase, and 5-ALA synthetase was demonstrated. Furthermore, PDT7 working as a genetic amplifier had been designed for E. coli cell-based biosensors, which illustrated the opportunities in the future of PDT7 used in synthetic biology.
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Affiliation(s)
- Shih-I Tan
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan
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32
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Noh MH, Lim HG, Moon D, Park S, Jung GY. Auxotrophic Selection Strategy for Improved Production of Coenzyme B 12 in Escherichia coli. iScience 2020; 23:100890. [PMID: 32086013 PMCID: PMC7033360 DOI: 10.1016/j.isci.2020.100890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/17/2020] [Accepted: 02/03/2020] [Indexed: 02/02/2023] Open
Abstract
The production of coenzyme B12 using well-characterized microorganisms, such as Escherichia coli, has recently attracted considerable attention to meet growing demands of coenzyme B12 in various applications. In the present study, we designed an auxotrophic selection strategy and demonstrated the enhanced production of coenzyme B12 using a previously engineered coenzyme B12-producing E. coli strain. To select a high producer, the coenzyme B12-independent methionine synthase (metE) gene was deleted in E. coli, thus limiting its methionine synthesis to only that via coenzyme B12-dependent synthase (encoded by metH). Following the deletion of metE, significantly enhanced production of the specific coenzyme B12 validated the coenzyme B12-dependent auxotrophic growth. Further precise tuning of the auxotrophic system by varying the expression of metH substantially increased the cell biomass and coenzyme B12 production, suggesting that our strategy could be effectively applied to E. coli and other coenzyme B12-producing strains. The auxotrophic selection strategy was applied to coenzyme B12 production Coenzyme B12-independent methionine synthase was deleted for auxotroph system The auxotrophic strategy could significantly enhance the coenzyme B12 production Optimization of the auxotroph system further enhanced the coenzyme B12 production
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Affiliation(s)
- Myung Hyun Noh
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongsangbuk-do 37673, Korea
| | - Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongsangbuk-do 37673, Korea
| | - Daeyeong Moon
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongsangbuk-do 37673, Korea
| | - Sunghoon Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, 50 UNIST-Ro, Ulju-gun, Ulsan, Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongsangbuk-do 37673, Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongsangbuk-do 37673, Korea.
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33
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Usmani Z, Sharma M, Sudheer S, Gupta VK, Bhat R. Engineered Microbes for Pigment Production Using Waste Biomass. Curr Genomics 2020; 21:80-95. [PMID: 32655303 PMCID: PMC7324876 DOI: 10.2174/1389202921999200330152007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/08/2020] [Accepted: 03/16/2020] [Indexed: 12/17/2022] Open
Abstract
Agri-food waste biomass is the most abundant organic waste and has high valorisation potential for sustainable bioproducts development. These wastes are not only recyclable in nature but are also rich sources of bioactive carbohydrates, peptides, pigments, polyphenols, vitamins, natural antioxidants, etc. Bioconversion of agri-food waste to value-added products is very important towards zero waste and circular economy concepts. To reduce the environmental burden, food researchers are seeking strategies to utilize this waste for microbial pigments production and further biotechnological exploitation in functional foods or value-added products. Microbes are valuable sources for a range of bioactive molecules, including microbial pigments production through fermentation and/or utilisation of waste. Here, we have reviewed some of the recent advancements made in important bioengineering technologies to develop engineered microbial systems for enhanced pigments production using agri-food wastes biomass/by-products as substrates in a sustainable way.
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Affiliation(s)
| | - Minaxi Sharma
- Address correspondence to these authors at the ERA Chair for Food (By-) Products Valorization Technologies- VALORTECH, Estonian University of Life Sciences, Kreutzwaldi 56/5, 51006, Tartu, Estonia; Tel/Fax: +372 7313927; E-mails: ;, ;
| | | | | | - Rajeev Bhat
- Address correspondence to these authors at the ERA Chair for Food (By-) Products Valorization Technologies- VALORTECH, Estonian University of Life Sciences, Kreutzwaldi 56/5, 51006, Tartu, Estonia; Tel/Fax: +372 7313927; E-mails: ;, ;
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34
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Song JW, Seo JH, Oh DK, Bornscheuer UT, Park JB. Design and engineering of whole-cell biocatalytic cascades for the valorization of fatty acids. Catal Sci Technol 2020. [DOI: 10.1039/c9cy01802f] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This review presents the key factors to construct a productive whole-cell biocatalytic cascade exemplified for the biotransformation of renewable fatty acids.
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Affiliation(s)
- Ji-Won Song
- Department of Food Science and Engineering
- Ewha Womans University
- Seoul 03760
- Republic of Korea
| | - Joo-Hyun Seo
- Department of Bio and Fermentation Convergence Technology
- Kookmin University
- Seoul 02707
- Republic of Korea
| | - Doek-Kun Oh
- Department of Bioscience and Biotechnology
- Konkuk University
- Seoul 143-701
- Republic of Korea
| | - Uwe T. Bornscheuer
- Institute of Biochemistry
- Department of Biotechnology & Enzyme Catalysis
- Greifswald University
- 17487 Greifswald
- Germany
| | - Jin-Byung Park
- Department of Food Science and Engineering
- Ewha Womans University
- Seoul 03760
- Republic of Korea
- Institute of Molecular Microbiology and Biosystems Engineering
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35
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Wang M, Yan Y, Wang R, Wang L, Zhou H, Li Y, Tang L, Xu Y, Jiang Y, Cui W, Qiao X. Simultaneous Detection of Bovine Rotavirus, Bovine Parvovirus, and Bovine Viral Diarrhea Virus Using a Gold Nanoparticle-Assisted PCR Assay With a Dual-Priming Oligonucleotide System. Front Microbiol 2019; 10:2884. [PMID: 31921061 PMCID: PMC6920155 DOI: 10.3389/fmicb.2019.02884] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 11/29/2019] [Indexed: 12/17/2022] Open
Abstract
Bovine rotavirus (BRV), bovine parvovirus (BPV), and bovine viral diarrhea virus (BVDV) are the pathogens that cause diarrhea primarily in newborn calves. A mixed infection of BRV, BPV, and BVDV makes clinical diagnosis difficult. In this study, we designed dual-priming oligonucleotide (DPO) primers the VP6 gene of BRV, VP2 gene of BPV, and 5′UTR gene of BVDV and synthesized gold nanoparticles (GNPs) with an average diameter of 10 nm. We combined the DPOs with the GNPs to develop a DPO-nanoPCR assay for detecting BRV, BPV, and BVDV. The annealing temperature, primer concentration, and GNP concentration were optimized for this assay. Compared to a conventional PCR assay, the DPO-nanoPCR assay allowed the use of a wider range of annealing temperatures (41–65°C) to effectively amplify target genes. PCR amplification was the most efficient at 56.2°C using conventional primers. The optimal volume of all the primers (10 μM) was 1.0 μL. The optimal volume of GNPs (10 nM) for all the reactions was 0.5 μL. The detection limits of DPO-nanoPCR for pMD19-T-VP6, pMD19-T-VP2, and pMD19-T-5′UTR were 9.40 × 102 copies/μL, 5.14 × 103 copies/μL, and 4.09 × 101 copies/μL, respectively; and those using conventional PCR were 9.40 × 104 copies/μL, 5.14 × 105 copies/μL, and 4.09 × 104 copies/μL, respectively. The sensitivity of DPO-nanoPCR was at least 100-fold higher than that of conventional PCR. The specificity detection showed that the DPO-nanoPCR was able to specifically detect BRV, BPV, and BVDV. Use of clinical samples indicated that target viruses can be detected accurately. Thus, DPO-nanoPCR is a new powerful, simple, specific, and sensitive tool for detecting mixed infections of BRV, BPV, and BVDV.
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Affiliation(s)
- Mengmeng Wang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Yue Yan
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Ruichong Wang
- Department for Radiological Protection, Heilongjiang Province Center for Disease Control and Prevention, Harbin, China
| | - Li Wang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Han Zhou
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Yijing Li
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Lijie Tang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Yigang Xu
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Yanping Jiang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Wen Cui
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Xinyuan Qiao
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
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Enhanced Lycopene Production in Escherichia coli by Expression of Two MEP Pathway Enzymes from Vibrio sp. Dhg. Catalysts 2019. [DOI: 10.3390/catal9121003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Microbial production is a promising method that can overcome major limitations in conventional methods of lycopene production, such as low yields and variations in product quality. Significant efforts have been made to improve lycopene production by engineering either the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway or mevalonate (MVA) pathway in microorganisms. To further improve lycopene production, it is critical to utilize metabolic enzymes with high specific activities. Two enzymes, 1-deoxy-d-xylulose-5-phosphate synthase (Dxs) and farnesyl diphosphate synthase (IspA), are required in lycopene production using MEP pathway. Here, we evaluated the activities of Dxs and IspA of Vibrio sp. dhg, a newly isolated and fast-growing microorganism. Considering that the MEP pathway is closely related to the cell membrane and electron transport chain, the activities of the two enzymes of Vibrio sp. dhg were expected to be higher than the enzymes of Escherichia coli. We found that Dxs and IspA in Vibrio sp. dhg exhibited 1.08-fold and 1.38-fold higher catalytic efficiencies, respectively. Consequently, the heterologous overexpression improved the specific lycopene production by 1.88-fold. Our findings could be widely utilized to enhance production of lycopene and other carotenoids.
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Systems Metabolic Engineering Strategies: Integrating Systems and Synthetic Biology with Metabolic Engineering. Trends Biotechnol 2019; 37:817-837. [DOI: 10.1016/j.tibtech.2019.01.003] [Citation(s) in RCA: 226] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/07/2019] [Accepted: 01/10/2019] [Indexed: 12/12/2022]
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High-throughput identification of microRNAs in Taenia hydatigena, a cestode threatening livestock breeding industry. INFECTION GENETICS AND EVOLUTION 2019; 75:103985. [PMID: 31362070 DOI: 10.1016/j.meegid.2019.103985] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/23/2019] [Accepted: 07/26/2019] [Indexed: 12/11/2022]
Abstract
Infection of Cysticercus tenuicollis, the larval stage of Taenia hydatigena, is extensively found in sheep and pigs and jeopardizes the breeding and meat industry. miRNAs are a subclass of small noncoding regulatory RNAs and closely associated with the pathogenesis and biology of parasites. Here, using HiSeq sequencing we identified 49 known and 2 potential novel miRNAs in C. tenuicollis, of which both thy-miR-71 and -87 were predominant. Using RT-qPCR, 6 selected miRNAs were validated, and thy-miR-71 and -miR-87 were confirmed to be highly expressed, with the copy number of approximately 82,340 ± 2079 and 19,580 ± 609 per 1 ng total RNA, respectively. Similar to other cestodes, T. hydatigena was predicted to have two conserved miRNA clusters thy-miR-71/2c/2b and thy-miR-4989/277, and three members of the former were confirmed to reside sequentially within the genomic region of 253 bp by PCR. The current data provide us a valuable resource for further studies of a role of miRNAs in T. hydatigena biology and infection.
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Xu JZ, Yu HB, Han M, Liu LM, Zhang WG. Metabolic engineering of glucose uptake systems in Corynebacterium glutamicum for improving the efficiency of l-lysine production. ACTA ACUST UNITED AC 2019; 46:937-949. [DOI: 10.1007/s10295-019-02170-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 03/27/2019] [Indexed: 11/25/2022]
Abstract
Abstract
Traditional amino acid producers typically exhibit the low glucose uptake rate and growth deficiency, resulting in a long fermentation time because of the accumulation of side mutations in breeding of strains. In this study, we demonstrate that the efficiency of l-lysine production in traditional l-lysine producer Corynebacterium glutamicum ZL-9 can be improved by rationally engineering glucose uptake systems. To do this, different bypasses for glucose uptake were investigated to reveal the best glucose uptake system for l-lysine production in traditional l-lysine producer. This study showed that overexpression of the key genes in PTSGlc or non-PTSGlc increased the glucose consumption, growth rate, and l-lysine production. However, increasing the function of PTSGlc in glucose uptake led to the increase of by-products, especially for plasmid-mediated expression system. Increasing the participation of non-PTSGlc in glucose utilization showed the best glucose uptake system for l-lysine production. The final strain ZL-92 with increasing the expression level of iolT1, iolT2 and ppgK could produce 201.6 ± 13.8 g/L of l-lysine with a productivity of 5.04 g/L/h and carbon yield of 0.65 g/(g glucose) in fed-batch culture. This is the first report of a rational modification of glucose uptake systems that improve the efficiency of l-lysine production through increasing the participation of non-PTSGlc in glucose utilization in traditional l-lysine producer. Similar strategies can be also used for producing other amino acids or their derivatives.
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Affiliation(s)
- Jian-Zhong Xu
- 0000 0001 0708 1323 grid.258151.a The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University 1800 Lihu Road 214122 Wuxi People’s Republic of China
| | - Hai-Bo Yu
- 0000 0001 0708 1323 grid.258151.a The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University 1800 Lihu Road 214122 Wuxi People’s Republic of China
| | - Mei Han
- 0000 0004 0431 6539 grid.469163.f Shanghai Business School 2271 Zhongsha West-Road 200235 Shanghai People’s Republic of China
| | - Li-Ming Liu
- 0000 0001 0708 1323 grid.258151.a State Key Laboratory of Food Science and Technology, School of Biotechnology Jiangnan University 1800 Lihu Road 214122 Wuxi People’s Republic of China
| | - Wei-Guo Zhang
- 0000 0001 0708 1323 grid.258151.a The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University 1800 Lihu Road 214122 Wuxi People’s Republic of China
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Lv Y, Qian S, Du G, Chen J, Zhou J, Xu P. Coupling feedback genetic circuits with growth phenotype for dynamic population control and intelligent bioproduction. Metab Eng 2019; 54:109-116. [DOI: 10.1016/j.ymben.2019.03.009] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/22/2019] [Accepted: 03/27/2019] [Indexed: 12/14/2022]
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41
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Multi-level engineering of Baeyer-Villiger monooxygenase-based Escherichia coli biocatalysts for the production of C9 chemicals from oleic acid. Metab Eng 2019; 54:137-144. [DOI: 10.1016/j.ymben.2019.03.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 03/29/2019] [Accepted: 03/31/2019] [Indexed: 12/12/2022]
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Zhang R, Yang Y, Wang J, Lin Y, Yan Y. Synthetic symbiosis combining plasmid displacement enables rapid construction of phenotype-stable strains. Metab Eng 2019; 55:85-91. [PMID: 31229565 DOI: 10.1016/j.ymben.2019.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/29/2019] [Accepted: 06/19/2019] [Indexed: 11/19/2022]
Abstract
Plasmid-based microbial systems have been a major workhorse for chemical and pharmaceutical production. The biosafety issues and elevated industrial cost of antibiotic usage have led to the development of alternative strategies for plasmid selection and maintenance. Such strategies, including auxotrophy complementation, post-segregational killing, operator-repressor and RNA-based interactions often require extensive engineering of various elements and may result in extra metabolic burden in the cells. Herein, we report a design of synthetic symbiosis combining plasmid displacement to construct a phenotype-stable microbial system. By sequestrating an endogenous essential gene folP, cells obtained long-term plasmid maintenance with minimum cost. The phenotype performance was also inherited for up to 80 generations demonstrated by the production of salicylic acid in Escherichia coli. Meanwhile, the temperature-induced curing method of the intermediate plasmids enables rapid engineering. This design can lead to broad applications as a reliable and convenient plasmid-based expression system.
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Affiliation(s)
- Ruihua Zhang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA
| | - Yaping Yang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA
| | - Jian Wang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA
| | - Yuheng Lin
- BiotecEra Inc, 220 Riverbend Road, 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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Lim HG, Kwak DH, Park S, Woo S, Yang JS, Kang CW, Kim B, Noh MH, Seo SW, Jung GY. Vibrio sp. dhg as a platform for the biorefinery of brown macroalgae. Nat Commun 2019; 10:2486. [PMID: 31171782 PMCID: PMC6554313 DOI: 10.1038/s41467-019-10371-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 05/08/2019] [Indexed: 12/14/2022] Open
Abstract
Although brown macroalgae holds potential as an alternative feedstock, its utilization by conventional microbial platforms has been limited due to the inability to metabolize one of the principal sugars, alginate. Here, we isolate Vibrio sp. dhg, a fast-growing bacterium that can efficiently assimilate alginate. Based on systematic characterization of the genomic information of Vibrio sp. dhg, we establish a genetic toolbox for its engineering. We also demonstrate its ability to rapidly produce ethanol, 2,3-butanediol, and lycopene from brown macroalgae sugar mixture with high productivities and yields. Collectively, Vibrio sp. dhg can be used as a platform for the efficient conversion of brown macroalgae sugars into diverse value-added biochemicals.
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Affiliation(s)
- Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea
| | - Dong Hun Kwak
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea
| | - Sungwoo Park
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Korea
| | - Sunghwa Woo
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea
| | - Jae-Seong Yang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea
| | - Chae Won Kang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea
| | - Beomhee Kim
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Korea
| | - Myung Hyun Noh
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Korea.
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea.
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea.
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